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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;documentation&quot;,&quot;context&quot;:&quot;product&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;documentation_link_product_navbar&quot;}" href="https://docs.github.com">
      Documentation

    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;github_skills&quot;,&quot;context&quot;:&quot;product&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;github_skills_link_product_navbar&quot;}" href="https://skills.github.com">
      GitHub Skills

    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
    <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
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  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;blog&quot;,&quot;context&quot;:&quot;product&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;blog_link_product_navbar&quot;}" href="https://github.blog">
      Blog

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</svg>
</a></li>

                </ul>
              </div>
          </div>
      </div>
</li>

                  <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
      <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
        Solutions
        <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1">
    <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path>
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      </button>
      <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 d-lg-flex flex-wrap dropdown-menu-wide">
          <div class="HeaderMenu-column px-lg-4 border-lg-right mb-4 mb-lg-0 pr-lg-7">
              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0 pb-lg-3 mb-3 mb-lg-0">
                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-company-size-heading">By company size</span>
                <ul class="list-style-none f5" aria-labelledby="solutions-by-company-size-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;enterprises&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;enterprises_link_solutions_navbar&quot;}" href="https://github.com/enterprise">
      Enterprises

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;small_and_medium_teams&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;small_and_medium_teams_link_solutions_navbar&quot;}" href="https://github.com/team">
      Small and medium teams

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;startups&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;startups_link_solutions_navbar&quot;}" href="https://github.com/enterprise/startups">
      Startups

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;nonprofits&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;nonprofits_link_solutions_navbar&quot;}" href="/solutions/industry/nonprofits">
      Nonprofits

    
</a></li>

                </ul>
              </div>
              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-use-case-heading">By use case</span>
                <ul class="list-style-none f5" aria-labelledby="solutions-by-use-case-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;devsecops&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;devsecops_link_solutions_navbar&quot;}" href="/solutions/use-case/devsecops">
      DevSecOps

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;devops&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;devops_link_solutions_navbar&quot;}" href="/solutions/use-case/devops">
      DevOps

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;ci_cd&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;ci_cd_link_solutions_navbar&quot;}" href="/solutions/use-case/ci-cd">
      CI/CD

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all_use_cases&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_use_cases_link_solutions_navbar&quot;}" href="/solutions/use-case">
      View all use cases

    
</a></li>

                </ul>
              </div>
          </div>
          <div class="HeaderMenu-column px-lg-4">
              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="solutions-by-industry-heading">By industry</span>
                <ul class="list-style-none f5" aria-labelledby="solutions-by-industry-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;healthcare&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;healthcare_link_solutions_navbar&quot;}" href="/solutions/industry/healthcare">
      Healthcare

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;financial_services&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;financial_services_link_solutions_navbar&quot;}" href="/solutions/industry/financial-services">
      Financial services

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;manufacturing&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;manufacturing_link_solutions_navbar&quot;}" href="/solutions/industry/manufacturing">
      Manufacturing

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;government&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;government_link_solutions_navbar&quot;}" href="/solutions/industry/government">
      Government

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all_industries&quot;,&quot;context&quot;:&quot;solutions&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_industries_link_solutions_navbar&quot;}" href="/solutions/industry">
      View all industries

    
</a></li>

                </ul>
              </div>
          </div>
         <div class="HeaderMenu-trailing-link rounded-bottom-2 flex-shrink-0 mt-lg-4 px-lg-4 py-4 py-lg-3 f5 text-semibold">
            <a href="/solutions">
              View all solutions
              <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-right HeaderMenu-trailing-link-icon">
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</svg>
</a>         </div>
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</li>

                    <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
      <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
        Resources
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</svg>
      </button>
      <div class="HeaderMenu-dropdown dropdown-menu rounded m-0 p-0 pt-2 pt-lg-4 position-relative position-lg-absolute left-0 left-lg-n3 pb-2 pb-lg-4 d-lg-flex flex-wrap dropdown-menu-wide">
          <div class="HeaderMenu-column px-lg-4 border-lg-right mb-4 mb-lg-0 pr-lg-7">
              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="resources-topics-heading">Topics</span>
                <ul class="list-style-none f5" aria-labelledby="resources-topics-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;ai&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;ai_link_resources_navbar&quot;}" href="/resources/articles/ai">
      AI

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;devops&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;devops_link_resources_navbar&quot;}" href="/resources/articles/devops">
      DevOps

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;security&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;security_link_resources_navbar&quot;}" href="/resources/articles/security">
      Security

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;software_development&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;software_development_link_resources_navbar&quot;}" href="/resources/articles/software-development">
      Software Development

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;view_all&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;view_all_link_resources_navbar&quot;}" href="/resources/articles">
      View all

    
</a></li>

                </ul>
              </div>
          </div>
          <div class="HeaderMenu-column px-lg-4">
              <div class="border-bottom pb-3 pb-lg-0 border-lg-bottom-0 border-bottom-0">
                    <span class="d-block h4 color-fg-default my-1" id="resources-explore-heading">Explore</span>
                <ul class="list-style-none f5" aria-labelledby="resources-explore-heading">
                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;learning_pathways&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;learning_pathways_link_resources_navbar&quot;}" href="https://resources.github.com/learn/pathways">
      Learning Pathways

    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
    <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
</svg>
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;events_amp_webinars&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;events_amp_webinars_link_resources_navbar&quot;}" href="https://resources.github.com">
      Events &amp; Webinars

    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
    <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
</svg>
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;ebooks_amp_whitepapers&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;ebooks_amp_whitepapers_link_resources_navbar&quot;}" href="https://github.com/resources/whitepapers">
      Ebooks &amp; Whitepapers

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;customer_stories&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;customer_stories_link_resources_navbar&quot;}" href="https://github.com/customer-stories">
      Customer Stories

    
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary Link--external" target="_blank" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;partners&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;partners_link_resources_navbar&quot;}" href="https://partner.github.com">
      Partners

    <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-link-external HeaderMenu-external-icon color-fg-subtle">
    <path d="M3.75 2h3.5a.75.75 0 0 1 0 1.5h-3.5a.25.25 0 0 0-.25.25v8.5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-3.5a.75.75 0 0 1 1.5 0v3.5A1.75 1.75 0 0 1 12.25 14h-8.5A1.75 1.75 0 0 1 2 12.25v-8.5C2 2.784 2.784 2 3.75 2Zm6.854-1h4.146a.25.25 0 0 1 .25.25v4.146a.25.25 0 0 1-.427.177L13.03 4.03 9.28 7.78a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042l3.75-3.75-1.543-1.543A.25.25 0 0 1 10.604 1Z"></path>
</svg>
</a></li>

                    <li>
  <a class="HeaderMenu-dropdown-link d-block no-underline position-relative py-2 Link--secondary" data-analytics-event="{&quot;location&quot;:&quot;navbar&quot;,&quot;action&quot;:&quot;executive_insights&quot;,&quot;context&quot;:&quot;resources&quot;,&quot;tag&quot;:&quot;link&quot;,&quot;label&quot;:&quot;executive_insights_link_resources_navbar&quot;}" href="https://github.com/solutions/executive-insights">
      Executive Insights

    
</a></li>

                </ul>
              </div>
          </div>
      </div>
</li>


                <li class="HeaderMenu-item position-relative flex-wrap flex-justify-between flex-items-center d-block d-lg-flex flex-lg-nowrap flex-lg-items-center js-details-container js-header-menu-item">
      <button type="button" class="HeaderMenu-link border-0 width-full width-lg-auto px-0 px-lg-2 py-lg-2 no-wrap d-flex flex-items-center flex-justify-between js-details-target" aria-expanded="false">
        Open Source
        <svg opacity="0.5" aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-chevron-down HeaderMenu-icon ml-1">
    <path d="M12.78 5.22a.749.749 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.06 0L3.22 6.28a.749.749 0 1 1 1.06-1.06L8 8.939l3.72-3.719a.749.749 0 0 1 1.06 0Z"></path>
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<template id="code-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code">
    <path d="m11.28 3.22 4.25 4.25a.75.75 0 0 1 0 1.06l-4.25 4.25a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734L13.94 8l-3.72-3.72a.749.749 0 0 1 .326-1.275.749.749 0 0 1 .734.215Zm-6.56 0a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042L2.06 8l3.72 3.72a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L.47 8.53a.75.75 0 0 1 0-1.06Z"></path>
</svg>
</template>

<template id="file-code-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-file-code">
    <path d="M4 1.75C4 .784 4.784 0 5.75 0h5.586c.464 0 .909.184 1.237.513l2.914 2.914c.329.328.513.773.513 1.237v8.586A1.75 1.75 0 0 1 14.25 15h-9a.75.75 0 0 1 0-1.5h9a.25.25 0 0 0 .25-.25V6h-2.75A1.75 1.75 0 0 1 10 4.25V1.5H5.75a.25.25 0 0 0-.25.25v2.5a.75.75 0 0 1-1.5 0Zm1.72 4.97a.75.75 0 0 1 1.06 0l2 2a.75.75 0 0 1 0 1.06l-2 2a.749.749 0 0 1-1.275-.326.749.749 0 0 1 .215-.734l1.47-1.47-1.47-1.47a.75.75 0 0 1 0-1.06ZM3.28 7.78 1.81 9.25l1.47 1.47a.751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018l-2-2a.75.75 0 0 1 0-1.06l2-2a.751.751 0 0 1 1.042.018.751.751 0 0 1 .018 1.042Zm8.22-6.218V4.25c0 .138.112.25.25.25h2.688l-.011-.013-2.914-2.914-.013-.011Z"></path>
</svg>
</template>

<template id="history-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-history">
    <path d="m.427 1.927 1.215 1.215a8.002 8.002 0 1 1-1.6 5.685.75.75 0 1 1 1.493-.154 6.5 6.5 0 1 0 1.18-4.458l1.358 1.358A.25.25 0 0 1 3.896 6H.25A.25.25 0 0 1 0 5.75V2.104a.25.25 0 0 1 .427-.177ZM7.75 4a.75.75 0 0 1 .75.75v2.992l2.028.812a.75.75 0 0 1-.557 1.392l-2.5-1A.751.751 0 0 1 7 8.25v-3.5A.75.75 0 0 1 7.75 4Z"></path>
</svg>
</template>

<template id="repo-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-repo">
    <path d="M2 2.5A2.5 2.5 0 0 1 4.5 0h8.75a.75.75 0 0 1 .75.75v12.5a.75.75 0 0 1-.75.75h-2.5a.75.75 0 0 1 0-1.5h1.75v-2h-8a1 1 0 0 0-.714 1.7.75.75 0 1 1-1.072 1.05A2.495 2.495 0 0 1 2 11.5Zm10.5-1h-8a1 1 0 0 0-1 1v6.708A2.486 2.486 0 0 1 4.5 9h8ZM5 12.25a.25.25 0 0 1 .25-.25h3.5a.25.25 0 0 1 .25.25v3.25a.25.25 0 0 1-.4.2l-1.45-1.087a.249.249 0 0 0-.3 0L5.4 15.7a.25.25 0 0 1-.4-.2Z"></path>
</svg>
</template>

<template id="bookmark-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-bookmark">
    <path d="M3 2.75C3 1.784 3.784 1 4.75 1h6.5c.966 0 1.75.784 1.75 1.75v11.5a.75.75 0 0 1-1.227.579L8 11.722l-3.773 3.107A.751.751 0 0 1 3 14.25Zm1.75-.25a.25.25 0 0 0-.25.25v9.91l3.023-2.489a.75.75 0 0 1 .954 0l3.023 2.49V2.75a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="plus-circle-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-plus-circle">
    <path d="M8 0a8 8 0 1 1 0 16A8 8 0 0 1 8 0ZM1.5 8a6.5 6.5 0 1 0 13 0 6.5 6.5 0 0 0-13 0Zm7.25-3.25v2.5h2.5a.75.75 0 0 1 0 1.5h-2.5v2.5a.75.75 0 0 1-1.5 0v-2.5h-2.5a.75.75 0 0 1 0-1.5h2.5v-2.5a.75.75 0 0 1 1.5 0Z"></path>
</svg>
</template>

<template id="circle-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-dot-fill">
    <path d="M8 4a4 4 0 1 1 0 8 4 4 0 0 1 0-8Z"></path>
</svg>
</template>

<template id="trash-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-trash">
    <path d="M11 1.75V3h2.25a.75.75 0 0 1 0 1.5H2.75a.75.75 0 0 1 0-1.5H5V1.75C5 .784 5.784 0 6.75 0h2.5C10.216 0 11 .784 11 1.75ZM4.496 6.675l.66 6.6a.25.25 0 0 0 .249.225h5.19a.25.25 0 0 0 .249-.225l.66-6.6a.75.75 0 0 1 1.492.149l-.66 6.6A1.748 1.748 0 0 1 10.595 15h-5.19a1.75 1.75 0 0 1-1.741-1.575l-.66-6.6a.75.75 0 1 1 1.492-.15ZM6.5 1.75V3h3V1.75a.25.25 0 0 0-.25-.25h-2.5a.25.25 0 0 0-.25.25Z"></path>
</svg>
</template>

<template id="team-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-people">
    <path d="M2 5.5a3.5 3.5 0 1 1 5.898 2.549 5.508 5.508 0 0 1 3.034 4.084.75.75 0 1 1-1.482.235 4 4 0 0 0-7.9 0 .75.75 0 0 1-1.482-.236A5.507 5.507 0 0 1 3.102 8.05 3.493 3.493 0 0 1 2 5.5ZM11 4a3.001 3.001 0 0 1 2.22 5.018 5.01 5.01 0 0 1 2.56 3.012.749.749 0 0 1-.885.954.752.752 0 0 1-.549-.514 3.507 3.507 0 0 0-2.522-2.372.75.75 0 0 1-.574-.73v-.352a.75.75 0 0 1 .416-.672A1.5 1.5 0 0 0 11 5.5.75.75 0 0 1 11 4Zm-5.5-.5a2 2 0 1 0-.001 3.999A2 2 0 0 0 5.5 3.5Z"></path>
</svg>
</template>

<template id="project-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-project">
    <path d="M1.75 0h12.5C15.216 0 16 .784 16 1.75v12.5A1.75 1.75 0 0 1 14.25 16H1.75A1.75 1.75 0 0 1 0 14.25V1.75C0 .784.784 0 1.75 0ZM1.5 1.75v12.5c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25V1.75a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25ZM11.75 3a.75.75 0 0 1 .75.75v7.5a.75.75 0 0 1-1.5 0v-7.5a.75.75 0 0 1 .75-.75Zm-8.25.75a.75.75 0 0 1 1.5 0v5.5a.75.75 0 0 1-1.5 0ZM8 3a.75.75 0 0 1 .75.75v3.5a.75.75 0 0 1-1.5 0v-3.5A.75.75 0 0 1 8 3Z"></path>
</svg>
</template>

<template id="pencil-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-pencil">
    <path d="M11.013 1.427a1.75 1.75 0 0 1 2.474 0l1.086 1.086a1.75 1.75 0 0 1 0 2.474l-8.61 8.61c-.21.21-.47.364-.756.445l-3.251.93a.75.75 0 0 1-.927-.928l.929-3.25c.081-.286.235-.547.445-.758l8.61-8.61Zm.176 4.823L9.75 4.81l-6.286 6.287a.253.253 0 0 0-.064.108l-.558 1.953 1.953-.558a.253.253 0 0 0 .108-.064Zm1.238-3.763a.25.25 0 0 0-.354 0L10.811 3.75l1.439 1.44 1.263-1.263a.25.25 0 0 0 0-.354Z"></path>
</svg>
</template>

<template id="copilot-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copilot">
    <path d="M7.998 15.035c-4.562 0-7.873-2.914-7.998-3.749V9.338c.085-.628.677-1.686 1.588-2.065.013-.07.024-.143.036-.218.029-.183.06-.384.126-.612-.201-.508-.254-1.084-.254-1.656 0-.87.128-1.769.693-2.484.579-.733 1.494-1.124 2.724-1.261 1.206-.134 2.262.034 2.944.765.05.053.096.108.139.165.044-.057.094-.112.143-.165.682-.731 1.738-.899 2.944-.765 1.23.137 2.145.528 2.724 1.261.566.715.693 1.614.693 2.484 0 .572-.053 1.148-.254 1.656.066.228.098.429.126.612.012.076.024.148.037.218.924.385 1.522 1.471 1.591 2.095v1.872c0 .766-3.351 3.795-8.002 3.795Zm0-1.485c2.28 0 4.584-1.11 5.002-1.433V7.862l-.023-.116c-.49.21-1.075.291-1.727.291-1.146 0-2.059-.327-2.71-.991A3.222 3.222 0 0 1 8 6.303a3.24 3.24 0 0 1-.544.743c-.65.664-1.563.991-2.71.991-.652 0-1.236-.081-1.727-.291l-.023.116v4.255c.419.323 2.722 1.433 5.002 1.433ZM6.762 2.83c-.193-.206-.637-.413-1.682-.297-1.019.113-1.479.404-1.713.7-.247.312-.369.789-.369 1.554 0 .793.129 1.171.308 1.371.162.181.519.379 1.442.379.853 0 1.339-.235 1.638-.54.315-.322.527-.827.617-1.553.117-.935-.037-1.395-.241-1.614Zm4.155-.297c-1.044-.116-1.488.091-1.681.297-.204.219-.359.679-.242 1.614.091.726.303 1.231.618 1.553.299.305.784.54 1.638.54.922 0 1.28-.198 1.442-.379.179-.2.308-.578.308-1.371 0-.765-.123-1.242-.37-1.554-.233-.296-.693-.587-1.713-.7Z"></path><path d="M6.25 9.037a.75.75 0 0 1 .75.75v1.501a.75.75 0 0 1-1.5 0V9.787a.75.75 0 0 1 .75-.75Zm4.25.75v1.501a.75.75 0 0 1-1.5 0V9.787a.75.75 0 0 1 1.5 0Z"></path>
</svg>
</template>

<template id="copilot-error-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copilot-error">
    <path d="M16 11.24c0 .112-.072.274-.21.467L13 9.688V7.862l-.023-.116c-.49.21-1.075.291-1.727.291-.198 0-.388-.009-.571-.029L6.833 5.226a4.01 4.01 0 0 0 .17-.782c.117-.935-.037-1.395-.241-1.614-.193-.206-.637-.413-1.682-.297-.683.076-1.115.231-1.395.415l-1.257-.91c.579-.564 1.413-.877 2.485-.996 1.206-.134 2.262.034 2.944.765.05.053.096.108.139.165.044-.057.094-.112.143-.165.682-.731 1.738-.899 2.944-.765 1.23.137 2.145.528 2.724 1.261.566.715.693 1.614.693 2.484 0 .572-.053 1.148-.254 1.656.066.228.098.429.126.612.012.076.024.148.037.218.924.385 1.522 1.471 1.591 2.095Zm-5.083-8.707c-1.044-.116-1.488.091-1.681.297-.204.219-.359.679-.242 1.614.091.726.303 1.231.618 1.553.299.305.784.54 1.638.54.922 0 1.28-.198 1.442-.379.179-.2.308-.578.308-1.371 0-.765-.123-1.242-.37-1.554-.233-.296-.693-.587-1.713-.7Zm2.511 11.074c-1.393.776-3.272 1.428-5.43 1.428-4.562 0-7.873-2.914-7.998-3.749V9.338c.085-.628.677-1.686 1.588-2.065.013-.07.024-.143.036-.218.029-.183.06-.384.126-.612-.18-.455-.241-.963-.252-1.475L.31 4.107A.747.747 0 0 1 0 3.509V3.49a.748.748 0 0 1 .625-.73c.156-.026.306.047.435.139l14.667 10.578a.592.592 0 0 1 .227.264.752.752 0 0 1 .046.249v.022a.75.75 0 0 1-1.19.596Zm-1.367-.991L5.635 7.964a5.128 5.128 0 0 1-.889.073c-.652 0-1.236-.081-1.727-.291l-.023.116v4.255c.419.323 2.722 1.433 5.002 1.433 1.539 0 3.089-.505 4.063-.934Z"></path>
</svg>
</template>

<template id="workflow-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-workflow">
    <path d="M0 1.75C0 .784.784 0 1.75 0h3.5C6.216 0 7 .784 7 1.75v3.5A1.75 1.75 0 0 1 5.25 7H4v4a1 1 0 0 0 1 1h4v-1.25C9 9.784 9.784 9 10.75 9h3.5c.966 0 1.75.784 1.75 1.75v3.5A1.75 1.75 0 0 1 14.25 16h-3.5A1.75 1.75 0 0 1 9 14.25v-.75H5A2.5 2.5 0 0 1 2.5 11V7h-.75A1.75 1.75 0 0 1 0 5.25Zm1.75-.25a.25.25 0 0 0-.25.25v3.5c0 .138.112.25.25.25h3.5a.25.25 0 0 0 .25-.25v-3.5a.25.25 0 0 0-.25-.25Zm9 9a.25.25 0 0 0-.25.25v3.5c0 .138.112.25.25.25h3.5a.25.25 0 0 0 .25-.25v-3.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="book-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-book">
    <path d="M0 1.75A.75.75 0 0 1 .75 1h4.253c1.227 0 2.317.59 3 1.501A3.743 3.743 0 0 1 11.006 1h4.245a.75.75 0 0 1 .75.75v10.5a.75.75 0 0 1-.75.75h-4.507a2.25 2.25 0 0 0-1.591.659l-.622.621a.75.75 0 0 1-1.06 0l-.622-.621A2.25 2.25 0 0 0 5.258 13H.75a.75.75 0 0 1-.75-.75Zm7.251 10.324.004-5.073-.002-2.253A2.25 2.25 0 0 0 5.003 2.5H1.5v9h3.757a3.75 3.75 0 0 1 1.994.574ZM8.755 4.75l-.004 7.322a3.752 3.752 0 0 1 1.992-.572H14.5v-9h-3.495a2.25 2.25 0 0 0-2.25 2.25Z"></path>
</svg>
</template>

<template id="code-review-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-code-review">
    <path d="M1.75 1h12.5c.966 0 1.75.784 1.75 1.75v8.5A1.75 1.75 0 0 1 14.25 13H8.061l-2.574 2.573A1.458 1.458 0 0 1 3 14.543V13H1.75A1.75 1.75 0 0 1 0 11.25v-8.5C0 1.784.784 1 1.75 1ZM1.5 2.75v8.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h6.5a.25.25 0 0 0 .25-.25v-8.5a.25.25 0 0 0-.25-.25H1.75a.25.25 0 0 0-.25.25Zm5.28 1.72a.75.75 0 0 1 0 1.06L5.31 7l1.47 1.47a.751.751 0 0 1-.018 1.042.751.751 0 0 1-1.042.018l-2-2a.75.75 0 0 1 0-1.06l2-2a.75.75 0 0 1 1.06 0Zm2.44 0a.75.75 0 0 1 1.06 0l2 2a.75.75 0 0 1 0 1.06l-2 2a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L10.69 7 9.22 5.53a.75.75 0 0 1 0-1.06Z"></path>
</svg>
</template>

<template id="codespaces-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-codespaces">
    <path d="M0 11.25c0-.966.784-1.75 1.75-1.75h12.5c.966 0 1.75.784 1.75 1.75v3A1.75 1.75 0 0 1 14.25 16H1.75A1.75 1.75 0 0 1 0 14.25Zm2-9.5C2 .784 2.784 0 3.75 0h8.5C13.216 0 14 .784 14 1.75v5a1.75 1.75 0 0 1-1.75 1.75h-8.5A1.75 1.75 0 0 1 2 6.75Zm1.75-.25a.25.25 0 0 0-.25.25v5c0 .138.112.25.25.25h8.5a.25.25 0 0 0 .25-.25v-5a.25.25 0 0 0-.25-.25Zm-2 9.5a.25.25 0 0 0-.25.25v3c0 .138.112.25.25.25h12.5a.25.25 0 0 0 .25-.25v-3a.25.25 0 0 0-.25-.25Z"></path><path d="M7 12.75a.75.75 0 0 1 .75-.75h4.5a.75.75 0 0 1 0 1.5h-4.5a.75.75 0 0 1-.75-.75Zm-4 0a.75.75 0 0 1 .75-.75h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1-.75-.75Z"></path>
</svg>
</template>

<template id="comment-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-comment">
    <path d="M1 2.75C1 1.784 1.784 1 2.75 1h10.5c.966 0 1.75.784 1.75 1.75v7.5A1.75 1.75 0 0 1 13.25 12H9.06l-2.573 2.573A1.458 1.458 0 0 1 4 13.543V12H2.75A1.75 1.75 0 0 1 1 10.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h2a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h4.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
</template>

<template id="comment-discussion-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-comment-discussion">
    <path d="M1.75 1h8.5c.966 0 1.75.784 1.75 1.75v5.5A1.75 1.75 0 0 1 10.25 10H7.061l-2.574 2.573A1.458 1.458 0 0 1 2 11.543V10h-.25A1.75 1.75 0 0 1 0 8.25v-5.5C0 1.784.784 1 1.75 1ZM1.5 2.75v5.5c0 .138.112.25.25.25h1a.75.75 0 0 1 .75.75v2.19l2.72-2.72a.749.749 0 0 1 .53-.22h3.5a.25.25 0 0 0 .25-.25v-5.5a.25.25 0 0 0-.25-.25h-8.5a.25.25 0 0 0-.25.25Zm13 2a.25.25 0 0 0-.25-.25h-.5a.75.75 0 0 1 0-1.5h.5c.966 0 1.75.784 1.75 1.75v5.5A1.75 1.75 0 0 1 14.25 12H14v1.543a1.458 1.458 0 0 1-2.487 1.03L9.22 12.28a.749.749 0 0 1 .326-1.275.749.749 0 0 1 .734.215l2.22 2.22v-2.19a.75.75 0 0 1 .75-.75h1a.25.25 0 0 0 .25-.25Z"></path>
</svg>
</template>

<template id="organization-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-organization">
    <path d="M1.75 16A1.75 1.75 0 0 1 0 14.25V1.75C0 .784.784 0 1.75 0h8.5C11.216 0 12 .784 12 1.75v12.5c0 .085-.006.168-.018.25h2.268a.25.25 0 0 0 .25-.25V8.285a.25.25 0 0 0-.111-.208l-1.055-.703a.749.749 0 1 1 .832-1.248l1.055.703c.487.325.779.871.779 1.456v5.965A1.75 1.75 0 0 1 14.25 16h-3.5a.766.766 0 0 1-.197-.026c-.099.017-.2.026-.303.026h-3a.75.75 0 0 1-.75-.75V14h-1v1.25a.75.75 0 0 1-.75.75Zm-.25-1.75c0 .138.112.25.25.25H4v-1.25a.75.75 0 0 1 .75-.75h2.5a.75.75 0 0 1 .75.75v1.25h2.25a.25.25 0 0 0 .25-.25V1.75a.25.25 0 0 0-.25-.25h-8.5a.25.25 0 0 0-.25.25ZM3.75 6h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5ZM3 3.75A.75.75 0 0 1 3.75 3h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 3 3.75Zm4 3A.75.75 0 0 1 7.75 6h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 7 6.75ZM7.75 3h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5ZM3 9.75A.75.75 0 0 1 3.75 9h.5a.75.75 0 0 1 0 1.5h-.5A.75.75 0 0 1 3 9.75ZM7.75 9h.5a.75.75 0 0 1 0 1.5h-.5a.75.75 0 0 1 0-1.5Z"></path>
</svg>
</template>

<template id="rocket-icon">
  <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-rocket">
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<template id="shield-check-icon">
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<template id="server-icon">
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<template id="globe-icon">
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<template id="issue-opened-icon">
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<template id="device-mobile-icon">
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<template id="package-icon">
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<template id="credit-card-icon">
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<template id="play-icon">
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<template id="gift-icon">
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<template id="code-square-icon">
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<template id="device-desktop-icon">
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        <div class="position-relative">
                <ul
                  role="listbox"
                  class="ActionListWrap QueryBuilder-ListWrap"
                  aria-label="Suggestions"
                  data-action="
                    combobox-commit:query-builder#comboboxCommit
                    mousedown:query-builder#resultsMousedown
                  "
                  data-target="query-builder.resultsList"
                  data-persist-list=false
                  id="query-builder-test-results"
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        </div>
      <div class="FormControl-inlineValidation" id="validation-632f5e5a-5ed2-42a1-95a6-b12246360193" hidden="hidden">
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          <svg aria-hidden="true" height="12" viewBox="0 0 12 12" version="1.1" width="12" data-view-component="true" class="octicon octicon-alert-fill">
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          <div class="d-flex flex-row color-fg-muted px-3 text-small color-bg-default search-feedback-prompt">
            <a target="_blank" href="https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax" data-view-component="true" class="Link color-fg-accent text-normal ml-2">Search syntax tips</a>            <div class="d-flex flex-1"></div>
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  <div data-action="click:qbsearch-input#retract" class="dark-backdrop position-fixed" hidden data-target="qbsearch-input.darkBackdrop"></div>
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<dialog-helper>
  <dialog data-target="qbsearch-input.feedbackDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="feedback-dialog" aria-modal="true" aria-labelledby="feedback-dialog-title" aria-describedby="feedback-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll">
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      <h1 class="Overlay-title " id="feedback-dialog-title">
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      <button data-close-dialog-id="feedback-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
    <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path>
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      <scrollable-region data-labelled-by="feedback-dialog-title">
        <div data-view-component="true" class="Overlay-body">        <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="code-search-feedback-form" data-turbo="false" action="/search/feedback" accept-charset="UTF-8" method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="jsbxLn9MmAvI1iaYZ+MX1GZidZ0+vwtaBocOHpDN27HtQ6VzNGD2+EVzjd5jcthXCYtbWqqk1glYtXGCnJNx0A==" />
          <p>We read every piece of feedback, and take your input very seriously.</p>
          <textarea name="feedback" class="form-control width-full mb-2" style="height: 120px" id="feedback"></textarea>
          <input name="include_email" id="include_email" aria-label="Include my email address so I can be contacted" class="form-control mr-2" type="checkbox">
          <label for="include_email" style="font-weight: normal">Include my email address so I can be contacted</label>
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    <custom-scopes data-target="qbsearch-input.customScopesManager">
    
<dialog-helper>
  <dialog data-target="custom-scopes.customScopesModalDialog" data-action="close:qbsearch-input#handleDialogClose cancel:qbsearch-input#handleDialogClose" id="custom-scopes-dialog" aria-modal="true" aria-labelledby="custom-scopes-dialog-title" aria-describedby="custom-scopes-dialog-description" data-view-component="true" class="Overlay Overlay-whenNarrow Overlay--size-medium Overlay--motion-scaleFade Overlay--disableScroll">
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  <div class="Overlay-headerContentWrap">
    <div class="Overlay-titleWrap">
      <h1 class="Overlay-title " id="custom-scopes-dialog-title">
        Saved searches
      </h1>
        <h2 id="custom-scopes-dialog-description" class="Overlay-description">Use saved searches to filter your results more quickly</h2>
    </div>
    <div class="Overlay-actionWrap">
      <button data-close-dialog-id="custom-scopes-dialog" aria-label="Close" type="button" data-view-component="true" class="close-button Overlay-closeButton"><svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-x">
    <path d="M3.72 3.72a.75.75 0 0 1 1.06 0L8 6.94l3.22-3.22a.749.749 0 0 1 1.275.326.749.749 0 0 1-.215.734L9.06 8l3.22 3.22a.749.749 0 0 1-.326 1.275.749.749 0 0 1-.734-.215L8 9.06l-3.22 3.22a.751.751 0 0 1-1.042-.018.751.751 0 0 1-.018-1.042L6.94 8 3.72 4.78a.75.75 0 0 1 0-1.06Z"></path>
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      <scrollable-region data-labelled-by="custom-scopes-dialog-title">
        <div data-view-component="true" class="Overlay-body">        <div data-target="custom-scopes.customScopesModalDialogFlash"></div>

        <div hidden class="create-custom-scope-form" data-target="custom-scopes.createCustomScopeForm">
        <!-- '"` --><!-- </textarea></xmp> --></option></form><form id="custom-scopes-dialog-form" data-turbo="false" action="/search/custom_scopes" accept-charset="UTF-8" method="post"><input type="hidden" data-csrf="true" name="authenticity_token" value="72UqUmuV/REY+nPwBQBD2lrFvYmNyxjgQJL7YNW0W59S9pDl8kvOqcxbHXQYtS2b5n/9rzbM8SCuNe/4BSnz9w==" />
          <div data-target="custom-scopes.customScopesModalDialogFlash"></div>

          <input type="hidden" id="custom_scope_id" name="custom_scope_id" data-target="custom-scopes.customScopesIdField">

          <div class="form-group">
            <label for="custom_scope_name">Name</label>
            <auto-check src="/search/custom_scopes/check_name" required only-validate-on-blur="false">
              <input
                type="text"
                name="custom_scope_name"
                id="custom_scope_name"
                data-target="custom-scopes.customScopesNameField"
                class="form-control"
                autocomplete="off"
                placeholder="github-ruby"
                required
                maxlength="50">
              <input type="hidden" data-csrf="true" value="i3YlXdFxc0JYbkpW4M97dVpNF8rQCnnd+nrwIayI0oXuTtaCLUxOndPuVA3FBgDoSJ8xseRwX2HzQrvoP8euBw==" />
            </auto-check>
          </div>

          <div class="form-group">
            <label for="custom_scope_query">Query</label>
            <input
              type="text"
              name="custom_scope_query"
              id="custom_scope_query"
              data-target="custom-scopes.customScopesQueryField"
              class="form-control"
              autocomplete="off"
              placeholder="(repo:mona/a OR repo:mona/b) AND lang:python"
              required
              maxlength="500">
          </div>

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The package is able to calculate OFL, ABC represented #\r","#  as a fraction of the OFL F, and F rebuild represented as a fixed     #\r","#  reduction in F during the specified rebuild period if needed.        #\r","#                                                                       #\r","##---------------------------------------------------------------------##\r","#                                                                       #\r","#  Author: Nathan Vaughan                                               #\r","#  Last update date: 10/15/21                                           #\r","#  Contact: nathan.vaughan@noaa.gov                                     #\r","#                                                                       #\r","##---------------------------------------------------------------------##\r","#\r","#   Disclaimer\r","#\r","#   \"The United States Department of Commerce (DOC) GitHub project code \r","#    is provided on an \"as is\" basis and the user assumes responsibility \r","#    for its use. DOC has relinquished control of the information and no \r","#    longer has responsibility to protect the integrity, confidentiality, \r","#    or availability of the information. Any claims against the Department \r","#    of Commerce stemming from the use of its GitHub project will be \r","#    governed by all applicable Federal law. Any reference to specific \r","#    commercial products, processes, or services by service mark, trademark, \r","#    manufacturer, or otherwise, does not constitute or imply their endorsement, \r","#    recommendation or favoring by the Department of Commerce. The Department \r","#    of Commerce seal and logo, or the seal and logo of a DOC bureau, shall \r","#    not be used in any manner to imply endorsement of any commercial \r","#    product or activity by DOC or the United States Government.\"\r","#\r","#\r","##                                                                       #\r","##---------------------------------------------------------------------##\r","##\r","\r","# This is now a generalized function to run projections that should work for most species. \r","# The function is now designed to mostly read out settings from the forecast file the \r","# same way you would generally set things up for a base SS projection.\r","# The only additional inputs needed are a proportion for F.ABC relative to F.OFL if \r","# ABC projections are desired and a rebuild target year if rebuilding projections are desired.\r","#\r","\r","run.projections\u003c-function(assessment_dir, #Here you set the location of a previously fit SS3.3 stock assessment to perform projections\r","                          ABC_Fraction = NULL, #Set the ABC target as a fraction of the OFL target if NULL will not fit ABC projections\r","                          Rebuild_yr = NULL, #Set the rebuild target year if NULL will not fit rebuild projections\r","                          Calc_F0 = FALSE, #Should an F=0 projection be performed\r","                          Const_Catch = NULL, #Constant catch target in mt. If constant catch is chosen no other simulations will run (i.e. benchmark, OFL, etc)  \r","                          F_max = FALSE, #If true and forecast method is Fmsy will replace Fmsy with Fmax search (maximum yield per recruit)\r","                          Depletion.Threshold = 0.0001, # These are all just thresholds for when \r","                          Annual.F.Threshold = 0.0001, # targets are acceptably achieved these default to a .01% change\r","                          Allocation.Threshold = 0.0001, # increase them if run is too slow or reduce to improve fit if run is fast.\r","                          Step.Threshold = 0.0001, #\r","                          Benchmark_complete = FALSE, #Set to true if you already have a fit Benchmark run but want to add or adjust an ABC or Rebuild run\r","                          Make_plots = FALSE, #Should plots be created (this is useful for diagnostics but can cause annoying errors if plot window is small)\r","                          Calc_Hessian = FALSE, #Should the hessian inversion be completed for runs once converged. TODO: NOT YET IMPLEMENTED!!!\r","                          Do_Pstar = FALSE, #If TRUE then ABC_Fraction above will instead be the P* probability of overfishing limit for ABC calculation. TODO: NOT YET IMPLEMENTED!!!\r","                          Years_report = 20, #How many years of projection to include in stored OFL and ABC reporting. (All forecast years data will still be available in report file) \r","                          Years_projection = 100, #How many years of projection to run (need enough to reach equilibrium) 100 is safe but may not be sufficient for some long lived species.\r","                          run_in_MSE = FALSE,\r","                          starting_Forecatch = NULL,\r","                          MSY_step = 0.1,\r","                          SS_exe = NULL\r","                          ) \r","{\r","  \r","  projection_results \u003c- list()\r","  \r","  \r","  \r","  #SSMSE::report_message(\"Running the allocation forecasting function.\") \r","  \r","  #Removed these as inputs as they are not needed yet, could add back to input options later\r"," \r","  oldwd\u003c-getwd()\r","  \r","  library(r4ss)\r","  #Set large max print to avoid issues with writing out a large forecast file.\r","  options(max.print = 1000000)\r","  setwd(paste0(assessment_dir))\r","  assessment_dir \u003c- getwd()\r","  #Read in all the model files and results \r","  start \u003c- SS_readstarter()\r","  dat \u003c- SS_readdat(file = start$datfile, version = 3.3)\r","  ctl \u003c- SS_readctl(file = start$ctlfile, version = 3.3, use_datlist = TRUE, datlist = dat)\r","  results \u003c- SS_output(dir = getwd(), covar = FALSE)\r","  forecast \u003c- SS_readforecast() \r","  \r","  if(!is.null(SS_exe)){\r","    \r","  }else if(file.exists(\"ss.exe\")){\r","    SS_exe \u003c- \"ss\"\r","  } else if(file.exists(\"ss3.exe\")){\r","    SS_exe \u003c- \"ss3\"\r","  } else if(file.exists(\"ss_opt.exe\")){\r","    SS_exe \u003c- \"ss_opt\"\r","  } else if(file.exists(\"ss3_opt.exe\")){\r","    SS_exe \u003c- \"ss3_opt\"\r","  } else if(file.exists(\"ss3_win.exe\")){\r","    SS_exe \u003c- \"ss3_win\"\r","  }else{\r","    stop(\"Error: Couldn't find an expected SS executable name\")\r","  }\r","  \r","  if(file.exists(\"ss.par\")){\r","    par_name \u003c- \"ss.par\"\r","  }else if(file.exists(\"ss3.par\")){\r","    par_name \u003c- \"ss3.par\"\r","  }else{\r","    stop(\"Error: No par file found with name ss.par or ss3.par\")\r","  }\r","  \r","  parlist \u003c- SS_readpar_3.30(parfile = par_name, datsource = dat, ctlsource = ctl)\r","  \r","  \r","  if(!is.null(Const_Catch)){\r","    Const_Catch \u003c- sort(Const_Catch)\r","  }\r","  \r","  #First set up a working director for running projections in (to avoid overwriting the base files with a failed model run)\r","  #then copy all of the assessment files to this working folder (ignore any output directories that have been previously created)\r","  if(Benchmark_complete == FALSE){\r","  if(dir.exists(file.path(getwd(),\"Working_dir\"))){\r","    unlink(file.path(getwd(),\"Working_dir\"), recursive = TRUE)\r","  }\r","  dir.create(file.path(getwd(),\"Working_dir\"))\r","  temp.files \u003c- list.files(path=assessment_dir)\r","  folders \u003c- c(which(temp.files==\"Benchmark_target\"), which(temp.files==\"OFL_target\"), which(temp.files==\"ABC_target\"), which(temp.files==\"Rebuild_target\"), which(temp.files==\"F0_target\"), which(temp.files==\"Working_dir\"))\r","  if(length(folders)\u003e0){\r","    temp.files \u003c- temp.files[-folders]\r","  }\r","  file.copy(from = file.path(getwd(),temp.files), to = file.path(getwd(),\"Working_dir\",temp.files))\r","  }else{\r","    temp.files \u003c- list.files(path=file.path(getwd(),\"Working_dir\"))\r","    folders \u003c- c(which(temp.files==\"Benchmark_target\"), which(temp.files==\"OFL_target\"), which(temp.files==\"ABC_target\"), which(temp.files==\"Rebuild_target\"), which(temp.files==\"F0_target\"), which(temp.files==\"Working_dir\"))\r","    if(length(folders)\u003e0){\r","      temp.files \u003c- temp.files[-folders]\r","    }\r","    unlink(file.path(getwd(),\"Working_dir/\",temp.files))\r","    temp.files \u003c- list.files(path=file.path(getwd(),\"Benchmark_target\"))\r","    file.copy(from = file.path(getwd(),\"Benchmark_target\",temp.files), to = file.path(getwd(),\"Working_dir\",temp.files))\r","  }\r","  \r","  #Set the new working directory \r","  setwd(file.path(getwd(),\"Working_dir\"))\r","  \r","  #Modify assessment files to produce expected timeseries length and outputs\r","  #need enough projection years to allow equilibrium to be achieved\r","  forecast[[\"Nforecastyrs\"]] \u003c- Years_projection\r","  \r","  #If fitting the Benchmark/OFL values then save the specified recruitment source for catches \r","  #and set to 0 (S/R curve) in order to first calculate benchmarks\r","  catch_rec \u003c- forecast$fcast_rec_option\r","  if(Benchmark_complete==FALSE){\r","    forecast$fcast_rec_option \u003c- 0\r","  }\r","  \r","  #Need to set recdevs and implementation error for all projection years \r","  #so that reading from par file is possible\r","  expected_forecast_rec_length \u003c- length((min(dat[[\"endyr\"]],ctl[[\"MainRdevYrLast\"]])+1):(dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]]))\r","  if(!is.null(parlist$recdev_forecast)){\r","    if(length(parlist$recdev_forecast[,1])!=expected_forecast_rec_length){\r","      temp_recs\u003c-parlist$recdev_forecast[,2]\r","      parlist$recdev_forecast \u003c- matrix(NA, nrow = expected_forecast_rec_length, ncol = 2)\r","      parlist$recdev_forecast[,1] \u003c- (min(dat[[\"endyr\"]],ctl[[\"MainRdevYrLast\"]])+1):(dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]])\r","      parlist$recdev_forecast[,2] \u003c- rep(0,expected_forecast_rec_length)\r","      parlist$recdev_forecast[1:length(temp_recs),2] \u003c- temp_recs\r","      colnames(parlist$recdev_forecast) \u003c- c(\"year\",\"recdev\")\r","    }\r","  }else{\r","    parlist$recdev_forecast \u003c- matrix(NA, nrow = expected_forecast_rec_length, ncol = 2)\r","    parlist$recdev_forecast[,1] \u003c- (min(dat[[\"endyr\"]],ctl[[\"MainRdevYrLast\"]])+1):(dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]])\r","    parlist$recdev_forecast[,2] \u003c- rep(0,expected_forecast_rec_length)\r","    colnames(parlist$recdev_forecast) \u003c- c(\"year\",\"recdev\")\r","  }\r","  \r","  # if(!is.null(parlist$Fcast_impl_error)){\r","  parlist$Fcast_impl_error \u003c- matrix(NA, nrow = forecast[[\"Nforecastyrs\"]], ncol = 2)\r","  parlist$Fcast_impl_error[,1] \u003c- (dat[[\"endyr\"]]+1):(dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]])\r","  parlist$Fcast_impl_error[,2] \u003c- rep(0,forecast[[\"Nforecastyrs\"]])\r","  colnames(parlist$Fcast_impl_error) \u003c- c(\"year\",\"impl_error\")\r","  if(forecast[[\"stddev_of_log_catch_ratio\"]]==0){\r","    forecast[[\"stddev_of_log_catch_ratio\"]]\u003c-0.001\r","  }\r","  \r","  #Adjust the starter file to read from par file, perform no fitting (This should already have been done),\r","  #and set the depletion value to be relative to unexploited biomass and have no scaling \r","  #(so that correct depletion target can be found).\r","  start$init_values_src \u003c- 1\r","  start$last_estimation_phase \u003c- 0\r","  start$depl_basis \u003c- 1\r","  start$depl_denom_frac \u003c- 1\r","  start$SPR_basis \u003c- 4\r","  start$F_report_units \u003c- 1\r","  start$F_report_basis \u003c- 0\r","  \r","  #Get the timeseries of historic/projected catches and F\r","  TimeFit \u003c- results$timeseries\r","  \r","  #Identify the column numbers for Catch, F, SSB, Recruits, etc\r","  Catch_cols \u003c- grep(\"retain(B)\", names(TimeFit), fixed = TRUE)\r","  Dead_cols \u003c- grep(\"dead(B)\", names(TimeFit), fixed = TRUE)\r","  CatchN_cols \u003c- grep(\"retain(N)\", names(TimeFit), fixed = TRUE)\r","  DeadN_cols \u003c- grep(\"dead(N)\", names(TimeFit), fixed = TRUE)\r","  F_cols \u003c- grep(\"F\", names(TimeFit), fixed = TRUE)\r","  if(length(F_cols)==0){\r","    F_cols \u003c- grep(\"Hrate\", names(TimeFit), fixed = TRUE)\r","  }\r","  TimeFit2 \u003c- aggregate(TimeFit[,sort(c(2,4,7,Catch_cols,Dead_cols,CatchN_cols,DeadN_cols,F_cols))],by=list(TimeFit$Yr,TimeFit$Seas),FUN=sum,na.rm=TRUE)[,-c(3,4,5)]\r","  names(TimeFit2)[c(1,2)] \u003c- c(\"Yr\", \"Seas\")\r","  \r","  Catch_cols2 \u003c- grep(\"retain(B)\", names(TimeFit2), fixed = TRUE)\r","  Dead_cols2 \u003c- grep(\"dead(B)\", names(TimeFit2), fixed = TRUE)\r","  CatchN_cols2 \u003c- grep(\"retain(N)\", names(TimeFit2), fixed = TRUE)\r","  DeadN_cols2 \u003c- grep(\"dead(N)\", names(TimeFit2), fixed = TRUE)\r","  F_cols2 \u003c- grep(\"F\", names(TimeFit2), fixed = TRUE)\r","  if(length(F_cols2)==0){\r","    F_cols2 \u003c- grep(\"Hrate\", names(TimeFit2), fixed = TRUE)\r","  }\r","  \r","  TimeFit3 \u003c- aggregate(TimeFit[,sort(c(2,7,8,Catch_cols,Dead_cols,CatchN_cols,DeadN_cols,F_cols))],by=list(TimeFit$Yr),FUN=sum,na.rm=TRUE)[,-2]\r","  names(TimeFit3)[c(1)] \u003c- c(\"Yr\")\r","  Virgin_bio \u003c- TimeFit3$SpawnBio[1]\r","  \r","  Catch_cols3 \u003c- grep(\"retain(B)\", names(TimeFit3), fixed = TRUE)\r","  Dead_cols3 \u003c- grep(\"dead(B)\", names(TimeFit3), fixed = TRUE)\r","  CatchN_cols3 \u003c- grep(\"retain(N)\", names(TimeFit3), fixed = TRUE)\r","  DeadN_cols3 \u003c- grep(\"dead(N)\", names(TimeFit3), fixed = TRUE)\r","  F_cols3 \u003c- grep(\"F\", names(TimeFit3), fixed = TRUE)\r","  if(length(F_cols3)==0){\r","    F_cols3 \u003c- grep(\"Hrate\", names(TimeFit3), fixed = TRUE)\r","  }\r","  \r","  achieved.report \u003c- TimeFit2[0,1:8]\r","  colnames(achieved.report)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"retain(B)\",\"dead(B)\",\"retain(N)\",\"dead(N)\",\"F\")\r","  for(i in 1:length(F_cols2)){\r","    temp.data \u003c- TimeFit2[,1:8]\r","    temp.data[,3] \u003c- i \r","    temp.data[,4] \u003c- TimeFit2[,Catch_cols2[i]]\r","    temp.data[,5] \u003c- TimeFit2[,Dead_cols2[i]]\r","    temp.data[,6] \u003c- TimeFit2[,CatchN_cols2[i]]\r","    temp.data[,7] \u003c- TimeFit2[,DeadN_cols2[i]]\r","    temp.data[,8] \u003c- TimeFit2[,F_cols2[i]]\r","    colnames(temp.data)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"retain(B)\",\"dead(B)\",\"retain(N)\",\"dead(N)\",\"F\")\r","    achieved.report \u003c- rbind(achieved.report,temp.data)\r","  }\r","  achieved.report\u003c-achieved.report[order(achieved.report$Year,achieved.report$Seas,achieved.report$Fleet),]\r","  \r","  #Set all future projections to fish at constant apical F that matches recent years\r","  #get the years of timeseries F's based on the forecast year range\r","  if(is.data.frame(forecast[[\"Fcast_years\"]])){\r","    min_fcast_yr \u003c- forecast[[\"Fcast_years\"]][forecast[[\"Fcast_years\"]][,'MG_type']==11,'st_year']\r","    if(min_fcast_yr==-999){\r","      min_fcast_yr \u003c- dat[[\"styr\"]]\r","    }else if(min_fcast_yr \u003c= 0){\r","      min_fcast_yr \u003c- dat[[\"endyr\"]] + min_fcast_yr\r","    }\r","    \r","    max_fcast_yr \u003c- forecast[[\"Fcast_years\"]][forecast[[\"Fcast_years\"]][,'MG_type']==11,'end_year']\r","    if(max_fcast_yr \u003c= 0){\r","      max_fcast_yr \u003c- dat[[\"endyr\"]] + max_fcast_yr\r","    }\r","    \r","  }else{ \r","    if(forecast[[\"Fcast_years\"]][3]==-999){\r","      min_fcast_yr \u003c- dat[[\"styr\"]]\r","    }else if(forecast[[\"Fcast_years\"]][3]\u003e0){\r","      min_fcast_yr \u003c- forecast[[\"Fcast_years\"]][3]\r","    }else{\r","      min_fcast_yr \u003c- dat[[\"endyr\"]]+forecast[[\"Fcast_years\"]][3]\r","    }\r","    \r","    if(forecast[[\"Fcast_years\"]][4]\u003e0){\r","      max_fcast_yr \u003c- forecast[[\"Fcast_years\"]][4]\r","    }else{\r","      max_fcast_yr \u003c- dat[[\"endyr\"]]+forecast[[\"Fcast_years\"]][4]\r","    }\r","  }\r","  TargetYears \u003c- TimeFit2[TimeFit2$Yr\u003e=min_fcast_yr \u0026 TimeFit2$Yr\u003c=max_fcast_yr,]\r","  TargetYears \u003c- TargetYears[,c(2,F_cols2)]\r","  seasons \u003c- unique(TargetYears[,1])\r","  F_by_Fleet_seas \u003c- as.data.frame(matrix(apply(TargetYears[TargetYears[,1]==seasons[1],,drop=FALSE], 2, mean),nrow=1,ncol=(length(F_cols)+1)))\r","  if(length(seasons)\u003e1){\r","    for(i in seasons[-1]){\r","      F_by_Fleet_seas \u003c- rbind(F_by_Fleet_seas,apply(TargetYears[TargetYears[,1]==i,,drop=FALSE], 2, mean))\r","    }\r","  }\r","  Forecast_target \u003c- forecast[[\"Forecast\"]]\r","  if(!is.element(Forecast_target,c(1,2,3))){\r","    stop(\"forecast should be set to either 1, 2, or 3 so we know what the target is\")\r","  }\r","  \r","  if(is.null(starting_Forecatch)){\r","    #Build a projection forcast matrix of F values by fleet/season/year which will adjusted to achieve target stock status, F, and allocations.\r","    forecast_F\u003c-matrix(1,nrow=forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols),ncol=5)\r","    forecast_F[,1]\u003c-sort(rep((dat[[\"endyr\"]]+1):(dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]]),length(seasons)*length(F_cols)))\r","    forecast_F[,2]\u003c-rep(sort(rep(seasons,length(F_cols))),forecast[[\"Nforecastyrs\"]])\r","    forecast_F[,3]\u003c-rep(sort(which(dat$fleetinfo$type!=3)),forecast[[\"Nforecastyrs\"]]*(length(seasons)))\r","    for(i in seasons){\r","      forecast_F[forecast_F[,2]==i,4]\u003c-unlist(rep(F_by_Fleet_seas[F_by_Fleet_seas[,1]==i,-1],forecast[[\"Nforecastyrs\"]]))\r","      forecast_F[forecast_F[,2]==i,5]\u003c-rep(99,length(F_cols)*forecast[[\"Nforecastyrs\"]])\r","    }\r","    forecast_F\u003c-as.data.frame(forecast_F)\r","    colnames(forecast_F)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"Catch or F\",\"Basis\")\r","    forecast_F[,\"Catch or F\"] \u003c- forecast_F[,\"Catch or F\"] + 0.00000001\r","  }else{\r","    if(dim(starting_Forecatch)[1]!=forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols)){\r","      stop(\"Error: You input a starting forecatch matrix but it is not the correct length n_years*n_fleets*n_seasons.\")\r","    }\r","    if(dim(starting_Forecatch)[2]!=5){\r","      stop(\"Error: You input a starting forecatch matrix but it does not have 5 columns Year, Season, Fleet, Catch, Basis.\")\r","    }\r","    if(length(dim(starting_Forecatch))!=2){\r","      stop(\"Error: You input a starting forecatch but it is not a matrix\")\r","    }\r","    forecast_F \u003c- starting_Forecatch\r","    colnames(forecast_F)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"Catch or F\",\"Basis\")\r","  }\r","  \r","  adjusted_F_OFL\u003c-1:(forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","\r","  #Extract fixed forecast values from the forecast file these will be fixed at these values for the projections\r","  #This is used to implement recent catches or fixed harvest from an independent fleet such as shrimp bycatch.\r","  if(!is.null(forecast[[\"ForeCatch\"]])){\r","    Fixed_catch_basis \u003c- forecast[[\"InputBasis\"]]\r","    Fixed_catch_target \u003c- forecast[[\"ForeCatch\"]]\r","    fixed_ref \u003c- seq_along(Fixed_catch_target[,1])\r","    if(length(names(Fixed_catch_target))==4){\r","      new_names \u003c- c(names(Fixed_catch_target),\"Basis\")\r","      Fixed_catch_target \u003c- cbind(Fixed_catch_target,rep(Fixed_catch_basis,length(Fixed_catch_target[,1])))\r","      names(Fixed_catch_target) \u003c- new_names\r","    }\r","    for(i in seq_along(Fixed_catch_target[,1])){\r","      fixed_ref[i]\u003c-which(forecast_F[,1]==Fixed_catch_target[i,1] \u0026 \r","                          forecast_F[,2]==Fixed_catch_target[i,2] \u0026 \r","                          forecast_F[,3]==Fixed_catch_target[i,3])\r","    }\r","    \r","    #Replace the temporary average F values with specified fixed inputs\r","    forecast_F[fixed_ref,c(4,5)]\u003c-Fixed_catch_target[,c(4,5)]\r","    adjusted_F_OFL\u003c-adjusted_F_OFL[-fixed_ref]\r","    if(length(adjusted_F_OFL)==0){stop(\"all F's are fixed nothing to estimate\")}\r","  }else{\r","    fixed_ref\u003c-NULL\r","  }\r","  \r","\r","  if(!is.null(Rebuild_yr)){\r","    #This reference identifies inputs subject to a rebuilding period F \r","    rebuild_ref \u003c- which(forecast_F[,1]\u003c=Rebuild_yr)\r","    if(length(rebuild_ref)\u003e0){\r","      adjusted_OFL_F_Rebuild\u003c-adjusted_F_OFL[adjusted_F_OFL\u003emax(rebuild_ref)]\r","      adjusted_Rebuild_F_Rebuild\u003c-rebuild_ref\r","      if(!is.null(fixed_ref)){\r","        adjusted_Rebuild_F_Rebuild\u003c-adjusted_Rebuild_F_Rebuild[-fixed_ref]\r","      }\r","    }\r","  }else{\r","    adjusted_OFL_F_Rebuild \u003c- adjusted_F_OFL\r","    adjusted_Rebuild_F_Rebuild \u003c- NULL\r","    rebuild_ref \u003c- NULL\r","  }\r","  #Here all input values are assigned to an allocation group if needed and\r","  #relative landings targets are identified\r","  n_groups \u003c- forecast[[\"N_allocation_groups\"]]\r","  groups \u003c- rep(0,length(F_cols))\r","  fleets_by_group \u003c- list()\r","  Allocations \u003c- forecast_F[,c(1,2,3,4,5,5)]\r","  Allocations[,c(4)] \u003c- 0\r","  Allocations[,c(5,6)] \u003c- 1\r","  names(Allocations) \u003c- c(\"Year\",\"Seas\",\"Fleet\",\"Group\",\"Target\",\"Achieved\")\r","  if(n_groups\u003e0){\r","    for(i in seq_along(forecast[[\"fleet_assignment_to_allocation_group\"]][,\"Fleet\"])){\r","      groups[forecast[[\"fleet_assignment_to_allocation_group\"]][i,\"Fleet\"]] \u003c- forecast[[\"fleet_assignment_to_allocation_group\"]][i,\"Group\"]\r","      Allocations[Allocations[,\"Fleet\"]==forecast[[\"fleet_assignment_to_allocation_group\"]][i,\"Fleet\"],4] \u003c- forecast[[\"fleet_assignment_to_allocation_group\"]][i,\"Group\"]\r","    }\r","    \r","    alloc \u003c- forecast[[\"allocation_among_groups\"]][order(forecast[[\"allocation_among_groups\"]][,\"Year\"]),]\r","    for(i in seq_along(alloc[,1])){\r","      for(j in seq_along(alloc[i,-1])){\r","        Allocations[Allocations[,1]\u003e=alloc[,\"Year\"] \u0026 Allocations[,4]==j,5] \u003c- alloc[i,(j+1)]/sum(alloc[i,-1])\r","      }\r","    }\r","    \r","    for(i in 1:n_groups){\r","      fleets_by_group[[i]]\u003c-which(is.element(which(dat$fleetinfo$type!=3),which(groups==i)))\r","    }\r","  }\r","  \r","  forecast[[\"Forecast\"]] \u003c- 4\r","  forecast[[\"InputBasis\"]] \u003c- -1\r","  forecast[[\"ForeCatch\"]] \u003c- forecast_F\r","  forecast[[\"FirstYear_for_caps_and_allocations\"]] \u003c- (dat[[\"endyr\"]]+forecast[[\"Nforecastyrs\"]]+1)\r","  \r","  keepFitting \u003c- TRUE\r","  loop \u003c- 0\r","  subloop \u003c- 0\r","  F_maxed \u003c- 100000\r","  \r","  F_adjust1 \u003c- F_adjust2 \u003c- 1\r","  F_adjust3 \u003c- rep(1,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","  search_step \u003c- MSY_step \r","  Fmult1 \u003c- Fmult2 \u003c- Fmult3 \u003c- Fmult4 \u003c- rep(1.01,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","  Fmult2a \u003c- Fmult2b \u003c- 1\r","  First_run\u003c-TRUE\r","  \r","  if(!is.null(Const_Catch)){\r","    forecast$fcast_rec_option \u003c- catch_rec\r","    SS_writepar_3.30(parlist = parlist,outfile=par_name,overwrite = TRUE)\r","    SS_writeforecast(mylist=forecast,overwrite = TRUE)\r","    SS_writestarter(mylist=start,overwrite = TRUE)\r","    \r","    if(run_in_MSE==TRUE){\r","      SSMSE:::run_EM(EM_dir = getwd(), verbose = TRUE, check_converged = TRUE)\r","    }else{\r","      shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\" -nohess\",sep=\"\"))\r","    }\r","    #Begin the search in the Benchmark phase\r","    fitting_Benchmark \u003c- FALSE\r","    fitting_OFL \u003c- FALSE\r","    fitting_ABC \u003c- FALSE\r","    fitting_Rebuild \u003c- FALSE\r","    fitting_F0 \u003c- FALSE\r","    fitting_Fixed_Catch \u003c- TRUE\r","    CC_loop \u003c- 1\r","    Catch_Target \u003c- rep(Const_Catch[CC_loop],forecast[[\"Nforecastyrs\"]])\r","    Catch_trunc \u003c- 0\r","    method \u003c- \"fixed_catch\"\r","  }else if(Benchmark_complete == FALSE){\r","    #Save all the modified files and then perform a base run of SS so that output is specified correctly with \r","    #a forecast[[\"Nforecastyrs\"]] year projection series.\r","    \r","    SS_writepar_3.30(parlist = parlist, outfile = par_name, overwrite = TRUE)\r","    SS_writeforecast(mylist=forecast,overwrite = TRUE)\r","    SS_writestarter(mylist=start,overwrite = TRUE)\r","    \r","    if(run_in_MSE==TRUE){\r","      SSMSE:::run_EM(EM_dir = getwd(), verbose = TRUE, check_converged = TRUE)\r","    }else{\r","      shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\" -nohess\",sep=\"\"))\r","    }\r","    #Begin the search in the Benchmark phase\r","    fitting_Benchmark \u003c- TRUE\r","    fitting_OFL \u003c- FALSE\r","    fitting_ABC \u003c- FALSE\r","    fitting_Rebuild \u003c- FALSE\r","    fitting_F0 \u003c- FALSE\r","    fitting_Fixed_Catch \u003c- FALSE\r","    \r","    MSY.Fit \u003c- data.frame(catch=c(0),Ave.F=c(0),depletion=c(0),target.depletion=c(0))\r","    method \u003c- \"Benchmark\"\r","    \r","  }else{\r","    #Save all the modified files and then set search to begin in OFL phase \r","    \r","    start \u003c- SS_readstarter()\r","    dat \u003c- SS_readdat(file = start$datfile, version = 3.3)\r","    ctl \u003c- SS_readctl(file = start$ctlfile, version = 3.3, use_datlist = TRUE, datlist = dat)\r","    results \u003c- SS_output(dir = getwd(), covar = FALSE)\r","    forecast \u003c- SS_readforecast() \r","    parlist \u003c- SS_readpar_3.30(parfile = par_name, datsource = dat, ctlsource = ctl)\r","    \r","    forecast$fcast_rec_option \u003c- catch_rec\r","    SS_writeforecast(mylist=forecast,overwrite = TRUE)\r","    \r","    fitting_Benchmark \u003c- FALSE\r","    fitting_OFL \u003c- TRUE\r","\t  fitting_ABC \u003c- FALSE\r","    fitting_Rebuild \u003c- FALSE\r","    fitting_F0 \u003c- FALSE\r","    fitting_Fixed_Catch \u003c- FALSE\r","    method \u003c- \"OFL\"\r","  }\r","  \r","  #Set up plot window for production of search diagnostic plots depending on target specifications\r","  #These plots were largely for diagnostic testing during code development but can allow you to see what\r","  #is going wrong if a future bug does occur.\r","  if(Make_plots==TRUE){\r","    if(Forecast_target==2 \u0026 fitting_Benchmark==TRUE){\r","      par(mfrow=c(5,2))\r","    }else{\r","      par(mfrow=c(4,2))\r","    }\r","  }\r","  #Now start a loop of projecting and modifying fixed F's until the desired \r","  #landings projections are achieved\r","  while(keepFitting){\r","    #Read in the SS results for landings and stock status to determine if desired\r","    #targets have been achieved\r","    resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","    TimeFit \u003c- resultsFit[[\"timeseries\"]]\r","    TimeFit \u003c- TimeFit[TimeFit[,\"Yr\"]\u003edat[[\"endyr\"]],]\r","    SPRfit \u003c- resultsFit[[\"sprseries\"]]\r","    SPRfit \u003c- SPRfit[SPRfit[,\"Yr\"]\u003edat[[\"endyr\"]],]\r","    loop \u003c- loop + 1\r","    if(Make_plots==TRUE){\r","      par(mar=c(4,3,3,2))\r","      plot(SPRfit[SPRfit[,\"Yr\"]\u003e=dat[[\"endyr\"]],\"F_report\"],xlab=\"year\",ylab=\"F\",main = paste0(method,\" loop = \",loop))\r","      plot(SPRfit[SPRfit[,\"Yr\"]\u003e=dat[[\"endyr\"]],\"Deplete\"],xlab=\"year\",ylab=\"Depletion\",main = paste0(method,\" loop = \",loop))\r","    }\r","    \r","    #Identify the column numbers for Catch, F, SSB, Recruits, etc\r","    Catch_cols \u003c- grep(\"retain(B)\", names(TimeFit), fixed = TRUE)\r","    Dead_cols \u003c- grep(\"dead(B)\", names(TimeFit), fixed = TRUE)\r","    CatchN_cols \u003c- grep(\"retain(N)\", names(TimeFit), fixed = TRUE)\r","    DeadN_cols \u003c- grep(\"dead(N)\", names(TimeFit), fixed = TRUE)\r","    F_cols \u003c- grep(\"F\", names(TimeFit), fixed = TRUE)\r","    if(length(F_cols)==0){\r","      F_cols \u003c- grep(\"Hrate\", names(TimeFit), fixed = TRUE)\r","    }\r","    \r","    TimeFit2 \u003c- aggregate(TimeFit[,sort(c(2,4,7,Catch_cols,Dead_cols,CatchN_cols,DeadN_cols,F_cols))],by=list(TimeFit$Yr,TimeFit$Seas),FUN=sum,na.rm=TRUE)[,-c(3,4,5)]\r","    names(TimeFit2)[c(1,2)] \u003c- c(\"Yr\", \"Seas\")\r","    \r","    Catch_cols2 \u003c- grep(\"retain(B)\", names(TimeFit2), fixed = TRUE)\r","    Dead_cols2 \u003c- grep(\"dead(B)\", names(TimeFit2), fixed = TRUE)\r","    CatchN_cols2 \u003c- grep(\"retain(N)\", names(TimeFit2), fixed = TRUE)\r","    DeadN_cols2 \u003c- grep(\"dead(N)\", names(TimeFit2), fixed = TRUE)\r","    F_cols2 \u003c- grep(\"F\", names(TimeFit2), fixed = TRUE)\r","    if(length(F_cols2)==0){\r","      F_cols2 \u003c- grep(\"Hrate\", names(TimeFit2), fixed = TRUE)\r","    }\r","    \r","    TimeFit3 \u003c- aggregate(TimeFit[,sort(c(2,7,8,Catch_cols,Dead_cols,CatchN_cols,DeadN_cols,F_cols))],by=list(TimeFit$Yr),FUN=sum,na.rm=TRUE)[,-2]\r","    names(TimeFit3)[c(1)] \u003c- c(\"Yr\")\r","    \r","    Catch_cols3 \u003c- grep(\"retain(B)\", names(TimeFit3), fixed = TRUE)\r","    Dead_cols3 \u003c- grep(\"dead(B)\", names(TimeFit3), fixed = TRUE)\r","    CatchN_cols3 \u003c- grep(\"retain(N)\", names(TimeFit3), fixed = TRUE)\r","    DeadN_cols3 \u003c- grep(\"dead(N)\", names(TimeFit3), fixed = TRUE)\r","    F_cols3 \u003c- grep(\"F\", names(TimeFit3), fixed = TRUE)\r","    if(length(F_cols3)==0){\r","      F_cols3 \u003c- grep(\"Hrate\", names(TimeFit3), fixed = TRUE)\r","    }\r","    \r","    achieved.report \u003c- TimeFit2[0,1:8]\r","    colnames(achieved.report)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"retain(B)\",\"dead(B)\",\"retain(N)\",\"dead(N)\",\"F\")\r","    for(i in 1:length(F_cols2)){\r","      temp.data \u003c- TimeFit2[,1:8]\r","      temp.data[,3] \u003c- i \r","      temp.data[,4] \u003c- TimeFit2[,Catch_cols2[i]]\r","      temp.data[,5] \u003c- TimeFit2[,Dead_cols2[i]]\r","      temp.data[,6] \u003c- TimeFit2[,CatchN_cols2[i]]\r","      temp.data[,7] \u003c- TimeFit2[,DeadN_cols2[i]]\r","      temp.data[,8] \u003c- TimeFit2[,F_cols2[i]]\r","      colnames(temp.data)\u003c-c(\"Year\",\"Seas\",\"Fleet\",\"retain(B)\",\"dead(B)\",\"retain(N)\",\"dead(N)\",\"F\")\r","      achieved.report \u003c- rbind(achieved.report,temp.data)\r","    }\r","    achieved.report\u003c-achieved.report[order(achieved.report$Year,achieved.report$Seas,achieved.report$Fleet),]\r","    \r","    if(fitting_Rebuild==TRUE){\r","      terminal_year \u003c- min(length(SPRfit$Yr[SPRfit$Yr\u003c=Rebuild_yr])+5, Years_projection) #min to ensure report years beyond projection length not requested\r","    }else{\r","      terminal_year \u003c- min(Years_report, Years_projection) #min to ensure report years beyond projection length not requested\r","    }\r","    \r","    Achieved.Catch \u003c- apply(TimeFit3[,Catch_cols3,drop=FALSE],1,sum)[1:terminal_year]\r","    Achieved.Catch.All \u003c- apply(TimeFit3[,Catch_cols3,drop=FALSE],1,sum)\r","    Achieved.SSBratio \u003c- TimeFit3$SpawnBio[1:terminal_year]/Virgin_bio\r","    Achieved.SPR \u003c- TimeFit3$SpawnBio[1:terminal_year]/TimeFit3$Recruit_0[1:terminal_year]\r","    Achieved.SSB \u003c- TimeFit3$SpawnBio[1:terminal_year]\r","    Achieved.Rec \u003c- TimeFit3$Recruit_0[1:terminal_year]\r","    Achieved.F \u003c- SPRfit$F_report[1:terminal_year]\r","    if(is.null(Achieved.F)){\r","      Achieved.F \u003c- SPRfit$F_std[1:terminal_year]\r","    }\r","    #If reading in results of a previous OFL run then set the F_OFL and F.ABC values before begining ABC/Rebuild loops\r","   \r","    if(Benchmark_complete==TRUE \u0026 First_run==TRUE){\r","      F_report\u003c-SPRfit$F_report\r","      if(is.null(F_report)){\r","        F_report\u003c-SPRfit$F_std\r","      }\r","      FScale\u003c-median(F_report[(length(F_report)-0.5*Years_projection):length(F_report)])\r","      F_OFL\u003c-FScale\r","      if(!is.null(ABC_Fraction)){\r","        F.ABC\u003c-ABC_Fraction*FScale\r","      }else{\r","        F.ABC\u003c-FScale\r","      }\r","      First_run\u003c-FALSE\r","      Depletion\u003c-TimeFit3$SpawnBio/Virgin_bio\r","      Target.Depletion \u003c- median(Depletion[(length(Depletion)-29):length(Depletion)])\r","      Target.Rebuild \u003c- median(Depletion[(length(Depletion)-29):length(Depletion)])\r","      \r","      Achieved.Catch.equil \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/10\r","      \r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_Benchmark\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group.equil \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3[fleets_by_group[[i]]]])/10\r","          projection_results[[\"Group_Catch_Equil_Benchmark\"]][[i]]\u003c-Achieved.Catch.group.equil\r","          \r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_Benchmark\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      Achieved.SSBratio.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)])/Virgin_bio\r","      Achieved.SPR.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)]/TimeFit3$Recruit_0[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)]) #median(SPRfit$SPR[(length(SPRfit$SPR)-9):length(SPRfit$SPR)])\r","      Achieved.SSB.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)])\r","      Achieved.Rec.equil \u003c- median(TimeFit3$Recruit_0[(length(TimeFit3$Recruit_0)-9):length(TimeFit3$Recruit_0)])\r","      \r","      projection_results[[\"Catch_equil_Benchmark\"]] \u003c- Achieved.Catch.equil\r","      projection_results[[\"F_equil_Benchmark\"]] \u003c- F_OFL\r","      projection_results[[\"Depletion_equil_Benchmark\"]] \u003c- Achieved.SSBratio.equil\r","      projection_results[[\"SSB_equil_Benchmark\"]] \u003c- Achieved.SSB.equil\r","      projection_results[[\"SPR_equil_Benchmark\"]] \u003c- Achieved.SPR.equil\r","      projection_results[[\"Recruitment_equil_Benchmark\"]] \u003c- Achieved.Rec.equil\r","      \r","      projection_results[[\"Forecatch_Benchmark\"]] \u003c- achieved.report\r","      \r","      projection_results[[\"Catch_Benchmark\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_Benchmark\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_Benchmark\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_Benchmark\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_Benchmark\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_Benchmark\"]] \u003c- Achieved.Rec\r","    }\r","    \r","    if(is.na(max(abs(achieved.report[,'F']-forecast_F[,\"Catch or F\"])[adjusted_F_OFL]))){\r","      if(fitting_Fixed_Catch==TRUE){\r","        if(Catch_trunc \u003e= (forecast$Nforecastyrs - 20)){\r","          Catch_trunc \u003c- Catch_trunc + 1\r","        }else{\r","          Catch_trunc \u003c- Catch_trunc + 5\r","        }\r","        Catch_Target[(forecast$Nforecastyrs-c((Catch_trunc-1):0))] \u003c- 0\r","        forecast_F[(length(forecast_F[,1])-c((Catch_trunc*length(seasons)*length(F_cols)-1):0)),4] \u003c- 0\r","      }\r","      forecast_F[,4] \u003c- forecast_F[,4]*0.5\r","      loop \u003c- loop - 1\r","    }else{\r","      \r","    if(max(abs(achieved.report[,'F']-forecast_F[,\"Catch or F\"])[adjusted_F_OFL])\u003e0.1){\r","      if(fitting_Fixed_Catch==TRUE){\r","        if(Catch_trunc \u003e= (forecast$Nforecastyrs - 20)){\r","          Catch_trunc \u003c- Catch_trunc + 1\r","        }else{\r","          Catch_trunc \u003c- Catch_trunc + 5\r","        }\r","        Catch_Target[(forecast$Nforecastyrs-c((Catch_trunc-1):0))] \u003c- 0\r","        forecast_F[(length(forecast_F[,1])-c((Catch_trunc*length(seasons)*length(F_cols)-1):0)),4] \u003c- 0\r","      }\r","      F_maxed \u003c- max(achieved.report[,'F'])\r","      forecast_F[,4] \u003c- achieved.report[,'F']\r","      loop \u003c- loop - 1\r","    }else {\r","    if(fitting_Benchmark==TRUE){\r","      \r","      #Calculate the average F at equilibrium that all F's will be scaled to in order\r","      #to achieve equal F in every year. As depletion approaches the target value this \r","      #F will approach F(OFL).\r","       \r","      \r","      F_report\u003c-SPRfit$F_report\r","      if(is.null(F_report)){\r","        F_report\u003c-SPRfit$F_std\r","      }\r","      FScale\u003c-median(F_report[(length(F_report)-0.5*Years_projection):length(F_report)])\r","      F_OFL\u003c-FScale\r","      if(!is.null(ABC_Fraction)){\r","        F.ABC\u003c-ABC_Fraction*FScale\r","      }else{\r","        F.ABC\u003c-FScale\r","      }\r","      \r","      Achieved.Catch.equil \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/10\r","      Achieved.SSBratio.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)])/Virgin_bio\r","      Achieved.SPR.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)]/TimeFit3$Recruit_0[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)]) #median(SPRfit$SPR[(length(SPRfit$SPR)-9):length(SPRfit$SPR)])\r","      Achieved.SSB.equil \u003c- median(TimeFit3$SpawnBio[(length(TimeFit3$SpawnBio)-9):length(TimeFit3$SpawnBio)])\r","      Achieved.Rec.equil \u003c- median(TimeFit3$Recruit_0[(length(TimeFit3$Recruit_0)-9):length(TimeFit3$Recruit_0)])\r","      \r","      \r","      \r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_Benchmark\"]]\u003c-list()\r","        projection_results[[\"Group_Catch_Equil_Benchmark\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group.equil \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3[fleets_by_group[[i]]]])/10\r","          projection_results[[\"Group_Catch_Equil_Benchmark\"]][[i]]\u003c-Achieved.Catch.group.equil\r","          \r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_Benchmark\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      projection_results[[\"Catch_equil_Benchmark\"]] \u003c- Achieved.Catch.equil\r","      projection_results[[\"F_equil_Benchmark\"]] \u003c- F_OFL\r","      projection_results[[\"Depletion_equil_Benchmark\"]] \u003c- Achieved.SSBratio.equil\r","      projection_results[[\"SSB_equil_Benchmark\"]] \u003c- Achieved.SSB.equil\r","      projection_results[[\"SPR_equil_Benchmark\"]] \u003c- Achieved.SPR.equil\r","      projection_results[[\"Recruitment_equil_Benchmark\"]] \u003c- Achieved.Rec.equil\r","      \r","      projection_results[[\"Forecatch_Benchmark\"]] \u003c- achieved.report\r","      \r","      projection_results[[\"Catch_Benchmark\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_Benchmark\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_Benchmark\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_Benchmark\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_Benchmark\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_Benchmark\"]] \u003c- Achieved.Rec\r","      #Calculate depletion target adjustment scale depending on the specified target (SPR ratio, SSB ratio, or true MSY)   \r","      if(Forecast_target==1){\r","        search_step\u003c-0.00001\r","        Target.Depletion \u003c- forecast[[\"SPRtarget\"]]\r","        Depletion\u003c-SPRfit$SPR\r","        \r","        Achieved.Depletion \u003c- median(Depletion[(length(Depletion)-29):length(Depletion)])\r","        \r","        Achieved.Depletion \u003c- min(Achieved.Depletion,max(Target.Depletion,0.9))\r","        \r","        DepletionScale \u003c- (1-Target.Depletion)/(1-Achieved.Depletion)\r","        \r","        if(FScale==0){\r","          if(DepletionScale\u003c=1.0001){\r","            DepletionScale\u003c-1\r","          }else{\r","            FScale\u003c-0.0001\r","            F_OFL\u003c-FScale\r","            if(!is.null(ABC_Fraction)){\r","              F.ABC\u003c-ABC_Fraction*FScale\r","            }else{\r","              F.ABC\u003c-FScale\r","            }\r","          }\r","        }else{\r","          DepletionScale \u003c- (-log(1-((1-exp(-FScale))*DepletionScale))/FScale)\r","        }\r","        \r","        Depletion_R\u003c-TimeFit3$SpawnBio/Virgin_bio\r","        Target.Rebuild \u003c- median(Depletion_R[(length(Depletion_R)-9):length(Depletion_R)])\r","        \r","      }else if(Forecast_target==2){\r","        Depletion \u003c- TimeFit3$SpawnBio/Virgin_bio\r","        Achieved.Depletion \u003c- median(Depletion[(length(Depletion)-29):length(Depletion)])\r","        Achieved.Depletion \u003c- min(Achieved.Depletion,.9)\r","        if(First_run == TRUE){\r","          Target.Depletion \u003c- forecast[[\"Btarget\"]]\r","          First_run \u003c- FALSE\r","        }\r","        Target.Rebuild \u003c- Target.Depletion\r","        Achieved.SSB \u003c- Achieved.Depletion\r","        if(max(abs(1-Fmult3))\u003eAllocation.Threshold | \r","\t\t       max(abs(1-Fmult2))\u003eAnnual.F.Threshold | \r","\t\t       max(abs(1-Fmult1))\u003eDepletion.Threshold){\r","          loop\u003c-loop-1\r","          subloop\u003c-subloop+1\r","          if(F_max==TRUE){\r","            Achieved.Catch \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/\r","\t\t\t                  sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),\"Recruit_0\"])\r","          }else{\r","            Achieved.Catch \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/10\r","          }\r","          MSY.Fit[1,] \u003c- c(Achieved.Catch,FScale,Achieved.Depletion,Target.Depletion)\r","        }else{\r","          subloop\u003c-0\r","          if(F_max==TRUE){\r","            Achieved.Catch \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/\r","\t\t\t                  sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),\"Recruit_0\"])\r","          }else{\r","            Achieved.Catch \u003c- sum(TimeFit3[(length(TimeFit3[,1])-9):length(TimeFit3[,1]),Catch_cols3])/10\r","          }\r","          MSY.Fit \u003c- rbind(MSY.Fit[1,],MSY.Fit)\r","          MSY.Fit[1,] \u003c- c(Achieved.Catch,FScale,Achieved.Depletion,Target.Depletion)\r","          if(loop\u003e1){\r","            if(Achieved.Catch\u003cLast_Achieved_Catch){\r","              search_step \u003c- -0.5*search_step\r","            }\r","          \r","            Target.Depletion \u003c- Target.Depletion+search_step\r","            \r","            min_diff \u003c- which(abs(MSY.Fit[,4]-Target.Depletion)\u003c0.001)\r","            if(length(min_diff)\u003e0){\r","              Old.Catch \u003c- MSY.Fit[min_diff[1],1]\r","              if(Old.Catch\u003cAchieved.Catch){\r","                search_step \u003c- -0.5*search_step\r","              }\r","              Target.Depletion \u003c- Target.Depletion+search_step\r","              Achieved.Catch \u003c- Old.Catch\r","            }\r","          }else{\r","            steps \u003c- seq(0.1,0.9,0.1)\r","            New.Target.Depletion \u003c- steps[which(abs(steps-Target.Depletion)==min(abs(steps-Target.Depletion)))[1]]\r","            if(New.Target.Depletion\u003cTarget.Depletion){\r","              search_step \u003c- -1*search_step\r","            }\r","            Target.Depletion \u003c- New.Target.Depletion\r","          }\r","          Last_Achieved_Catch \u003c- Achieved.Catch\r","        }\r","        DepletionScale \u003c- (1-Target.Depletion)/(1-Achieved.Depletion)\r","        \r","        if(FScale==0){\r","          if(DepletionScale\u003c=1.0001){\r","            DepletionScale\u003c-1\r","          }else{\r","            FScale\u003c-0.0001\r","            F_OFL\u003c-FScale\r","            if(!is.null(ABC_Fraction)){\r","              F.ABC\u003c-ABC_Fraction*FScale\r","            }else{\r","              F.ABC\u003c-FScale\r","            }\r","          }\r","        }\r","        \r","        if(Make_plots==TRUE){\r","          par(mar=c(4,3,3,2))\r","          if(F_max==TRUE){\r","            plot(x=TimeFit3[,\"Yr\"],y=apply(TimeFit3[,Catch_cols3,drop=FALSE],1,sum)/TimeFit3[,\"Recruit_0\"],\r","  \t\t       xlab=\"year\",ylab=\"Total Yield Per Recruit\",main = paste0(method,\" loop = \",loop,\".\",subloop))\r","            plot(x=MSY.Fit[,\"depletion\"],y=MSY.Fit[,\"catch\"],xlim=c(0.9*min(MSY.Fit[,3:4]),1.1*max(MSY.Fit[,3:4])),\r","  \t\t       xlab=\"Esimated depletion\",ylab=\"Total Yield Per Recruit\",main = paste0(method,\" loop = \",loop,\".\",subloop))\r","            lines(x=c(MSY.Fit[1,c(4,4)]),y=c(0,2*max(MSY.Fit[,\"catch\"])),col=\"dark red\")\r","            points(x=MSY.Fit[1,3],y=MSY.Fit[1,1],pch=16,col=\"dark blue\")\r","          }else{\r","            plot(x=TimeFit3[,\"Yr\"],y=apply(TimeFit3[,Catch_cols3,drop=FALSE],1,sum),\r","  \t\t       xlab=\"year\",ylab=\"Total Yield\",main = paste0(method,\" loop = \",loop,\".\",subloop))\r","            plot(x=MSY.Fit[,\"depletion\"],y=MSY.Fit[,\"catch\"],xlim=c(0.9*min(MSY.Fit[,3:4]),1.1*max(MSY.Fit[,3:4])),\r","  \t\t       xlab=\"Esimated depletion\",ylab=\"Total Yield\",main = paste0(method,\" loop = \",loop,\".\",subloop))\r","            lines(x=c(MSY.Fit[1,c(4,4)]),y=c(0,2*max(MSY.Fit[,\"catch\"])),col=\"dark red\")\r","            points(x=MSY.Fit[1,3],y=MSY.Fit[1,1],pch=16,col=\"dark blue\")\r","          }\r","        }\r","      }else if(Forecast_target==3){\r","        search_step\u003c-0.00001\r","        Target.Depletion \u003c- forecast[[\"Btarget\"]]\r","        Target.Rebuild \u003c- forecast[[\"Btarget\"]]\r","        Depletion\u003c-TimeFit3$SpawnBio/Virgin_bio\r","        Achieved.Depletion \u003c- median(Depletion[(length(Depletion)-29):length(Depletion)])\r","        Achieved.Depletion \u003c- min(Achieved.Depletion,max(0.9,Target.Depletion))\r","        DepletionScale \u003c- (1-Target.Depletion)/(1-Achieved.Depletion)\r","        \r","        if(FScale==0){\r","          if(DepletionScale\u003c=1.0001){\r","            DepletionScale\u003c-1\r","          }else{\r","            FScale\u003c-0.0001\r","            F_OFL\u003c-FScale\r","            if(!is.null(ABC_Fraction)){\r","              F.ABC\u003c-ABC_Fraction*FScale\r","            }else{\r","              F.ABC\u003c-FScale\r","            }\r","          }\r","        }else{\r","          DepletionScale \u003c- (-log(1-((1-exp(-FScale))*DepletionScale))/FScale)\r","        }\r","        \r","      }\r","    }else if(fitting_OFL==TRUE){\r","      search_step\u003c-0.00001 #Set search step to small value so it doesn't trigger continued loops this value is only needed during the Benchmark MSY search\r","      DepletionScale\u003c-1 #Set depletion scale to 1 so it doesn't trigger continued loops now that Benchmark search is complete\r","      FScale\u003c-F_OFL #Set the F target to F.OFL for rescaling annual F values\r","      \r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_OFL\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_OFL\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      projection_results[[\"Catch_OFL\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_OFL\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_OFL\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_OFL\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_OFL\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_OFL\"]] \u003c- Achieved.Rec\r","      projection_results[[\"Forecatch_OFL\"]] \u003c- achieved.report\r","      \r","    }else if(fitting_ABC==TRUE){\r","      search_step\u003c-0.00001 #Set search step to small value so it doesn't trigger continued loops this value is only needed during the Benchmark MSY search\r","      DepletionScale\u003c-1 #Set depletion scale to 1 so it doesn't trigger continued loops now that Benchmark search is complete\r","      FScale\u003c-F.ABC #Set the F target to F.ABC for rescaling annual F values\r","      \r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_ABC\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_ABC\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      projection_results[[\"Catch_ABC\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_ABC\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_ABC\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_ABC\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_ABC\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_ABC\"]] \u003c- Achieved.Rec\r","      projection_results[[\"Forecatch_ABC\"]] \u003c- achieved.report\r","    }else if(fitting_F0==TRUE){\r","      search_step\u003c-0.00001 #Set search step to small value so it doesn't trigger continued loops this value is only needed during the Benchmark MSY search\r","      DepletionScale\u003c-1 #Set depletion scale to 1 so it doesn't trigger continued loops now that Benchmark search is complete\r","      FScale\u003c-0 #Set the F target to 0 for rescaling annual F values\r","      \r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_F0\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_F0\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      projection_results[[\"Catch_F0\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_F0\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_F0\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_F0\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_F0\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_F0\"]] \u003c- Achieved.Rec\r","      projection_results[[\"Forecatch_F0\"]] \u003c- achieved.report\r","    }else if(fitting_Rebuild==TRUE){\r","      search_step\u003c-0.00001 #Set search step to small value so it doesn't trigger continued loops this value is only needed during the Benchmark MSY search\r","      DepletionScale\u003c-1 #Set depletion scale to 1 so it doesn't trigger continued loops now that Benchmark search is complete\r","      FScale\u003c-F_OFL #Set the F target to F_OFL for rescaling annual F values in years after the rebuild period.\r","      F_report\u003c-SPRfit$F_report\r","      if(is.null(F_report)){\r","        F_report\u003c-SPRfit$F_std\r","      }\r","      F_Rebuild_Scale\u003c-F_report[SPRfit$Yr==Rebuild_yr]\r","      Depletion\u003c-TimeFit3$SpawnBio/Virgin_bio\r","      Achieved.Rebuild \u003c- mean(Depletion[SPRfit$Yr==Rebuild_yr])\r","      \r","      Rebuild.Scale \u003c- (1-Target.Rebuild)/(1-Achieved.Rebuild)\r","      Rebuild.Ratio \u003c- Rebuild.Scale\r","      Rebuild.Scale \u003c- min(-log(1-((1-exp(-F_Rebuild_Scale))*Rebuild.Scale)),FScale)\r","      if(Rebuild.Scale \u003c 0.00001 \u0026 Rebuild.Ratio \u003c 1){\r","        Rebuild.Scale \u003c- 0\r","      }\r","      if(n_groups\u003e1){\r","        projection_results[[\"Group_Catch_Rebuild\"]]\u003c-list()\r","        for(i in 1:n_groups){\r","          Achieved.Catch.group \u003c- apply(TimeFit3[1:terminal_year,Catch_cols3[fleets_by_group[[i]]],drop=FALSE],1,sum)\r","          projection_results[[\"Group_Catch_Rebuild\"]][[i]]\u003c-Achieved.Catch.group\r","        }\r","      }\r","      \r","      projection_results[[\"Catch_Rebuild\"]] \u003c- Achieved.Catch\r","      projection_results[[\"F_Rebuild\"]] \u003c- Achieved.F\r","      projection_results[[\"Depletion_Rebuild\"]] \u003c- Achieved.SSBratio\r","      projection_results[[\"SSB_Rebuild\"]] \u003c- Achieved.SSB\r","      projection_results[[\"SPR_Rebuild\"]] \u003c- Achieved.SPR\r","      projection_results[[\"Recruitment_Rebuild\"]] \u003c- Achieved.Rec\r","      projection_results[[\"Forecatch_Rebuild\"]] \u003c- achieved.report\r","    }else if (fitting_Fixed_Catch==TRUE){\r","      \r","      search_step\u003c-0.00001 #Set search step to small value so it doesn't trigger continued loops this value is only needed during the Benchmark MSY search\r","      DepletionScale\u003c-1 #Set depletion scale to 1 so it doesn't trigger continued loops now that Benchmark search is complete\r","      FScale\u003c-0 #Set the F target to F_OFL for rescaling annual F values in years after the rebuild period.\r","      \r","      Fmult4 \u003c- rep(Catch_Target/Achieved.Catch.All,each=(length(seasons)*length(F_cols)))\r","      \r","      Fmult4 \u003c- ifelse(forecast_F[,4]\u003e=1.5,ifelse(Fmult4\u003e1,1,Fmult4),Fmult4)\r","      \r","      Fmult4[is.na(Fmult4)] \u003c- 1\r","      \r","      projection_results[[paste0(\"Catch_FixedCatch_\",CC_loop)]] \u003c- Achieved.Catch\r","      projection_results[[paste0(\"F_FixedCatch_\",CC_loop)]] \u003c- Achieved.F\r","      projection_results[[paste0(\"Depletion_FixedCatch_\",CC_loop)]] \u003c- Achieved.SSBratio\r","      projection_results[[paste0(\"SSB_FixedCatch_\",CC_loop)]] \u003c- Achieved.SSB\r","      projection_results[[paste0(\"SPR_FixedCatch_\",CC_loop)]] \u003c- Achieved.SPR\r","      projection_results[[paste0(\"Recruitment_FixedCatch_\",CC_loop)]] \u003c- Achieved.Rec\r","      projection_results[[paste0(\"Forecatch_FixedCatch_\",CC_loop)]] \u003c- achieved.report\r","    }\r","    \r","    #Fmult2 calculations define the multiplier for adjusting annual F values\r","    #Zero catch years are identified first to prevent divide by zero errors in the scaling and\r","    #to tell the search algorithm that the target has been achieved\r","\r","    if(is.null(SPRfit$F_report)){\r","      zero_catch \u003c- which(SPRfit$F_std[sort(rep(seq_along(SPRfit$F_std),length(seasons)*length(F_cols)))]==0)\r","    }else{\r","      zero_catch \u003c- which(SPRfit$F_report[sort(rep(seq_along(SPRfit$F_report),length(seasons)*length(F_cols)))]==0)\r","    }\r","    if(fitting_Fixed_Catch==FALSE){\r","      if(length(zero_catch)\u003e0){\r","        if(FScale==0){\r","          Fmult2[zero_catch] \u003c- 1\r","          Fmult2[-zero_catch] \u003c- 0\r","        }else{\r","          Fmult2[zero_catch] \u003c- 2\r","          if(is.null(SPRfit$F_report)){\r","            temp_F \u003c- SPRfit$F_std[sort(rep(seq_along(SPRfit$F_std),length(seasons)*length(F_cols)))][-zero_catch]\r","          }else{\r","            temp_F \u003c- SPRfit$F_report[sort(rep(seq_along(SPRfit$F_report),length(seasons)*length(F_cols)))][-zero_catch]\r","          }\r","          temp_F[temp_F\u003e1.5] \u003c- 1.5\r","          temp_F[temp_F\u003c(min(0.001,FScale))] \u003c- min(0.001,FScale)\r","          Fmult2[-zero_catch] \u003c- FScale/temp_F\r","        }\r","      }else if(FScale==0){\r","        Fmult2[] \u003c- 0\r","      }else{\r","        if(is.null(SPRfit$F_report)){\r","          temp_F \u003c- SPRfit$F_std[sort(rep(seq_along(SPRfit$F_std),length(seasons)*length(F_cols)))]\r","        }else{\r","          temp_F \u003c- SPRfit$F_report[sort(rep(seq_along(SPRfit$F_report),length(seasons)*length(F_cols)))]\r","        }\r","        temp_F[temp_F\u003e1.5] \u003c- 1.5\r","        temp_F[temp_F\u003c(min(0.001,FScale))] \u003c- min(0.001,FScale)\r","        Fmult2 \u003c- FScale/temp_F\r","      }\r","    }else{\r","      Fmult2 \u003c- rep(1,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","    }\r","    \r","    #If in a rebuild search phase the rebuild years are now adjusted independently of the later F_OFL years\r","    if(fitting_Rebuild==TRUE){\r","      if(is.null(SPRfit$F_report)){\r","        temp_F \u003c- SPRfit$F_std[sort(rep(seq_along(SPRfit$F_std),length(seasons)*length(F_cols)))][adjusted_Rebuild_F_Rebuild]\r","      }else{\r","        temp_F \u003c- SPRfit$F_report[sort(rep(seq_along(SPRfit$F_report),length(seasons)*length(F_cols)))][adjusted_Rebuild_F_Rebuild]\r","      }\r","      zero_rebuild \u003c- which(temp_F==0)\r","      if(length(zero_rebuild)\u003e0){\r","        if(Rebuild.Scale==0){\r","          Fmult2[adjusted_Rebuild_F_Rebuild[zero_rebuild]] \u003c- 1\r","          Fmult2[adjusted_Rebuild_F_Rebuild[-zero_rebuild]] \u003c- 0\r","        }else{\r","          Fmult2[adjusted_Rebuild_F_Rebuild[zero_rebuild]] \u003c- 2\r","          temp_F[temp_F\u003e1.5] \u003c- 1.5\r","          temp_F[temp_F\u003c(min(0.001,Rebuild.Scale))] \u003c- min(0.001,Rebuild.Scale)\r","          Fmult2[adjusted_Rebuild_F_Rebuild[-zero_rebuild]] \u003c- Rebuild.Scale/temp_F[-zero_rebuild]\r","        }\r","      }else if(Rebuild.Scale==0){\r","        Fmult2[adjusted_Rebuild_F_Rebuild] \u003c- 0\r","      }else{\r","        temp_F[temp_F\u003e1.5] \u003c- 1.5\r","        temp_F[temp_F\u003c(min(0.001,Rebuild.Scale))] \u003c- min(0.001,Rebuild.Scale)\r","        Fmult2[adjusted_Rebuild_F_Rebuild] \u003c- Rebuild.Scale/temp_F\r","      }\r","    }\r","    \r","    #Here a range of adjustments are made to the F step sizes based on the expected vs achieved change in F from\r","    #the previous step. i.e. if the last change only had half the impact expected on F then the next step will\r","    #be modified to make the next change in F twice as large as the raw change in F estimated.\r","    \r","    if(fitting_Fixed_Catch==FALSE){\r","      if((loop\u003e1 |  subloop\u003e2) \u0026 DepletionScale\u003e0 \u0026 DepletionScale!=1 \u0026 fitting_Benchmark==TRUE \u0026 (Forecast_target!=2 | subloop\u003e2)){\r","        F_adjust1 \u003c- (F_adjust1 + 1)/2\r","        F_adjust1 \u003c- F_adjust1*(Last_Mult1-1)/(Last_Mult1-DepletionScale)\r","        \r","        if(is.infinite(F_adjust1)){\r","          F_adjust1 \u003c- 1\r","        }else if(F_adjust1\u003e0){\r","          if(DepletionScale\u003c1){\r","            DepletionScale \u003c- exp(log(DepletionScale)*F_adjust1)\r","          }\r","          if(DepletionScale\u003e1){\r","            DepletionScale \u003c- ((DepletionScale-1)*F_adjust1+1)\r","          }\r","        }else{\r","          F_adjust1 \u003c- 1\r","        }\r","      }else if(loop\u003e1 \u0026 min(Fmult2)\u003e0 \u0026 (fitting_OFL==TRUE | fitting_ABC==TRUE) \u0026 median(Fmult2[adjusted_F_OFL])!=1){\r","        F_adjust2 \u003c- (F_adjust2 + 1)/2\r","        F_adjust2 \u003c- F_adjust2*(Last_Mult2-1)/(Last_Mult2-median(Fmult2[adjusted_F_OFL]))\r","        \r","        if(is.infinite(F_adjust2)){\r","          F_adjust2 \u003c- 1\r","        }else if(F_adjust2 \u003e 0){\r","          if(length(Fmult2[Fmult2\u003c1])\u003e0){\r","            Fmult2[Fmult2\u003c1] \u003c- exp(log(Fmult2[Fmult2\u003c1])*F_adjust2)\r","          }\r","          if(length(Fmult2[Fmult2\u003e1])\u003e0){\r","            Fmult2[Fmult2\u003e1] \u003c- ((Fmult2[Fmult2\u003e1]-1)*F_adjust2+1)\r","          }\r","        }else{\r","          F_adjust2 \u003c- 1\r","        }\r","      }else if(loop\u003e1 \u0026 min(Fmult2)\u003e0 \u0026 fitting_Rebuild==TRUE \u0026 median(Fmult2[adjusted_Rebuild_F_Rebuild])!=1 \u0026 median(Fmult2[adjusted_OFL_F_Rebuild])!=1){\r","        F_adjust2a \u003c- (Last_Mult2a-1)/(Last_Mult2a-median(Fmult2[adjusted_Rebuild_F_Rebuild]))\r","        F_adjust2b \u003c- (Last_Mult2b-1)/(Last_Mult2b-median(Fmult2[adjusted_OFL_F_Rebuild]))\r","        if(!is.na(F_adjust2a)){\r","          \r","          if(is.infinite(F_adjust2a)){\r","            F_adjust2a \u003c- 1\r","          }else if(F_adjust2a \u003e 0){\r","          if(exists(\"Fmult2a\")){\r","            Fmult2a \u003c- (Fmult2a + 1)/2\r","          }\r","          Fmult2a \u003c- Fmult2[adjusted_Rebuild_F_Rebuild]\r","          if(length(Fmult2a[Fmult2a\u003c1])\u003e0){\r","            Fmult2a[Fmult2a\u003c1] \u003c- exp(log(Fmult2a[Fmult2a\u003c1])*F_adjust2a)\r","          }\r","          if(length(Fmult2a[Fmult2a\u003e1])\u003e0){\r","            Fmult2a[Fmult2a\u003e1] \u003c- ((Fmult2a[Fmult2a\u003e1]-1)*F_adjust2a+1)\r","          }\r","          Fmult2[adjusted_Rebuild_F_Rebuild] \u003c- Fmult2a\r","        }else{\r","          F_adjust2a \u003c- 1\r","        }}else{\r","          F_adjust2a \u003c- 1\r","        }\r","        if(!is.na(F_adjust2b)){\r","          if(is.infinite(F_adjust2b)){\r","            F_adjust2b \u003c- 1\r","          }else if(F_adjust2b \u003e 0){\r","          if(exists(\"Fmult2b\")){\r","            Fmult2b \u003c- (Fmult2b + 1)/2\r","          }\r","          Fmult2b \u003c- Fmult2[adjusted_OFL_F_Rebuild]\r","          if(length(Fmult2b[Fmult2b\u003c1])\u003e0){\r","            Fmult2b[Fmult2b\u003c1] \u003c- exp(log(Fmult2b[Fmult2b\u003c1])*F_adjust2b)\r","          }\r","          if(length(Fmult2b[Fmult2b\u003e1])\u003e0){\r","            Fmult2b[Fmult2b\u003e1] \u003c- ((Fmult2b[Fmult2b\u003e1]-1)*F_adjust2b+1)\r","          }\r","          Fmult2[adjusted_OFL_F_Rebuild] \u003c- Fmult2b\r","        }else{\r","          F_adjust2b \u003c- 1\r","        }}else{\r","          F_adjust2b \u003c- 1\r","        }\r","      }\r","    }\r","    Fmult1 \u003c- rep(DepletionScale,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","   \r","\t#Here the achieved catch fractions by fishing sector and year are calculated and compared relative \r","\t#to the target allocations. An adjustment multiplier is then computed to adjust fleet Fs closer to a\r","\t#value expected to achieve the target allocations.\r","    if(FScale \u003e 0){               \r","      if(n_groups\u003e0){\r","        Catch_temp \u003c- TimeFit3[,Catch_cols3]\r","        Catch_tot \u003c- apply(Catch_temp[,unlist(fleets_by_group),drop=FALSE],1,sum)\r","        for(i in 1:n_groups){\r","          sort.mat \u003c- matrix(NA, nrow = forecast[[\"Nforecastyrs\"]]*length(seasons)*length(which(groups==i)), ncol = 2)\r","          sort.mat[,1] \u003c- rep(1:forecast[[\"Nforecastyrs\"]],length(seasons)*length(which(groups==i)))\r","          sort.mat[,2] \u003c- rep(apply(Catch_temp[,fleets_by_group[[i]],drop=FALSE],1,sum)/Catch_tot,length(seasons)*length(which(groups==i)))\r","          sort.mat \u003c- sort.mat[order(sort.mat[,1]),]\r","          Allocations[Allocations[,4]==i,6] \u003c- sort.mat[,2]\r","        }\r","      }\r","      Fmult3 \u003c- (0.5*(Allocations[,5]/Allocations[,6]-1)+1)\r","    }else{\r","      Fmult3 \u003c- rep(1,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","    }\r","\t  \r","    if(fitting_Rebuild==TRUE){\r","      if(Rebuild.Scale==0){\r","          Fmult3[adjusted_Rebuild_F_Rebuild] \u003c- 1\r","        }\r","    }\r","    \r","    if(fitting_Fixed_Catch==FALSE){\r","      Fmult4 \u003c- rep(1,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols))\r","    }\r","    \r","    \r","    \r","\t#Adjust any multipliers of fixed catch values to 1 so that the \r","    #search algorithm will consider them to have achieved their target\t\r","    if(!is.null(fixed_ref)){\r","      Fmult1[fixed_ref] \u003c- 1\r","      Fmult2[fixed_ref] \u003c- 1\r","      Fmult3[fixed_ref] \u003c- 1\r","      Fmult4[fixed_ref] \u003c- 1\r","    }\r","    Comb_Mult \u003c- Fmult1*Fmult2*Fmult3*Fmult4\r","    Comb_Mult[which(forecast_F[,4]\u003e=F_maxed)] \u003c- 1\r","    \r","    #Record the previous adjustment values so they can be used to optimize \r","    #step sizes to speed up target convergence\t\r","    Last_Mult1 \u003c- DepletionScale\r","    Last_Mult2 \u003c- median(Fmult2[adjusted_F_OFL])\r","    if(!is.null(rebuild_ref)){\r","    Last_Mult2a \u003c- median(Fmult2[adjusted_Rebuild_F_Rebuild])\r","    Last_Mult2b \u003c- median(Fmult2[adjusted_OFL_F_Rebuild])\r","    }else{\r","      Last_Mult2a \u003c- 1\r","      Last_Mult2b \u003c- 1\r","    }\r","\t#Plot out progess in achieving targets. This is primarily for diagnosis of a \r","\t#run that is failing to converge on an answer in a reasonable period of time.\r","    if(Make_plots==TRUE){\r","      par(mar=c(4,3,3,2))\r","      col_options \u003c- c(\"black\",\"dark red\",\"dark green\",\"dark blue\",\"orange\",\"purple\",\"red\",\"green\",\"blue\",\"brown\",\"pink\",\"yellow\",colors())\r","      point_options \u003c- c(16,15,17,18,8,9,10,11,12,13,0,1,2,3,4,5,6,14,21,22,23,24,25,19,20)\r","      plot(Fmult1,xlab=\"year/season/fleet\",ylab=\"Depletion Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","      plot(rep(F_adjust1,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols)),xlab=\"year/season/fleet\",ylab=\"Depletion Optimization Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","      plot(Fmult2,xlab=\"year/season/fleet\",ylab=\"F Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","      plot(rep(F_adjust2,forecast[[\"Nforecastyrs\"]]*length(seasons)*length(F_cols)),xlab=\"year/season/fleet\",ylab=\"F Optimization Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","      plot(Fmult3,xlab=\"year/season/fleet\",ylab=\"Allocation Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","      plot(F_adjust3,xlab=\"year/season/fleet\",ylab=\"Allocation Optimization Adjustment\",col=rep(col_options[seq_along(F_cols)],forecast[[\"Nforecastyrs\"]]*length(seasons)),pch=rep(sort(rep(point_options[seq_along(seasons)],length(F_cols))),forecast[[\"Nforecastyrs\"]]),main = paste0(method,\" loop = \",loop))\r","    }\r","\t#Check if all targets have been achieved and if so stop fitting\r","    if(max(abs(1-Fmult1))\u003e=Depletion.Threshold | max(abs(1-Fmult2))\u003e=Annual.F.Threshold | max(abs(1-Fmult3))\u003e=Allocation.Threshold | max(abs(1-Fmult4))\u003e=Annual.F.Threshold | abs(search_step)\u003eStep.Threshold | loop \u003c 2){keepFitting\u003c-TRUE}else{keepFitting\u003c-FALSE}\r","    if(FScale==0 \u0026 loop\u003e2 \u0026 fitting_Fixed_Catch==FALSE){keepFitting\u003c-FALSE}\r","    \r","\t#Here we check that no Fs have been reduced to zero that need some catch\r","\t#If that has occured repace the zero F with a small starting value 0.05 so that the \r","\t#search algorithm can act on it to achieve the true target value.\r","\t#This is needed if the ABC loop was used to perform a zero catch run and then \r","\t#rebuild run is performed starting from those zero values\r","    zero_Fs \u003c- which(forecast_F[,4]==0)\r","    increase_Fs \u003c- which(Comb_Mult\u003e1)\r","    if(length(zero_Fs)\u003e0 \u0026 length(increase_Fs)\u003e0){\r","      mod_Fs \u003c- zero_Fs[is.element(zero_Fs,increase_Fs)]\r","      if(length(mod_Fs)\u003e0){\r","        forecast_F[mod_Fs,4] \u003c- 0.05\r","        Comb_Mult[mod_Fs] \u003c- 1\r","      }\r","    }\r","    forecast_F[,4] \u003c- forecast_F[,4]*Comb_Mult\r","   } }\r","\t#Now adjust the previous F values by the estimated multiplier to create a \r","\t#new estimate of the target Fs, make sure to overwrite any fixed catches \r","\t#with their original values.\r","    \r","    if(!is.null(fixed_ref)){\r","      forecast_F[fixed_ref,4] \u003c- Fixed_catch_target[,4]\r","    }\r","    forecast[[\"ForeCatch\"]] \u003c- forecast_F\r","    #Write the modified forecast data out to a file and rerun projections\r","    unlink(paste0(getwd(),\"/forecast.ss\"))\r","    SS_writeforecast(mylist=forecast,overwrite = TRUE)\r","    \r","    if(run_in_MSE==TRUE){\r","      SSMSE:::run_EM(EM_dir = getwd(), verbose = TRUE, check_converged = TRUE)\r","    }else{\r","      shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\" -nohess\",sep=\"\"))\r","    }\r","    #If all values have converged check if this is the OFL, ABC, or Rebuild loop\r","    if(keepFitting==FALSE){\r","      if(fitting_Fixed_Catch){\r","        \r","        \r","        \r","        if(Calc_Hessian==TRUE | Do_Pstar==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[paste0(\"Param_CC_\",CC_loop)]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[paste0(\"F_sd_CC_\",CC_loop)]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[paste0(\"SSB_sd_CC_\",CC_loop)]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[paste0(\"Recr_sd_CC_\",CC_loop)]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[paste0(\"ForeCatchF_CC_\",CC_loop)]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[paste0(\"ForeCatchF_CC_\",CC_loop)]] \u003c- projection_results[[paste0(\"ForeCatchF_CC_\",CC_loop)]][-grep(\"annF_\",projection_results[[paste0(\"ForeCatchF_CC_\",CC_loop)]][,\"Label\"]),]\r","          projection_results[[paste0(\"ForeCatchDead_CC_\",CC_loop)]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[paste0(\"ForeCatchRetained_CC_\",CC_loop)]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        \r","        if(dir.exists(paste0(assessment_dir,\"/CC_\",CC_loop))){\r","          unlink(paste0(assessment_dir,\"/CC_\",CC_loop),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/CC_\",CC_loop))\r","        temp.files \u003c- list.files(path=paste0(assessment_dir,\"/Working_dir\"))\r","        file.copy(from=paste0(assessment_dir,'/Working_dir/',temp.files),to=paste0(assessment_dir,\"/CC_\",CC_loop,\"/\",temp.files))\r","        \r","        if(length(Const_Catch)\u003eCC_loop){\r","          CC_loop \u003c- CC_loop + 1\r","          Catch_Target \u003c- rep(Const_Catch[CC_loop],forecast[[\"Nforecastyrs\"]])\r","          if(Catch_trunc \u003e 0){\r","            Catch_Target[(forecast$Nforecastyrs-c((Catch_trunc-1):0))] \u003c- 0\r","          }\r","          keepFitting \u003c- TRUE\r","        }\r","      }else if(fitting_Benchmark==TRUE){\r","        fitting_Benchmark \u003c- FALSE\r","        fitting_OFL \u003c- TRUE\r","        par(mfrow=c(4,2))\r","        loop \u003c- 0\r","        method \u003c- \"OFL\"\r","        keepFitting \u003c- TRUE\r","        \r","        if(Calc_Hessian==TRUE | Do_Pstar==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[\"Param_Benchmark\"]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[\"F_sd_Benchmark\"]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[\"SSB_sd_Benchmark\"]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"Recr_sd_Benchmark\"]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_Benchmark\"]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_Benchmark\"]] \u003c- projection_results[[\"ForeCatchF_Benchmark\"]][-grep(\"annF_\",projection_results[[\"ForeCatchF_Benchmark\"]][,\"Label\"]),]\r","          projection_results[[\"ForeCatchDead_Benchmark\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchRetained_Benchmark\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        #Write out the Benchmark results to a new folder (replace any old folder that exists)\r","        if(dir.exists(paste0(assessment_dir,\"/Benchmark_target\"))){\r","          unlink(paste0(assessment_dir,\"/Benchmark_target\"),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/Benchmark_target\"))\r","        temp.files \u003c- list.files(path=paste0(assessment_dir,\"/Working_dir\"))\r","        file.copy(from=paste0(assessment_dir,'/Working_dir/',temp.files),to=paste0(assessment_dir,\"/Benchmark_target/\",temp.files))\r","        \r","        forecast$fcast_rec_option \u003c- catch_rec \r","        SS_writeforecast(mylist=forecast,overwrite = TRUE)\r","      }else if(fitting_OFL==TRUE){\r","        fitting_OFL \u003c- FALSE\r","        par(mfrow=c(4,2))\r","        \r","        if(Calc_Hessian==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[\"Param_OFL\"]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[\"F_sd_OFL\"]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[\"SSB_sd_OFL\"]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"Recr_sd_OFL\"]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_OFL\"]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_OFL\"]] \u003c- projection_results[[\"ForeCatchF_OFL\"]][-grep(\"annF_\",projection_results[[\"ForeCatchF_OFL\"]][,\"Label\"]),]\r","          projection_results[[\"ForeCatchDead_OFL\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchRetained_OFL\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        \r","        if(!is.null(ABC_Fraction)){\r","          #If in the OLF loop then reset to keep fitting and change the target from OFL to ABC\r","          loop \u003c- 0\r","          method \u003c- \"ABC\"\r","          keepFitting \u003c- TRUE\r","          fitting_ABC \u003c- TRUE\r","        }else if(!is.null(Rebuild_yr)){\r","          #If in the OLF loop then reset to keep fitting and change the target from OFL to Rebuild\r","          loop \u003c- 0\r","          method \u003c- \"Rebuild\"\r","          keepFitting \u003c- TRUE\r","          fitting_Rebuild \u003c- TRUE\r","        }else if(Calc_F0==TRUE){\r","          loop \u003c- 0\r","          method \u003c- \"F0\"\r","          keepFitting \u003c- TRUE\r","          fitting_F0 \u003c- TRUE\r","        }\r","        #Write out the OFL results to a new folder (replace any old folder that exists)\r","        if(dir.exists(paste0(assessment_dir,\"/OFL_target\"))){\r","          unlink(paste0(assessment_dir,\"/OFL_target\"),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/OFL_target\"))\r","        temp.files \u003c- list.files(path=paste0(assessment_dir,\"/Working_dir\"))\r","        file.copy(from=paste0(assessment_dir,'/Working_dir/',temp.files),to=paste0(assessment_dir,\"/OFL_target/\",temp.files))\r","      }else if(fitting_ABC==TRUE){\r","        fitting_ABC \u003c- FALSE\r","        \r","        if(Calc_Hessian==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[\"Param_ABC\"]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[\"F_sd_ABC\"]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[\"SSB_sd_ABC\"]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"Recr_sd_ABC\"]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_ABC\"]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_ABC\"]] \u003c- projection_results[[\"ForeCatchF_ABC\"]][-grep(\"annF_\",projection_results[[\"ForeCatchF_ABC\"]][,\"Label\"]),]\r","          projection_results[[\"ForeCatchDead_ABC\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchRetained_ABC\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        \r","        if(!is.null(Rebuild_yr)){\r","          #If in the ABC loop then reset to keep fitting and change the target from ABC to Rebuild\r","          loop \u003c- 0\r","          method \u003c- \"Rebuild\"\r","          keepFitting \u003c- TRUE\r","          fitting_Rebuild \u003c- TRUE\r","        }else if(Calc_F0==TRUE){\r","          loop \u003c- 0\r","          method \u003c- \"F0\"\r","          keepFitting \u003c- TRUE\r","          fitting_F0 \u003c- TRUE\r","        }\r","        #If on the ABC loop write out the P* results to a new folder (replace any old folder that exists)\r","        if(dir.exists(paste0(assessment_dir,\"/ABC_target\"))){\r","          unlink(paste0(assessment_dir,\"/ABC_target\"),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/ABC_target\"))\r","        temp.files \u003c- list.files(path=paste0(assessment_dir,\"/Working_dir\"))\r","        file.copy(from=paste0(assessment_dir,'/Working_dir/',temp.files),to=paste0(assessment_dir,\"/ABC_target/\",temp.files))\r","      }else if(fitting_Rebuild==TRUE){\r","        fitting_Rebuild \u003c- FALSE\r","        \r","        if(Calc_Hessian==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[\"Param_Rebuild\"]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[\"F_sd_Rebuild\"]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[\"SSB_sd_Rebuild\"]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"Recr_sd_Rebuild\"]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_Rebuild\"]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_Rebuild\"]] \u003c- projection_results[[\"ForeCatchF_Rebuild\"]][-grep(\"annF_\",projection_results[[\"ForeCatchF_Rebuild\"]][,\"Label\"]),]\r","          projection_results[[\"ForeCatchDead_Rebuild\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchRetained_Rebuild\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        \r","        if(Calc_F0==TRUE){\r","          loop \u003c- 0\r","          method \u003c- \"F0\"\r","          keepFitting \u003c- TRUE\r","          fitting_F0 \u003c- TRUE\r","        }\r","        #If on the Rebuild loop write out the Rebuild results to a new folder (replace any old folder that exists) and end the fitting process\r","        if(dir.exists(paste0(assessment_dir,\"/Rebuild_target\"))){\r","          unlink(paste0(assessment_dir,\"/Rebuild_target\"),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/Rebuild_target\"))\r","        temp.files \u003c- list.files(path=paste0(assessment_dir,\"/Working_dir\"))\r","        file.copy(from=paste0(assessment_dir,'/Working_dir/',temp.files),to=paste0(assessment_dir,\"/Rebuild_target/\",temp.files))\r","      }else if(fitting_F0==TRUE){\r","        \r","        if(Calc_Hessian==TRUE){\r","          start$last_estimation_phase \u003c- 10\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","          \r","          if(run_in_MSE==TRUE){\r","            SSMSE:::run_EM(EM_dir = getwd(), hess=TRUE, verbose = TRUE, check_converged = TRUE)\r","          }else{\r","            shell(paste(\"cd /d \",getwd(),\" \u0026\u0026 \",SS_exe,\"\",sep=\"\"))\r","          }\r","          \r","          resultsFit \u003c- SS_output(dir=getwd(),covar=FALSE)\r","          \r","          projection_results[[\"Param_F0\"]] \u003c- resultsFit$parameters[,c(2,3,11,12)]\r","          projection_results[[\"F_sd_F0\"]] \u003c- resultsFit$parameters[grep(\"F_fleet\",resultsFit$parameters$Label),c(2,3,11,12)]\r","          projection_results[[\"SSB_sd_F0\"]] \u003c- resultsFit$derived_quants[grep(\"SSB_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"Recr_sd_F0\"]] \u003c- resultsFit$derived_quants[grep(\"Recr_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_F0\"]] \u003c- resultsFit$derived_quants[grep(\"F_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchF_F0\"]] \u003c- projection_results[[\"ForeCatchF_F0\"]][-grep(\"annF_\",projection_results[[\"ForeCatchF_F0\"]][,\"Label\"]),]\r","          projection_results[[\"ForeCatchDead_F0\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatch_\",resultsFit$derived_quants$Label),1:3]\r","          projection_results[[\"ForeCatchRetained_F0\"]] \u003c- resultsFit$derived_quants[grep(\"ForeCatchret_\",resultsFit$derived_quants$Label),1:3]\r","          \r","          start$last_estimation_phase \u003c- 0\r","          SS_writestarter(mylist=start,overwrite = TRUE)\r","        }\r","        \r","        if(dir.exists(paste0(assessment_dir,\"/F0_target\"))){\r","          unlink(paste0(assessment_dir,\"/F0_target\"),recursive = TRUE)\r","        }\r","        dir.create(paste0(assessment_dir,\"/F0_target\"))\r","        temp.files 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style="padding-right:16px">964</div><div data-line-number="965" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">965</div><div data-line-number="966" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">966</div><div data-line-number="967" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">967</div><div data-line-number="968" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">968</div><div data-line-number="969" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">969</div><div data-line-number="970" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">970</div><div data-line-number="971" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">971</div><div data-line-number="972" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">972</div><div data-line-number="973" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">973</div><div data-line-number="974" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">974</div><div data-line-number="975" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">975</div><div data-line-number="976" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">976</div><div data-line-number="977" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">977</div><div data-line-number="978" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">978</div><div data-line-number="979" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">979</div><div data-line-number="980" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">980</div><div data-line-number="981" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">981</div><div data-line-number="982" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">982</div><div data-line-number="983" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">983</div><div data-line-number="984" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">984</div><div data-line-number="985" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">985</div><div data-line-number="986" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">986</div><div data-line-number="987" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">987</div><div data-line-number="988" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">988</div><div data-line-number="989" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">989</div><div data-line-number="990" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">990</div><div data-line-number="991" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">991</div><div data-line-number="992" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">992</div><div data-line-number="993" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">993</div><div data-line-number="994" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">994</div><div data-line-number="995" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">995</div><div data-line-number="996" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">996</div><div data-line-number="997" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">997</div><div data-line-number="998" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">998</div><div data-line-number="999" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">999</div><div data-line-number="1000" class="child-of-line-45  react-line-number react-code-text" style="padding-right:16px">1000</div></div><div class="react-code-lines"><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC1" class="react-file-line html-div" data-testid="code-cell" data-line-number="1" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#---------------------------------------------------------------------##</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC2" class="react-file-line html-div" data-testid="code-cell" data-line-number="2" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>                                                                       #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC3" class="react-file-line html-div" data-testid="code-cell" data-line-number="3" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  SS projection package to achieve target equilibrium stock status,    #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC4" class="react-file-line html-div" data-testid="code-cell" data-line-number="4" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  constant annual fishing mortality rate, fixed group catch            #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC5" class="react-file-line html-div" data-testid="code-cell" data-line-number="5" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  allocations, and historic relative fishing effort between fleets     #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC6" class="react-file-line html-div" data-testid="code-cell" data-line-number="6" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  within groups. The package is able to calculate OFL, ABC represented #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC7" class="react-file-line html-div" data-testid="code-cell" data-line-number="7" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  as a fraction of the OFL F, and F rebuild represented as a fixed     #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC8" class="react-file-line html-div" data-testid="code-cell" data-line-number="8" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  reduction in F during the specified rebuild period if needed.        #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC9" class="react-file-line html-div" data-testid="code-cell" data-line-number="9" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>                                                                       #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC10" class="react-file-line html-div" data-testid="code-cell" data-line-number="10" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#---------------------------------------------------------------------##</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC11" class="react-file-line html-div" data-testid="code-cell" data-line-number="11" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>                                                                       #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC12" class="react-file-line html-div" data-testid="code-cell" data-line-number="12" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  Author: Nathan Vaughan                                               #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC13" class="react-file-line html-div" data-testid="code-cell" data-line-number="13" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  Last update date: 10/15/21                                           #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC14" class="react-file-line html-div" data-testid="code-cell" data-line-number="14" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>  Contact: nathan.vaughan@noaa.gov                                     #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC15" class="react-file-line html-div" data-testid="code-cell" data-line-number="15" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>                                                                       #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC16" class="react-file-line html-div" data-testid="code-cell" data-line-number="16" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#---------------------------------------------------------------------##</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC17" class="react-file-line html-div" data-testid="code-cell" data-line-number="17" style="position:relative"><span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC18" class="react-file-line html-div" data-testid="code-cell" data-line-number="18" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>   Disclaimer</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC19" class="react-file-line html-div" data-testid="code-cell" data-line-number="19" style="position:relative"><span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC20" class="react-file-line html-div" data-testid="code-cell" data-line-number="20" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>   &quot;The United States Department of Commerce (DOC) GitHub project code </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC21" class="react-file-line html-div" data-testid="code-cell" data-line-number="21" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    is provided on an &quot;as is&quot; basis and the user assumes responsibility </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC22" class="react-file-line html-div" data-testid="code-cell" data-line-number="22" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    for its use. DOC has relinquished control of the information and no </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC23" class="react-file-line html-div" data-testid="code-cell" data-line-number="23" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    longer has responsibility to protect the integrity, confidentiality, </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC24" class="react-file-line html-div" data-testid="code-cell" data-line-number="24" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    or availability of the information. Any claims against the Department </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC25" class="react-file-line html-div" data-testid="code-cell" data-line-number="25" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    of Commerce stemming from the use of its GitHub project will be </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC26" class="react-file-line html-div" data-testid="code-cell" data-line-number="26" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    governed by all applicable Federal law. Any reference to specific </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC27" class="react-file-line html-div" data-testid="code-cell" data-line-number="27" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    commercial products, processes, or services by service mark, trademark, </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC28" class="react-file-line html-div" data-testid="code-cell" data-line-number="28" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    manufacturer, or otherwise, does not constitute or imply their endorsement, </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC29" class="react-file-line html-div" data-testid="code-cell" data-line-number="29" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    recommendation or favoring by the Department of Commerce. The Department </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC30" class="react-file-line html-div" data-testid="code-cell" data-line-number="30" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    of Commerce seal and logo, or the seal and logo of a DOC bureau, shall </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC31" class="react-file-line html-div" data-testid="code-cell" data-line-number="31" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    not be used in any manner to imply endorsement of any commercial </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC32" class="react-file-line html-div" data-testid="code-cell" data-line-number="32" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>    product or activity by DOC or the United States Government.&quot;</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC33" class="react-file-line html-div" data-testid="code-cell" data-line-number="33" style="position:relative"><span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC34" class="react-file-line html-div" data-testid="code-cell" data-line-number="34" style="position:relative"><span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC35" class="react-file-line html-div" data-testid="code-cell" data-line-number="35" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#                                                                       #</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC36" class="react-file-line html-div" data-testid="code-cell" data-line-number="36" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#---------------------------------------------------------------------##</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC37" class="react-file-line html-div" data-testid="code-cell" data-line-number="37" style="position:relative"><span class="pl-c"><span class="pl-c">#</span>#</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC38" class="react-file-line html-div" data-testid="code-cell" data-line-number="38" style="position:relative">
</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC39" class="react-file-line html-div" data-testid="code-cell" data-line-number="39" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> This is now a generalized function to run projections that should work for most species. </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC40" class="react-file-line html-div" data-testid="code-cell" data-line-number="40" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> The function is now designed to mostly read out settings from the forecast file the </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC41" class="react-file-line html-div" data-testid="code-cell" data-line-number="41" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> same way you would generally set things up for a base SS projection.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC42" class="react-file-line html-div" data-testid="code-cell" data-line-number="42" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> The only additional inputs needed are a proportion for F.ABC relative to F.OFL if </span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC43" class="react-file-line html-div" data-testid="code-cell" data-line-number="43" style="position:relative"><span class="pl-c"><span class="pl-c">#</span> ABC projections are desired and a rebuild target year if rebuilding projections are desired.</span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC44" class="react-file-line html-div" data-testid="code-cell" data-line-number="44" style="position:relative"><span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC45" class="react-file-line html-div" data-testid="code-cell" data-line-number="45" style="position:relative">
</div></div></div><div class="react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC46" class="react-file-line html-div" data-testid="code-cell" data-line-number="46" style="position:relative"><span class="pl-en">run.projections</span><span class="pl-k">&lt;-</span><span class="pl-k">function</span>(<span class="pl-smi">assessment_dir</span>, <span class="pl-c"><span class="pl-c">#</span>Here you set the location of a previously fit SS3.3 stock assessment to perform projections</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC47" class="react-file-line html-div" data-testid="code-cell" data-line-number="47" style="position:relative">                          <span class="pl-v">ABC_Fraction</span> <span class="pl-k">=</span> <span class="pl-c1">NULL</span>, <span class="pl-c"><span class="pl-c">#</span>Set the ABC target as a fraction of the OFL target if NULL will not fit ABC projections</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC48" class="react-file-line html-div" data-testid="code-cell" data-line-number="48" style="position:relative">                          <span class="pl-v">Rebuild_yr</span> <span class="pl-k">=</span> <span class="pl-c1">NULL</span>, <span class="pl-c"><span class="pl-c">#</span>Set the rebuild target year if NULL will not fit rebuild projections</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC49" class="react-file-line html-div" data-testid="code-cell" data-line-number="49" style="position:relative">                          <span class="pl-v">Calc_F0</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>Should an F=0 projection be performed</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC50" class="react-file-line html-div" data-testid="code-cell" data-line-number="50" style="position:relative">                          <span class="pl-v">Const_Catch</span> <span class="pl-k">=</span> <span class="pl-c1">NULL</span>, <span class="pl-c"><span class="pl-c">#</span>Constant catch target in mt. If constant catch is chosen no other simulations will run (i.e. benchmark, OFL, etc)  </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC51" class="react-file-line html-div" data-testid="code-cell" data-line-number="51" style="position:relative">                          <span class="pl-v">F_max</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>If true and forecast method is Fmsy will replace Fmsy with Fmax search (maximum yield per recruit)</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC52" class="react-file-line html-div" data-testid="code-cell" data-line-number="52" style="position:relative">                          <span class="pl-v">Depletion.Threshold</span> <span class="pl-k">=</span> <span class="pl-c1">0.0001</span>, <span class="pl-c"><span class="pl-c">#</span> These are all just thresholds for when </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC53" class="react-file-line html-div" data-testid="code-cell" data-line-number="53" style="position:relative">                          <span class="pl-v">Annual.F.Threshold</span> <span class="pl-k">=</span> <span class="pl-c1">0.0001</span>, <span class="pl-c"><span class="pl-c">#</span> targets are acceptably achieved these default to a .01% change</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC54" class="react-file-line html-div" data-testid="code-cell" data-line-number="54" style="position:relative">                          <span class="pl-v">Allocation.Threshold</span> <span class="pl-k">=</span> <span class="pl-c1">0.0001</span>, <span class="pl-c"><span class="pl-c">#</span> increase them if run is too slow or reduce to improve fit if run is fast.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC55" class="react-file-line html-div" data-testid="code-cell" data-line-number="55" style="position:relative">                          <span class="pl-v">Step.Threshold</span> <span class="pl-k">=</span> <span class="pl-c1">0.0001</span>, <span class="pl-c"><span class="pl-c">#</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC56" class="react-file-line html-div" data-testid="code-cell" data-line-number="56" style="position:relative">                          <span class="pl-v">Benchmark_complete</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>Set to true if you already have a fit Benchmark run but want to add or adjust an ABC or Rebuild run</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC57" class="react-file-line html-div" data-testid="code-cell" data-line-number="57" style="position:relative">                          <span class="pl-v">Make_plots</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>Should plots be created (this is useful for diagnostics but can cause annoying errors if plot window is small)</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC58" class="react-file-line html-div" data-testid="code-cell" data-line-number="58" style="position:relative">                          <span class="pl-v">Calc_Hessian</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>Should the hessian inversion be completed for runs once converged. TODO: NOT YET IMPLEMENTED!!!</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC59" class="react-file-line html-div" data-testid="code-cell" data-line-number="59" style="position:relative">                          <span class="pl-v">Do_Pstar</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>, <span class="pl-c"><span class="pl-c">#</span>If TRUE then ABC_Fraction above will instead be the P* probability of overfishing limit for ABC calculation. TODO: NOT YET IMPLEMENTED!!!</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC60" class="react-file-line html-div" data-testid="code-cell" data-line-number="60" style="position:relative">                          <span class="pl-v">Years_report</span> <span class="pl-k">=</span> <span class="pl-c1">20</span>, <span class="pl-c"><span class="pl-c">#</span>How many years of projection to include in stored OFL and ABC reporting. (All forecast years data will still be available in report file) </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC61" class="react-file-line html-div" data-testid="code-cell" data-line-number="61" style="position:relative">                          <span class="pl-v">Years_projection</span> <span class="pl-k">=</span> <span class="pl-c1">100</span>, <span class="pl-c"><span class="pl-c">#</span>How many years of projection to run (need enough to reach equilibrium) 100 is safe but may not be sufficient for some long lived species.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC62" class="react-file-line html-div" data-testid="code-cell" data-line-number="62" style="position:relative">                          <span class="pl-v">run_in_MSE</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>,</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC63" class="react-file-line html-div" data-testid="code-cell" data-line-number="63" style="position:relative">                          <span class="pl-v">starting_Forecatch</span> <span class="pl-k">=</span> <span class="pl-c1">NULL</span>,</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC64" class="react-file-line html-div" data-testid="code-cell" data-line-number="64" style="position:relative">                          <span class="pl-v">MSY_step</span> <span class="pl-k">=</span> <span class="pl-c1">0.1</span>,</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC65" class="react-file-line html-div" data-testid="code-cell" data-line-number="65" style="position:relative">                          <span class="pl-v">SS_exe</span> <span class="pl-k">=</span> <span class="pl-c1">NULL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC66" class="react-file-line html-div" data-testid="code-cell" data-line-number="66" style="position:relative">                          ) </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC67" class="react-file-line html-div" data-testid="code-cell" data-line-number="67" style="position:relative">{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC68" class="react-file-line html-div" data-testid="code-cell" data-line-number="68" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC69" class="react-file-line html-div" data-testid="code-cell" data-line-number="69" style="position:relative">  <span class="pl-smi">projection_results</span> <span class="pl-k">&lt;-</span> <span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC70" class="react-file-line html-div" data-testid="code-cell" data-line-number="70" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC71" class="react-file-line html-div" data-testid="code-cell" data-line-number="71" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC72" class="react-file-line html-div" data-testid="code-cell" data-line-number="72" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC73" class="react-file-line html-div" data-testid="code-cell" data-line-number="73" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>SSMSE::report_message(&quot;Running the allocation forecasting function.&quot;) </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC74" class="react-file-line html-div" data-testid="code-cell" data-line-number="74" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC75" class="react-file-line html-div" data-testid="code-cell" data-line-number="75" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Removed these as inputs as they are not needed yet, could add back to input options later</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC76" class="react-file-line html-div" data-testid="code-cell" data-line-number="76" style="position:relative"> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC77" class="react-file-line html-div" data-testid="code-cell" data-line-number="77" style="position:relative">  <span class="pl-smi">oldwd</span><span class="pl-k">&lt;-</span>getwd()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC78" class="react-file-line html-div" data-testid="code-cell" data-line-number="78" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC79" class="react-file-line html-div" data-testid="code-cell" data-line-number="79" style="position:relative">  library(<span class="pl-smi">r4ss</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC80" class="react-file-line html-div" data-testid="code-cell" data-line-number="80" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Set large max print to avoid issues with writing out a large forecast file.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC81" class="react-file-line html-div" data-testid="code-cell" data-line-number="81" style="position:relative">  options(<span class="pl-v">max.print</span> <span class="pl-k">=</span> <span class="pl-c1">1000000</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC82" class="react-file-line html-div" data-testid="code-cell" data-line-number="82" style="position:relative">  setwd(paste0(<span class="pl-smi">assessment_dir</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC83" class="react-file-line html-div" data-testid="code-cell" data-line-number="83" style="position:relative">  <span class="pl-smi">assessment_dir</span> <span class="pl-k">&lt;-</span> getwd()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC84" class="react-file-line html-div" data-testid="code-cell" data-line-number="84" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Read in all the model files and results </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC85" class="react-file-line html-div" data-testid="code-cell" data-line-number="85" style="position:relative">  <span class="pl-smi">start</span> <span class="pl-k">&lt;-</span> SS_readstarter()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC86" class="react-file-line html-div" data-testid="code-cell" data-line-number="86" style="position:relative">  <span class="pl-smi">dat</span> <span class="pl-k">&lt;-</span> SS_readdat(<span class="pl-v">file</span> <span class="pl-k">=</span> <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">datfile</span>, <span class="pl-v">version</span> <span class="pl-k">=</span> <span class="pl-c1">3.3</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC87" class="react-file-line html-div" data-testid="code-cell" data-line-number="87" style="position:relative">  <span class="pl-smi">ctl</span> <span class="pl-k">&lt;-</span> SS_readctl(<span class="pl-v">file</span> <span class="pl-k">=</span> <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">ctlfile</span>, <span class="pl-v">version</span> <span class="pl-k">=</span> <span class="pl-c1">3.3</span>, <span class="pl-v">use_datlist</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>, <span class="pl-v">datlist</span> <span class="pl-k">=</span> <span class="pl-smi">dat</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC88" class="react-file-line html-div" data-testid="code-cell" data-line-number="88" style="position:relative">  <span class="pl-smi">results</span> <span class="pl-k">&lt;-</span> SS_output(<span class="pl-v">dir</span> <span class="pl-k">=</span> getwd(), <span class="pl-v">covar</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC89" class="react-file-line html-div" data-testid="code-cell" data-line-number="89" style="position:relative">  <span class="pl-smi">forecast</span> <span class="pl-k">&lt;-</span> SS_readforecast() </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC90" class="react-file-line html-div" data-testid="code-cell" data-line-number="90" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC91" class="react-file-line html-div" data-testid="code-cell" data-line-number="91" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">SS_exe</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC92" class="react-file-line html-div" data-testid="code-cell" data-line-number="92" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC93" class="react-file-line html-div" data-testid="code-cell" data-line-number="93" style="position:relative">  }<span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss.exe<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC94" class="react-file-line html-div" data-testid="code-cell" data-line-number="94" style="position:relative">    <span class="pl-smi">SS_exe</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC95" class="react-file-line html-div" data-testid="code-cell" data-line-number="95" style="position:relative">  } <span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss3.exe<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC96" class="react-file-line html-div" data-testid="code-cell" data-line-number="96" style="position:relative">    <span class="pl-smi">SS_exe</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss3<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC97" class="react-file-line html-div" data-testid="code-cell" data-line-number="97" style="position:relative">  } <span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss_opt.exe<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC98" class="react-file-line html-div" data-testid="code-cell" data-line-number="98" style="position:relative">    <span class="pl-smi">SS_exe</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss_opt<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC99" class="react-file-line html-div" data-testid="code-cell" data-line-number="99" style="position:relative">  } <span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss3_opt.exe<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC100" class="react-file-line html-div" data-testid="code-cell" data-line-number="100" style="position:relative">    <span class="pl-smi">SS_exe</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss3_opt<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC101" class="react-file-line html-div" data-testid="code-cell" data-line-number="101" style="position:relative">  } <span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss3_win.exe<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC102" class="react-file-line html-div" data-testid="code-cell" data-line-number="102" style="position:relative">    <span class="pl-smi">SS_exe</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss3_win<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC103" class="react-file-line html-div" data-testid="code-cell" data-line-number="103" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC104" class="react-file-line html-div" data-testid="code-cell" data-line-number="104" style="position:relative">    stop(<span class="pl-s"><span class="pl-pds">&quot;</span>Error: Couldn&#039;t find an expected SS executable name<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC105" class="react-file-line html-div" data-testid="code-cell" data-line-number="105" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC106" class="react-file-line html-div" data-testid="code-cell" data-line-number="106" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC107" class="react-file-line html-div" data-testid="code-cell" data-line-number="107" style="position:relative">  <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss.par<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC108" class="react-file-line html-div" data-testid="code-cell" data-line-number="108" style="position:relative">    <span class="pl-smi">par_name</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss.par<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC109" class="react-file-line html-div" data-testid="code-cell" data-line-number="109" style="position:relative">  }<span class="pl-k">else</span> <span class="pl-k">if</span>(file.exists(<span class="pl-s"><span class="pl-pds">&quot;</span>ss3.par<span class="pl-pds">&quot;</span></span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC110" class="react-file-line html-div" data-testid="code-cell" data-line-number="110" style="position:relative">    <span class="pl-smi">par_name</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>ss3.par<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC111" class="react-file-line html-div" data-testid="code-cell" data-line-number="111" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC112" class="react-file-line html-div" data-testid="code-cell" data-line-number="112" style="position:relative">    stop(<span class="pl-s"><span class="pl-pds">&quot;</span>Error: No par file found with name ss.par or ss3.par<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC113" class="react-file-line html-div" data-testid="code-cell" data-line-number="113" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC114" class="react-file-line html-div" data-testid="code-cell" data-line-number="114" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC115" class="react-file-line html-div" data-testid="code-cell" data-line-number="115" style="position:relative">  <span class="pl-smi">parlist</span> <span class="pl-k">&lt;-</span> SS_readpar_3.30(<span class="pl-v">parfile</span> <span class="pl-k">=</span> <span class="pl-smi">par_name</span>, <span class="pl-v">datsource</span> <span class="pl-k">=</span> <span class="pl-smi">dat</span>, <span class="pl-v">ctlsource</span> <span class="pl-k">=</span> <span class="pl-smi">ctl</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC116" class="react-file-line html-div" data-testid="code-cell" data-line-number="116" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC117" class="react-file-line html-div" data-testid="code-cell" data-line-number="117" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC118" class="react-file-line html-div" data-testid="code-cell" data-line-number="118" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">Const_Catch</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC119" class="react-file-line html-div" data-testid="code-cell" data-line-number="119" style="position:relative">    <span class="pl-smi">Const_Catch</span> <span class="pl-k">&lt;-</span> sort(<span class="pl-smi">Const_Catch</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC120" class="react-file-line html-div" data-testid="code-cell" data-line-number="120" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC121" class="react-file-line html-div" data-testid="code-cell" data-line-number="121" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC122" class="react-file-line html-div" data-testid="code-cell" data-line-number="122" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>First set up a working director for running projections in (to avoid overwriting the base files with a failed model run)</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC123" class="react-file-line html-div" data-testid="code-cell" data-line-number="123" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>then copy all of the assessment files to this working folder (ignore any output directories that have been previously created)</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC124" class="react-file-line html-div" data-testid="code-cell" data-line-number="124" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-smi">Benchmark_complete</span> <span class="pl-k">==</span> <span class="pl-c1">FALSE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC125" class="react-file-line html-div" data-testid="code-cell" data-line-number="125" style="position:relative">  <span class="pl-k">if</span>(dir.exists(file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC126" class="react-file-line html-div" data-testid="code-cell" data-line-number="126" style="position:relative">    unlink(file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>), <span class="pl-v">recursive</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC127" class="react-file-line html-div" data-testid="code-cell" data-line-number="127" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC128" class="react-file-line html-div" data-testid="code-cell" data-line-number="128" style="position:relative">  dir.create(file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC129" class="react-file-line html-div" data-testid="code-cell" data-line-number="129" style="position:relative">  <span class="pl-smi">temp.files</span> <span class="pl-k">&lt;-</span> list.files(<span class="pl-v">path</span><span class="pl-k">=</span><span class="pl-smi">assessment_dir</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC130" class="react-file-line html-div" data-testid="code-cell" data-line-number="130" style="position:relative">  <span class="pl-smi">folders</span> <span class="pl-k">&lt;-</span> c(which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Benchmark_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>OFL_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>ABC_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Rebuild_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>F0_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC131" class="react-file-line html-div" data-testid="code-cell" data-line-number="131" style="position:relative">  <span class="pl-k">if</span>(length(<span class="pl-smi">folders</span>)<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC132" class="react-file-line html-div" data-testid="code-cell" data-line-number="132" style="position:relative">    <span class="pl-smi">temp.files</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">temp.files</span>[<span class="pl-k">-</span><span class="pl-smi">folders</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC133" class="react-file-line html-div" data-testid="code-cell" data-line-number="133" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC134" class="react-file-line html-div" data-testid="code-cell" data-line-number="134" style="position:relative">  file.copy(<span class="pl-v">from</span> <span class="pl-k">=</span> file.path(getwd(),<span class="pl-smi">temp.files</span>), <span class="pl-v">to</span> <span class="pl-k">=</span> file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">temp.files</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC135" class="react-file-line html-div" data-testid="code-cell" data-line-number="135" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC136" class="react-file-line html-div" data-testid="code-cell" data-line-number="136" style="position:relative">    <span class="pl-smi">temp.files</span> <span class="pl-k">&lt;-</span> list.files(<span class="pl-v">path</span><span class="pl-k">=</span>file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC137" class="react-file-line html-div" data-testid="code-cell" data-line-number="137" style="position:relative">    <span class="pl-smi">folders</span> <span class="pl-k">&lt;-</span> c(which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Benchmark_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>OFL_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>ABC_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Rebuild_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>F0_target<span class="pl-pds">&quot;</span></span>), which(<span class="pl-smi">temp.files</span><span class="pl-k">==</span><span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC138" class="react-file-line html-div" data-testid="code-cell" data-line-number="138" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">folders</span>)<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC139" class="react-file-line html-div" data-testid="code-cell" data-line-number="139" style="position:relative">      <span class="pl-smi">temp.files</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">temp.files</span>[<span class="pl-k">-</span><span class="pl-smi">folders</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC140" class="react-file-line html-div" data-testid="code-cell" data-line-number="140" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC141" class="react-file-line html-div" data-testid="code-cell" data-line-number="141" style="position:relative">    unlink(file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir/<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">temp.files</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC142" class="react-file-line html-div" data-testid="code-cell" data-line-number="142" style="position:relative">    <span class="pl-smi">temp.files</span> <span class="pl-k">&lt;-</span> list.files(<span class="pl-v">path</span><span class="pl-k">=</span>file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Benchmark_target<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC143" class="react-file-line html-div" data-testid="code-cell" data-line-number="143" style="position:relative">    file.copy(<span class="pl-v">from</span> <span class="pl-k">=</span> file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Benchmark_target<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">temp.files</span>), <span class="pl-v">to</span> <span class="pl-k">=</span> file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">temp.files</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC144" class="react-file-line html-div" data-testid="code-cell" data-line-number="144" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC145" class="react-file-line html-div" data-testid="code-cell" data-line-number="145" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC146" class="react-file-line html-div" data-testid="code-cell" data-line-number="146" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Set the new working directory </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC147" class="react-file-line html-div" data-testid="code-cell" data-line-number="147" style="position:relative">  setwd(file.path(getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span>Working_dir<span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC148" class="react-file-line html-div" data-testid="code-cell" data-line-number="148" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC149" class="react-file-line html-div" data-testid="code-cell" data-line-number="149" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Modify assessment files to produce expected timeseries length and outputs</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC150" class="react-file-line html-div" data-testid="code-cell" data-line-number="150" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>need enough projection years to allow equilibrium to be achieved</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC151" class="react-file-line html-div" data-testid="code-cell" data-line-number="151" style="position:relative">  <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Years_projection</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC152" class="react-file-line html-div" data-testid="code-cell" data-line-number="152" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC153" class="react-file-line html-div" data-testid="code-cell" data-line-number="153" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>If fitting the Benchmark/OFL values then save the specified recruitment source for catches </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC154" class="react-file-line html-div" data-testid="code-cell" data-line-number="154" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>and set to 0 (S/R curve) in order to first calculate benchmarks</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC155" class="react-file-line html-div" data-testid="code-cell" data-line-number="155" style="position:relative">  <span class="pl-smi">catch_rec</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">fcast_rec_option</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC156" class="react-file-line html-div" data-testid="code-cell" data-line-number="156" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-smi">Benchmark_complete</span><span class="pl-k">==</span><span class="pl-c1">FALSE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC157" class="react-file-line html-div" data-testid="code-cell" data-line-number="157" style="position:relative">    <span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">fcast_rec_option</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC158" class="react-file-line html-div" data-testid="code-cell" data-line-number="158" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC159" class="react-file-line html-div" data-testid="code-cell" data-line-number="159" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC160" class="react-file-line html-div" data-testid="code-cell" data-line-number="160" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Need to set recdevs and implementation error for all projection years </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC161" class="react-file-line html-div" data-testid="code-cell" data-line-number="161" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>so that reading from par file is possible</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC162" class="react-file-line html-div" data-testid="code-cell" data-line-number="162" style="position:relative">  <span class="pl-smi">expected_forecast_rec_length</span> <span class="pl-k">&lt;-</span> length((min(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],<span class="pl-smi">ctl</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>MainRdevYrLast<span class="pl-pds">&quot;</span></span>]])<span class="pl-k">+</span><span class="pl-c1">1</span>)<span class="pl-k">:</span>(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC163" class="react-file-line html-div" data-testid="code-cell" data-line-number="163" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC164" class="react-file-line html-div" data-testid="code-cell" data-line-number="164" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">1</span>])<span class="pl-k">!=</span><span class="pl-smi">expected_forecast_rec_length</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC165" class="react-file-line html-div" data-testid="code-cell" data-line-number="165" style="position:relative">      <span class="pl-smi">temp_recs</span><span class="pl-k">&lt;-</span><span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">2</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC166" class="react-file-line html-div" data-testid="code-cell" data-line-number="166" style="position:relative">      <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span> <span class="pl-k">&lt;-</span> <span class="pl-k">matrix</span>(<span class="pl-c1">NA</span>, <span class="pl-v">nrow</span> <span class="pl-k">=</span> <span class="pl-smi">expected_forecast_rec_length</span>, <span class="pl-v">ncol</span> <span class="pl-k">=</span> <span class="pl-c1">2</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC167" class="react-file-line html-div" data-testid="code-cell" data-line-number="167" style="position:relative">      <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">1</span>] <span class="pl-k">&lt;-</span> (min(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],<span class="pl-smi">ctl</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>MainRdevYrLast<span class="pl-pds">&quot;</span></span>]])<span class="pl-k">+</span><span class="pl-c1">1</span>)<span class="pl-k">:</span>(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC168" class="react-file-line html-div" data-testid="code-cell" data-line-number="168" style="position:relative">      <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">2</span>] <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">0</span>,<span class="pl-smi">expected_forecast_rec_length</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC169" class="react-file-line html-div" data-testid="code-cell" data-line-number="169" style="position:relative">      <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[<span class="pl-c1">1</span><span class="pl-k">:</span>length(<span class="pl-smi">temp_recs</span>),<span class="pl-c1">2</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">temp_recs</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC170" class="react-file-line html-div" data-testid="code-cell" data-line-number="170" style="position:relative">      colnames(<span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>) <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>recdev<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC171" class="react-file-line html-div" data-testid="code-cell" data-line-number="171" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC172" class="react-file-line html-div" data-testid="code-cell" data-line-number="172" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC173" class="react-file-line html-div" data-testid="code-cell" data-line-number="173" style="position:relative">    <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span> <span class="pl-k">&lt;-</span> <span class="pl-k">matrix</span>(<span class="pl-c1">NA</span>, <span class="pl-v">nrow</span> <span class="pl-k">=</span> <span class="pl-smi">expected_forecast_rec_length</span>, <span class="pl-v">ncol</span> <span class="pl-k">=</span> <span class="pl-c1">2</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC174" class="react-file-line html-div" data-testid="code-cell" data-line-number="174" style="position:relative">    <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">1</span>] <span class="pl-k">&lt;-</span> (min(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],<span class="pl-smi">ctl</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>MainRdevYrLast<span class="pl-pds">&quot;</span></span>]])<span class="pl-k">+</span><span class="pl-c1">1</span>)<span class="pl-k">:</span>(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC175" class="react-file-line html-div" data-testid="code-cell" data-line-number="175" style="position:relative">    <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>[,<span class="pl-c1">2</span>] <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">0</span>,<span class="pl-smi">expected_forecast_rec_length</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC176" class="react-file-line html-div" data-testid="code-cell" data-line-number="176" style="position:relative">    colnames(<span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">recdev_forecast</span>) <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>recdev<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC177" class="react-file-line html-div" data-testid="code-cell" data-line-number="177" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC178" class="react-file-line html-div" data-testid="code-cell" data-line-number="178" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC179" class="react-file-line html-div" data-testid="code-cell" data-line-number="179" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span> if(!is.null(parlist$Fcast_impl_error)){</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC180" class="react-file-line html-div" data-testid="code-cell" data-line-number="180" style="position:relative">  <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">Fcast_impl_error</span> <span class="pl-k">&lt;-</span> <span class="pl-k">matrix</span>(<span class="pl-c1">NA</span>, <span class="pl-v">nrow</span> <span class="pl-k">=</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]], <span class="pl-v">ncol</span> <span class="pl-k">=</span> <span class="pl-c1">2</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC181" class="react-file-line html-div" data-testid="code-cell" data-line-number="181" style="position:relative">  <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">Fcast_impl_error</span>[,<span class="pl-c1">1</span>] <span class="pl-k">&lt;-</span> (<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-c1">1</span>)<span class="pl-k">:</span>(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC182" class="react-file-line html-div" data-testid="code-cell" data-line-number="182" style="position:relative">  <span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">Fcast_impl_error</span>[,<span class="pl-c1">2</span>] <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">0</span>,<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC183" class="react-file-line html-div" data-testid="code-cell" data-line-number="183" style="position:relative">  colnames(<span class="pl-smi">parlist</span><span class="pl-k">$</span><span class="pl-smi">Fcast_impl_error</span>) <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>impl_error<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC184" class="react-file-line html-div" data-testid="code-cell" data-line-number="184" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>stddev_of_log_catch_ratio<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC185" class="react-file-line html-div" data-testid="code-cell" data-line-number="185" style="position:relative">    <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>stddev_of_log_catch_ratio<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-c1">0.001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC186" class="react-file-line html-div" data-testid="code-cell" data-line-number="186" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC187" class="react-file-line html-div" data-testid="code-cell" data-line-number="187" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC188" class="react-file-line html-div" data-testid="code-cell" data-line-number="188" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Adjust the starter file to read from par file, perform no fitting (This should already have been done),</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC189" class="react-file-line html-div" data-testid="code-cell" data-line-number="189" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>and set the depletion value to be relative to unexploited biomass and have no scaling </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC190" class="react-file-line html-div" data-testid="code-cell" data-line-number="190" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>(so that correct depletion target can be found).</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC191" class="react-file-line html-div" data-testid="code-cell" data-line-number="191" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">init_values_src</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC192" class="react-file-line html-div" data-testid="code-cell" data-line-number="192" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">last_estimation_phase</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC193" class="react-file-line html-div" data-testid="code-cell" data-line-number="193" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">depl_basis</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC194" class="react-file-line html-div" data-testid="code-cell" data-line-number="194" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">depl_denom_frac</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC195" class="react-file-line html-div" data-testid="code-cell" data-line-number="195" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">SPR_basis</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">4</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC196" class="react-file-line html-div" data-testid="code-cell" data-line-number="196" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">F_report_units</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC197" class="react-file-line html-div" data-testid="code-cell" data-line-number="197" style="position:relative">  <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">F_report_basis</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC198" class="react-file-line html-div" data-testid="code-cell" data-line-number="198" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC199" class="react-file-line html-div" data-testid="code-cell" data-line-number="199" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Get the timeseries of historic/projected catches and F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC200" class="react-file-line html-div" data-testid="code-cell" data-line-number="200" style="position:relative">  <span class="pl-smi">TimeFit</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">results</span><span class="pl-k">$</span><span class="pl-smi">timeseries</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC201" class="react-file-line html-div" data-testid="code-cell" data-line-number="201" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC202" class="react-file-line html-div" data-testid="code-cell" data-line-number="202" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Identify the column numbers for Catch, F, SSB, Recruits, etc</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC203" class="react-file-line html-div" data-testid="code-cell" data-line-number="203" style="position:relative">  <span class="pl-smi">Catch_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC204" class="react-file-line html-div" data-testid="code-cell" data-line-number="204" style="position:relative">  <span class="pl-smi">Dead_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC205" class="react-file-line html-div" data-testid="code-cell" data-line-number="205" style="position:relative">  <span class="pl-smi">CatchN_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC206" class="react-file-line html-div" data-testid="code-cell" data-line-number="206" style="position:relative">  <span class="pl-smi">DeadN_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC207" class="react-file-line html-div" data-testid="code-cell" data-line-number="207" style="position:relative">  <span class="pl-smi">F_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC208" class="react-file-line html-div" data-testid="code-cell" data-line-number="208" style="position:relative">  <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC209" class="react-file-line html-div" data-testid="code-cell" data-line-number="209" style="position:relative">    <span class="pl-smi">F_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC210" class="react-file-line html-div" data-testid="code-cell" data-line-number="210" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC211" class="react-file-line html-div" data-testid="code-cell" data-line-number="211" style="position:relative">  <span class="pl-smi">TimeFit2</span> <span class="pl-k">&lt;-</span> aggregate(<span class="pl-smi">TimeFit</span>[,sort(c(<span class="pl-c1">2</span>,<span class="pl-c1">4</span>,<span class="pl-c1">7</span>,<span class="pl-smi">Catch_cols</span>,<span class="pl-smi">Dead_cols</span>,<span class="pl-smi">CatchN_cols</span>,<span class="pl-smi">DeadN_cols</span>,<span class="pl-smi">F_cols</span>))],<span class="pl-v">by</span><span class="pl-k">=</span><span class="pl-k">list</span>(<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span>,<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Seas</span>),<span class="pl-v">FUN</span><span class="pl-k">=</span><span class="pl-smi">sum</span>,<span class="pl-v">na.rm</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)[,<span class="pl-k">-</span>c(<span class="pl-c1">3</span>,<span class="pl-c1">4</span>,<span class="pl-c1">5</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC212" class="react-file-line html-div" data-testid="code-cell" data-line-number="212" style="position:relative">  names(<span class="pl-smi">TimeFit2</span>)[c(<span class="pl-c1">1</span>,<span class="pl-c1">2</span>)] <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC213" class="react-file-line html-div" data-testid="code-cell" data-line-number="213" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC214" class="react-file-line html-div" data-testid="code-cell" data-line-number="214" style="position:relative">  <span class="pl-smi">Catch_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC215" class="react-file-line html-div" data-testid="code-cell" data-line-number="215" style="position:relative">  <span class="pl-smi">Dead_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC216" class="react-file-line html-div" data-testid="code-cell" data-line-number="216" style="position:relative">  <span class="pl-smi">CatchN_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC217" class="react-file-line html-div" data-testid="code-cell" data-line-number="217" style="position:relative">  <span class="pl-smi">DeadN_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC218" class="react-file-line html-div" data-testid="code-cell" data-line-number="218" style="position:relative">  <span class="pl-smi">F_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC219" class="react-file-line html-div" data-testid="code-cell" data-line-number="219" style="position:relative">  <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols2</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC220" class="react-file-line html-div" data-testid="code-cell" data-line-number="220" style="position:relative">    <span class="pl-smi">F_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC221" class="react-file-line html-div" data-testid="code-cell" data-line-number="221" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC222" class="react-file-line html-div" data-testid="code-cell" data-line-number="222" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC223" class="react-file-line html-div" data-testid="code-cell" data-line-number="223" style="position:relative">  <span class="pl-smi">TimeFit3</span> <span class="pl-k">&lt;-</span> aggregate(<span class="pl-smi">TimeFit</span>[,sort(c(<span class="pl-c1">2</span>,<span class="pl-c1">7</span>,<span class="pl-c1">8</span>,<span class="pl-smi">Catch_cols</span>,<span class="pl-smi">Dead_cols</span>,<span class="pl-smi">CatchN_cols</span>,<span class="pl-smi">DeadN_cols</span>,<span class="pl-smi">F_cols</span>))],<span class="pl-v">by</span><span class="pl-k">=</span><span class="pl-k">list</span>(<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span>),<span class="pl-v">FUN</span><span class="pl-k">=</span><span class="pl-smi">sum</span>,<span class="pl-v">na.rm</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)[,<span class="pl-k">-</span><span class="pl-c1">2</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC224" class="react-file-line html-div" data-testid="code-cell" data-line-number="224" style="position:relative">  names(<span class="pl-smi">TimeFit3</span>)[c(<span class="pl-c1">1</span>)] <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC225" class="react-file-line html-div" data-testid="code-cell" data-line-number="225" style="position:relative">  <span class="pl-smi">Virgin_bio</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[<span class="pl-c1">1</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC226" class="react-file-line html-div" data-testid="code-cell" data-line-number="226" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC227" class="react-file-line html-div" data-testid="code-cell" data-line-number="227" style="position:relative">  <span class="pl-smi">Catch_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC228" class="react-file-line html-div" data-testid="code-cell" data-line-number="228" style="position:relative">  <span class="pl-smi">Dead_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC229" class="react-file-line html-div" data-testid="code-cell" data-line-number="229" style="position:relative">  <span class="pl-smi">CatchN_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC230" class="react-file-line html-div" data-testid="code-cell" data-line-number="230" style="position:relative">  <span class="pl-smi">DeadN_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC231" class="react-file-line html-div" data-testid="code-cell" data-line-number="231" style="position:relative">  <span class="pl-smi">F_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC232" class="react-file-line html-div" data-testid="code-cell" data-line-number="232" style="position:relative">  <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols3</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC233" class="react-file-line html-div" data-testid="code-cell" data-line-number="233" style="position:relative">    <span class="pl-smi">F_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC234" class="react-file-line html-div" data-testid="code-cell" data-line-number="234" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC235" class="react-file-line html-div" data-testid="code-cell" data-line-number="235" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC236" class="react-file-line html-div" data-testid="code-cell" data-line-number="236" style="position:relative">  <span class="pl-smi">achieved.report</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[<span class="pl-c1">0</span>,<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-c1">8</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC237" class="react-file-line html-div" data-testid="code-cell" data-line-number="237" style="position:relative">  colnames(<span class="pl-smi">achieved.report</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC238" class="react-file-line html-div" data-testid="code-cell" data-line-number="238" style="position:relative">  <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span>length(<span class="pl-smi">F_cols2</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC239" class="react-file-line html-div" data-testid="code-cell" data-line-number="239" style="position:relative">    <span class="pl-smi">temp.data</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-c1">8</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC240" class="react-file-line html-div" data-testid="code-cell" data-line-number="240" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">3</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">i</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC241" class="react-file-line html-div" data-testid="code-cell" data-line-number="241" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">Catch_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC242" class="react-file-line html-div" data-testid="code-cell" data-line-number="242" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">5</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">Dead_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC243" class="react-file-line html-div" data-testid="code-cell" data-line-number="243" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">6</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">CatchN_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC244" class="react-file-line html-div" data-testid="code-cell" data-line-number="244" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">7</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">DeadN_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC245" class="react-file-line html-div" data-testid="code-cell" data-line-number="245" style="position:relative">    <span class="pl-smi">temp.data</span>[,<span class="pl-c1">8</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">F_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC246" class="react-file-line html-div" data-testid="code-cell" data-line-number="246" style="position:relative">    colnames(<span class="pl-smi">temp.data</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC247" class="react-file-line html-div" data-testid="code-cell" data-line-number="247" style="position:relative">    <span class="pl-smi">achieved.report</span> <span class="pl-k">&lt;-</span> rbind(<span class="pl-smi">achieved.report</span>,<span class="pl-smi">temp.data</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC248" class="react-file-line html-div" data-testid="code-cell" data-line-number="248" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC249" class="react-file-line html-div" data-testid="code-cell" data-line-number="249" style="position:relative">  <span class="pl-smi">achieved.report</span><span class="pl-k">&lt;-</span><span class="pl-smi">achieved.report</span>[order(<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Year</span>,<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Seas</span>,<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Fleet</span>),]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC250" class="react-file-line html-div" data-testid="code-cell" data-line-number="250" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC251" class="react-file-line html-div" data-testid="code-cell" data-line-number="251" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Set all future projections to fish at constant apical F that matches recent years</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC252" class="react-file-line html-div" data-testid="code-cell" data-line-number="252" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>get the years of timeseries F&#039;s based on the forecast year range</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC253" class="react-file-line html-div" data-testid="code-cell" data-line-number="253" style="position:relative">  <span class="pl-k">if</span>(is.data.frame(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC254" class="react-file-line html-div" data-testid="code-cell" data-line-number="254" style="position:relative">    <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][,<span class="pl-s"><span class="pl-pds">&#039;</span>MG_type<span class="pl-pds">&#039;</span></span>]<span class="pl-k">==</span><span class="pl-c1">11</span>,<span class="pl-s"><span class="pl-pds">&#039;</span>st_year<span class="pl-pds">&#039;</span></span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC255" class="react-file-line html-div" data-testid="code-cell" data-line-number="255" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">min_fcast_yr</span><span class="pl-k">==</span><span class="pl-k">-</span><span class="pl-c1">999</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC256" class="react-file-line html-div" data-testid="code-cell" data-line-number="256" style="position:relative">      <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>styr<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC257" class="react-file-line html-div" data-testid="code-cell" data-line-number="257" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;</span><span class="pl-k">=</span> <span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC258" class="react-file-line html-div" data-testid="code-cell" data-line-number="258" style="position:relative">      <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">+</span> <span class="pl-smi">min_fcast_yr</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC259" class="react-file-line html-div" data-testid="code-cell" data-line-number="259" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC260" class="react-file-line html-div" data-testid="code-cell" data-line-number="260" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC261" class="react-file-line html-div" data-testid="code-cell" data-line-number="261" style="position:relative">    <span class="pl-smi">max_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][,<span class="pl-s"><span class="pl-pds">&#039;</span>MG_type<span class="pl-pds">&#039;</span></span>]<span class="pl-k">==</span><span class="pl-c1">11</span>,<span class="pl-s"><span class="pl-pds">&#039;</span>end_year<span class="pl-pds">&#039;</span></span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC262" class="react-file-line html-div" data-testid="code-cell" data-line-number="262" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">max_fcast_yr</span> <span class="pl-k">&lt;</span><span class="pl-k">=</span> <span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC263" class="react-file-line html-div" data-testid="code-cell" data-line-number="263" style="position:relative">      <span class="pl-smi">max_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">+</span> <span class="pl-smi">max_fcast_yr</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC264" class="react-file-line html-div" data-testid="code-cell" data-line-number="264" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC265" class="react-file-line html-div" data-testid="code-cell" data-line-number="265" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC266" class="react-file-line html-div" data-testid="code-cell" data-line-number="266" style="position:relative">  }<span class="pl-k">else</span>{ </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC267" class="react-file-line html-div" data-testid="code-cell" data-line-number="267" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">3</span>]<span class="pl-k">==</span><span class="pl-k">-</span><span class="pl-c1">999</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC268" class="react-file-line html-div" data-testid="code-cell" data-line-number="268" style="position:relative">      <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>styr<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC269" class="react-file-line html-div" data-testid="code-cell" data-line-number="269" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">3</span>]<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC270" class="react-file-line html-div" data-testid="code-cell" data-line-number="270" style="position:relative">      <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">3</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC271" class="react-file-line html-div" data-testid="code-cell" data-line-number="271" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC272" class="react-file-line html-div" data-testid="code-cell" data-line-number="272" style="position:relative">      <span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">3</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC273" class="react-file-line html-div" data-testid="code-cell" data-line-number="273" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC274" class="react-file-line html-div" data-testid="code-cell" data-line-number="274" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC275" class="react-file-line html-div" data-testid="code-cell" data-line-number="275" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">4</span>]<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC276" class="react-file-line html-div" data-testid="code-cell" data-line-number="276" style="position:relative">      <span class="pl-smi">max_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">4</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC277" class="react-file-line html-div" data-testid="code-cell" data-line-number="277" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC278" class="react-file-line html-div" data-testid="code-cell" data-line-number="278" style="position:relative">      <span class="pl-smi">max_fcast_yr</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Fcast_years<span class="pl-pds">&quot;</span></span>]][<span class="pl-c1">4</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC279" class="react-file-line html-div" data-testid="code-cell" data-line-number="279" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC280" class="react-file-line html-div" data-testid="code-cell" data-line-number="280" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC281" class="react-file-line html-div" data-testid="code-cell" data-line-number="281" style="position:relative">  <span class="pl-smi">TargetYears</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[<span class="pl-smi">TimeFit2</span><span class="pl-k">$</span><span class="pl-smi">Yr</span><span class="pl-k">&gt;</span><span class="pl-k">=</span><span class="pl-smi">min_fcast_yr</span> <span class="pl-k">&amp;</span> <span class="pl-smi">TimeFit2</span><span class="pl-k">$</span><span class="pl-smi">Yr</span><span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-smi">max_fcast_yr</span>,]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC282" class="react-file-line html-div" data-testid="code-cell" data-line-number="282" style="position:relative">  <span class="pl-smi">TargetYears</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TargetYears</span>[,c(<span class="pl-c1">2</span>,<span class="pl-smi">F_cols2</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC283" class="react-file-line html-div" data-testid="code-cell" data-line-number="283" style="position:relative">  <span class="pl-smi">seasons</span> <span class="pl-k">&lt;-</span> unique(<span class="pl-smi">TargetYears</span>[,<span class="pl-c1">1</span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC284" class="react-file-line html-div" data-testid="code-cell" data-line-number="284" style="position:relative">  <span class="pl-smi">F_by_Fleet_seas</span> <span class="pl-k">&lt;-</span> as.data.frame(<span class="pl-k">matrix</span>(apply(<span class="pl-smi">TargetYears</span>[<span class="pl-smi">TargetYears</span>[,<span class="pl-c1">1</span>]<span class="pl-k">==</span><span class="pl-smi">seasons</span>[<span class="pl-c1">1</span>],,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>], <span class="pl-c1">2</span>, <span class="pl-smi">mean</span>),<span class="pl-v">nrow</span><span class="pl-k">=</span><span class="pl-c1">1</span>,<span class="pl-v">ncol</span><span class="pl-k">=</span>(length(<span class="pl-smi">F_cols</span>)<span class="pl-k">+</span><span class="pl-c1">1</span>)))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC285" class="react-file-line html-div" data-testid="code-cell" data-line-number="285" style="position:relative">  <span class="pl-k">if</span>(length(<span class="pl-smi">seasons</span>)<span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC286" class="react-file-line html-div" data-testid="code-cell" data-line-number="286" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-smi">seasons</span>[<span class="pl-k">-</span><span class="pl-c1">1</span>]){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC287" class="react-file-line html-div" data-testid="code-cell" data-line-number="287" style="position:relative">      <span class="pl-smi">F_by_Fleet_seas</span> <span class="pl-k">&lt;-</span> rbind(<span class="pl-smi">F_by_Fleet_seas</span>,apply(<span class="pl-smi">TargetYears</span>[<span class="pl-smi">TargetYears</span>[,<span class="pl-c1">1</span>]<span class="pl-k">==</span><span class="pl-smi">i</span>,,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>], <span class="pl-c1">2</span>, <span class="pl-smi">mean</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC288" class="react-file-line html-div" data-testid="code-cell" data-line-number="288" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC289" class="react-file-line html-div" data-testid="code-cell" data-line-number="289" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC290" class="react-file-line html-div" data-testid="code-cell" data-line-number="290" style="position:relative">  <span class="pl-smi">Forecast_target</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecast<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC291" class="react-file-line html-div" data-testid="code-cell" data-line-number="291" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.element(<span class="pl-smi">Forecast_target</span>,c(<span class="pl-c1">1</span>,<span class="pl-c1">2</span>,<span class="pl-c1">3</span>))){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC292" class="react-file-line html-div" data-testid="code-cell" data-line-number="292" style="position:relative">    stop(<span class="pl-s"><span class="pl-pds">&quot;</span>forecast should be set to either 1, 2, or 3 so we know what the target is<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC293" class="react-file-line html-div" data-testid="code-cell" data-line-number="293" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC294" class="react-file-line html-div" data-testid="code-cell" data-line-number="294" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC295" class="react-file-line html-div" data-testid="code-cell" data-line-number="295" style="position:relative">  <span class="pl-k">if</span>(is.null(<span class="pl-smi">starting_Forecatch</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC296" class="react-file-line html-div" data-testid="code-cell" data-line-number="296" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Build a projection forcast matrix of F values by fleet/season/year which will adjusted to achieve target stock status, F, and allocations.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC297" class="react-file-line html-div" data-testid="code-cell" data-line-number="297" style="position:relative">    <span class="pl-smi">forecast_F</span><span class="pl-k">&lt;-</span><span class="pl-k">matrix</span>(<span class="pl-c1">1</span>,<span class="pl-v">nrow</span><span class="pl-k">=</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>),<span class="pl-v">ncol</span><span class="pl-k">=</span><span class="pl-c1">5</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC298" class="react-file-line html-div" data-testid="code-cell" data-line-number="298" style="position:relative">    <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">1</span>]<span class="pl-k">&lt;-</span>sort(rep((<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-c1">1</span>)<span class="pl-k">:</span>(<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC299" class="react-file-line html-div" data-testid="code-cell" data-line-number="299" style="position:relative">    <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">2</span>]<span class="pl-k">&lt;-</span>rep(sort(rep(<span class="pl-smi">seasons</span>,length(<span class="pl-smi">F_cols</span>))),<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC300" class="react-file-line html-div" data-testid="code-cell" data-line-number="300" style="position:relative">    <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">3</span>]<span class="pl-k">&lt;-</span>rep(sort(which(<span class="pl-smi">dat</span><span class="pl-k">$</span><span class="pl-smi">fleetinfo</span><span class="pl-k">$</span><span class="pl-smi">type</span><span class="pl-k">!=</span><span class="pl-c1">3</span>)),<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>(length(<span class="pl-smi">seasons</span>)))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC301" class="react-file-line html-div" data-testid="code-cell" data-line-number="301" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-smi">seasons</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC302" class="react-file-line html-div" data-testid="code-cell" data-line-number="302" style="position:relative">      <span class="pl-smi">forecast_F</span>[<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">2</span>]<span class="pl-k">==</span><span class="pl-smi">i</span>,<span class="pl-c1">4</span>]<span class="pl-k">&lt;-</span>unlist(rep(<span class="pl-smi">F_by_Fleet_seas</span>[<span class="pl-smi">F_by_Fleet_seas</span>[,<span class="pl-c1">1</span>]<span class="pl-k">==</span><span class="pl-smi">i</span>,<span class="pl-k">-</span><span class="pl-c1">1</span>],<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC303" class="react-file-line html-div" data-testid="code-cell" data-line-number="303" style="position:relative">      <span class="pl-smi">forecast_F</span>[<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">2</span>]<span class="pl-k">==</span><span class="pl-smi">i</span>,<span class="pl-c1">5</span>]<span class="pl-k">&lt;-</span>rep(<span class="pl-c1">99</span>,length(<span class="pl-smi">F_cols</span>)<span class="pl-k">*</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC304" class="react-file-line html-div" data-testid="code-cell" data-line-number="304" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC305" class="react-file-line html-div" data-testid="code-cell" data-line-number="305" style="position:relative">    <span class="pl-smi">forecast_F</span><span class="pl-k">&lt;-</span>as.data.frame(<span class="pl-smi">forecast_F</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC306" class="react-file-line html-div" data-testid="code-cell" data-line-number="306" style="position:relative">    colnames(<span class="pl-smi">forecast_F</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Basis<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC307" class="react-file-line html-div" data-testid="code-cell" data-line-number="307" style="position:relative">    <span class="pl-smi">forecast_F</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast_F</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>] <span class="pl-k">+</span> <span class="pl-c1">0.00000001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC308" class="react-file-line html-div" data-testid="code-cell" data-line-number="308" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC309" class="react-file-line html-div" data-testid="code-cell" data-line-number="309" style="position:relative">    <span class="pl-k">if</span>(dim(<span class="pl-smi">starting_Forecatch</span>)[<span class="pl-c1">1</span>]<span class="pl-k">!=</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC310" class="react-file-line html-div" data-testid="code-cell" data-line-number="310" style="position:relative">      stop(<span class="pl-s"><span class="pl-pds">&quot;</span>Error: You input a starting forecatch matrix but it is not the correct length n_years*n_fleets*n_seasons.<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC311" class="react-file-line html-div" data-testid="code-cell" data-line-number="311" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC312" class="react-file-line html-div" data-testid="code-cell" data-line-number="312" style="position:relative">    <span class="pl-k">if</span>(dim(<span class="pl-smi">starting_Forecatch</span>)[<span class="pl-c1">2</span>]<span class="pl-k">!=</span><span class="pl-c1">5</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC313" class="react-file-line html-div" data-testid="code-cell" data-line-number="313" style="position:relative">      stop(<span class="pl-s"><span class="pl-pds">&quot;</span>Error: You input a starting forecatch matrix but it does not have 5 columns Year, Season, Fleet, Catch, Basis.<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC314" class="react-file-line html-div" data-testid="code-cell" data-line-number="314" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC315" class="react-file-line html-div" data-testid="code-cell" data-line-number="315" style="position:relative">    <span class="pl-k">if</span>(length(dim(<span class="pl-smi">starting_Forecatch</span>))<span class="pl-k">!=</span><span class="pl-c1">2</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC316" class="react-file-line html-div" data-testid="code-cell" data-line-number="316" style="position:relative">      stop(<span class="pl-s"><span class="pl-pds">&quot;</span>Error: You input a starting forecatch but it is not a matrix<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC317" class="react-file-line html-div" data-testid="code-cell" data-line-number="317" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC318" class="react-file-line html-div" data-testid="code-cell" data-line-number="318" style="position:relative">    <span class="pl-smi">forecast_F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">starting_Forecatch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC319" class="react-file-line html-div" data-testid="code-cell" data-line-number="319" style="position:relative">    colnames(<span class="pl-smi">forecast_F</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Basis<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC320" class="react-file-line html-div" data-testid="code-cell" data-line-number="320" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC321" class="react-file-line html-div" data-testid="code-cell" data-line-number="321" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC322" class="react-file-line html-div" data-testid="code-cell" data-line-number="322" style="position:relative">  <span class="pl-smi">adjusted_F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span><span class="pl-k">:</span>(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC323" class="react-file-line html-div" data-testid="code-cell" data-line-number="323" style="position:relative">
</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC324" class="react-file-line html-div" data-testid="code-cell" data-line-number="324" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Extract fixed forecast values from the forecast file these will be fixed at these values for the projections</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC325" class="react-file-line html-div" data-testid="code-cell" data-line-number="325" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>This is used to implement recent catches or fixed harvest from an independent fleet such as shrimp bycatch.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC326" class="react-file-line html-div" data-testid="code-cell" data-line-number="326" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>ForeCatch<span class="pl-pds">&quot;</span></span>]])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC327" class="react-file-line html-div" data-testid="code-cell" data-line-number="327" style="position:relative">    <span class="pl-smi">Fixed_catch_basis</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>InputBasis<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC328" class="react-file-line html-div" data-testid="code-cell" data-line-number="328" style="position:relative">    <span class="pl-smi">Fixed_catch_target</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>ForeCatch<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC329" class="react-file-line html-div" data-testid="code-cell" data-line-number="329" style="position:relative">    <span class="pl-smi">fixed_ref</span> <span class="pl-k">&lt;-</span> seq_along(<span class="pl-smi">Fixed_catch_target</span>[,<span class="pl-c1">1</span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC330" class="react-file-line html-div" data-testid="code-cell" data-line-number="330" style="position:relative">    <span class="pl-k">if</span>(length(names(<span class="pl-smi">Fixed_catch_target</span>))<span class="pl-k">==</span><span class="pl-c1">4</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC331" class="react-file-line html-div" data-testid="code-cell" data-line-number="331" style="position:relative">      <span class="pl-smi">new_names</span> <span class="pl-k">&lt;-</span> c(names(<span class="pl-smi">Fixed_catch_target</span>),<span class="pl-s"><span class="pl-pds">&quot;</span>Basis<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC332" class="react-file-line html-div" data-testid="code-cell" data-line-number="332" style="position:relative">      <span class="pl-smi">Fixed_catch_target</span> <span class="pl-k">&lt;-</span> cbind(<span class="pl-smi">Fixed_catch_target</span>,rep(<span class="pl-smi">Fixed_catch_basis</span>,length(<span class="pl-smi">Fixed_catch_target</span>[,<span class="pl-c1">1</span>])))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC333" class="react-file-line html-div" data-testid="code-cell" data-line-number="333" style="position:relative">      names(<span class="pl-smi">Fixed_catch_target</span>) <span class="pl-k">&lt;-</span> <span class="pl-smi">new_names</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC334" class="react-file-line html-div" data-testid="code-cell" data-line-number="334" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC335" class="react-file-line html-div" data-testid="code-cell" data-line-number="335" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> seq_along(<span class="pl-smi">Fixed_catch_target</span>[,<span class="pl-c1">1</span>])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC336" class="react-file-line html-div" data-testid="code-cell" data-line-number="336" style="position:relative">      <span class="pl-smi">fixed_ref</span>[<span class="pl-smi">i</span>]<span class="pl-k">&lt;-</span>which(<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">1</span>]<span class="pl-k">==</span><span class="pl-smi">Fixed_catch_target</span>[<span class="pl-smi">i</span>,<span class="pl-c1">1</span>] <span class="pl-k">&amp;</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC337" class="react-file-line html-div" data-testid="code-cell" data-line-number="337" style="position:relative">                          <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">2</span>]<span class="pl-k">==</span><span class="pl-smi">Fixed_catch_target</span>[<span class="pl-smi">i</span>,<span class="pl-c1">2</span>] <span class="pl-k">&amp;</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC338" class="react-file-line html-div" data-testid="code-cell" data-line-number="338" style="position:relative">                          <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">3</span>]<span class="pl-k">==</span><span class="pl-smi">Fixed_catch_target</span>[<span class="pl-smi">i</span>,<span class="pl-c1">3</span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC339" class="react-file-line html-div" data-testid="code-cell" data-line-number="339" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC340" class="react-file-line html-div" data-testid="code-cell" data-line-number="340" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC341" class="react-file-line html-div" data-testid="code-cell" data-line-number="341" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Replace the temporary average F values with specified fixed inputs</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC342" class="react-file-line html-div" data-testid="code-cell" data-line-number="342" style="position:relative">    <span class="pl-smi">forecast_F</span>[<span class="pl-smi">fixed_ref</span>,c(<span class="pl-c1">4</span>,<span class="pl-c1">5</span>)]<span class="pl-k">&lt;-</span><span class="pl-smi">Fixed_catch_target</span>[,c(<span class="pl-c1">4</span>,<span class="pl-c1">5</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC343" class="react-file-line html-div" data-testid="code-cell" data-line-number="343" style="position:relative">    <span class="pl-smi">adjusted_F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">adjusted_F_OFL</span>[<span class="pl-k">-</span><span class="pl-smi">fixed_ref</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC344" class="react-file-line html-div" data-testid="code-cell" data-line-number="344" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">adjusted_F_OFL</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){stop(<span class="pl-s"><span class="pl-pds">&quot;</span>all F&#039;s are fixed nothing to estimate<span class="pl-pds">&quot;</span></span>)}</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC345" class="react-file-line html-div" data-testid="code-cell" data-line-number="345" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC346" class="react-file-line html-div" data-testid="code-cell" data-line-number="346" style="position:relative">    <span class="pl-smi">fixed_ref</span><span class="pl-k">&lt;-</span><span class="pl-c1">NULL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC347" class="react-file-line html-div" data-testid="code-cell" data-line-number="347" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC348" class="react-file-line html-div" data-testid="code-cell" data-line-number="348" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC349" class="react-file-line html-div" data-testid="code-cell" data-line-number="349" style="position:relative">
</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC350" class="react-file-line html-div" data-testid="code-cell" data-line-number="350" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">Rebuild_yr</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC351" class="react-file-line html-div" data-testid="code-cell" data-line-number="351" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>This reference identifies inputs subject to a rebuilding period F </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC352" class="react-file-line html-div" data-testid="code-cell" data-line-number="352" style="position:relative">    <span class="pl-smi">rebuild_ref</span> <span class="pl-k">&lt;-</span> which(<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">1</span>]<span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-smi">Rebuild_yr</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC353" class="react-file-line html-div" data-testid="code-cell" data-line-number="353" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">rebuild_ref</span>)<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC354" class="react-file-line html-div" data-testid="code-cell" data-line-number="354" style="position:relative">      <span class="pl-smi">adjusted_OFL_F_Rebuild</span><span class="pl-k">&lt;-</span><span class="pl-smi">adjusted_F_OFL</span>[<span class="pl-smi">adjusted_F_OFL</span><span class="pl-k">&gt;</span>max(<span class="pl-smi">rebuild_ref</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC355" class="react-file-line html-div" data-testid="code-cell" data-line-number="355" style="position:relative">      <span class="pl-smi">adjusted_Rebuild_F_Rebuild</span><span class="pl-k">&lt;-</span><span class="pl-smi">rebuild_ref</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC356" class="react-file-line html-div" data-testid="code-cell" data-line-number="356" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">fixed_ref</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC357" class="react-file-line html-div" data-testid="code-cell" data-line-number="357" style="position:relative">        <span class="pl-smi">adjusted_Rebuild_F_Rebuild</span><span class="pl-k">&lt;-</span><span class="pl-smi">adjusted_Rebuild_F_Rebuild</span>[<span class="pl-k">-</span><span class="pl-smi">fixed_ref</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC358" class="react-file-line html-div" data-testid="code-cell" data-line-number="358" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC359" class="react-file-line html-div" data-testid="code-cell" data-line-number="359" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC360" class="react-file-line html-div" data-testid="code-cell" data-line-number="360" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC361" class="react-file-line html-div" data-testid="code-cell" data-line-number="361" style="position:relative">    <span class="pl-smi">adjusted_OFL_F_Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">adjusted_F_OFL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC362" class="react-file-line html-div" data-testid="code-cell" data-line-number="362" style="position:relative">    <span class="pl-smi">adjusted_Rebuild_F_Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">NULL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC363" class="react-file-line html-div" data-testid="code-cell" data-line-number="363" style="position:relative">    <span class="pl-smi">rebuild_ref</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">NULL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC364" class="react-file-line html-div" data-testid="code-cell" data-line-number="364" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC365" class="react-file-line html-div" data-testid="code-cell" data-line-number="365" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Here all input values are assigned to an allocation group if needed and</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC366" class="react-file-line html-div" data-testid="code-cell" data-line-number="366" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>relative landings targets are identified</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC367" class="react-file-line html-div" data-testid="code-cell" data-line-number="367" style="position:relative">  <span class="pl-smi">n_groups</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>N_allocation_groups<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC368" class="react-file-line html-div" data-testid="code-cell" data-line-number="368" style="position:relative">  <span class="pl-smi">groups</span> <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">0</span>,length(<span class="pl-smi">F_cols</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC369" class="react-file-line html-div" data-testid="code-cell" data-line-number="369" style="position:relative">  <span class="pl-smi">fleets_by_group</span> <span class="pl-k">&lt;-</span> <span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC370" class="react-file-line html-div" data-testid="code-cell" data-line-number="370" style="position:relative">  <span class="pl-smi">Allocations</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast_F</span>[,c(<span class="pl-c1">1</span>,<span class="pl-c1">2</span>,<span class="pl-c1">3</span>,<span class="pl-c1">4</span>,<span class="pl-c1">5</span>,<span class="pl-c1">5</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC371" class="react-file-line html-div" data-testid="code-cell" data-line-number="371" style="position:relative">  <span class="pl-smi">Allocations</span>[,c(<span class="pl-c1">4</span>)] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC372" class="react-file-line html-div" data-testid="code-cell" data-line-number="372" style="position:relative">  <span class="pl-smi">Allocations</span>[,c(<span class="pl-c1">5</span>,<span class="pl-c1">6</span>)] <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC373" class="react-file-line html-div" data-testid="code-cell" data-line-number="373" style="position:relative">  names(<span class="pl-smi">Allocations</span>) <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Group<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Target<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Achieved<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC374" class="react-file-line html-div" data-testid="code-cell" data-line-number="374" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC375" class="react-file-line html-div" data-testid="code-cell" data-line-number="375" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> seq_along(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>fleet_assignment_to_allocation_group<span class="pl-pds">&quot;</span></span>]][,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC376" class="react-file-line html-div" data-testid="code-cell" data-line-number="376" style="position:relative">      <span class="pl-smi">groups</span>[<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>fleet_assignment_to_allocation_group<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">i</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>fleet_assignment_to_allocation_group<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">i</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Group<span class="pl-pds">&quot;</span></span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC377" class="react-file-line html-div" data-testid="code-cell" data-line-number="377" style="position:relative">      <span class="pl-smi">Allocations</span>[<span class="pl-smi">Allocations</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>]<span class="pl-k">==</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>fleet_assignment_to_allocation_group<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">i</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>],<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>fleet_assignment_to_allocation_group<span class="pl-pds">&quot;</span></span>]][<span class="pl-smi">i</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Group<span class="pl-pds">&quot;</span></span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC378" class="react-file-line html-div" data-testid="code-cell" data-line-number="378" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC379" class="react-file-line html-div" data-testid="code-cell" data-line-number="379" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC380" class="react-file-line html-div" data-testid="code-cell" data-line-number="380" style="position:relative">    <span class="pl-smi">alloc</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>allocation_among_groups<span class="pl-pds">&quot;</span></span>]][order(<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>allocation_among_groups<span class="pl-pds">&quot;</span></span>]][,<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>]),]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC381" class="react-file-line html-div" data-testid="code-cell" data-line-number="381" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> seq_along(<span class="pl-smi">alloc</span>[,<span class="pl-c1">1</span>])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC382" class="react-file-line html-div" data-testid="code-cell" data-line-number="382" style="position:relative">      <span class="pl-k">for</span>(<span class="pl-smi">j</span> <span class="pl-k">in</span> seq_along(<span class="pl-smi">alloc</span>[<span class="pl-smi">i</span>,<span class="pl-k">-</span><span class="pl-c1">1</span>])){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC383" class="react-file-line html-div" data-testid="code-cell" data-line-number="383" style="position:relative">        <span class="pl-smi">Allocations</span>[<span class="pl-smi">Allocations</span>[,<span class="pl-c1">1</span>]<span class="pl-k">&gt;</span><span class="pl-k">=</span><span class="pl-smi">alloc</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>] <span class="pl-k">&amp;</span> <span class="pl-smi">Allocations</span>[,<span class="pl-c1">4</span>]<span class="pl-k">==</span><span class="pl-smi">j</span>,<span class="pl-c1">5</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">alloc</span>[<span class="pl-smi">i</span>,(<span class="pl-smi">j</span><span class="pl-k">+</span><span class="pl-c1">1</span>)]<span class="pl-k">/</span>sum(<span class="pl-smi">alloc</span>[<span class="pl-smi">i</span>,<span class="pl-k">-</span><span class="pl-c1">1</span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC384" class="react-file-line html-div" data-testid="code-cell" data-line-number="384" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC385" class="react-file-line html-div" data-testid="code-cell" data-line-number="385" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC386" class="react-file-line html-div" data-testid="code-cell" data-line-number="386" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC387" class="react-file-line html-div" data-testid="code-cell" data-line-number="387" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC388" class="react-file-line html-div" data-testid="code-cell" data-line-number="388" style="position:relative">      <span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span>which(is.element(which(<span class="pl-smi">dat</span><span class="pl-k">$</span><span class="pl-smi">fleetinfo</span><span class="pl-k">$</span><span class="pl-smi">type</span><span class="pl-k">!=</span><span class="pl-c1">3</span>),which(<span class="pl-smi">groups</span><span class="pl-k">==</span><span class="pl-smi">i</span>)))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC389" class="react-file-line html-div" data-testid="code-cell" data-line-number="389" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC390" class="react-file-line html-div" data-testid="code-cell" data-line-number="390" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC391" class="react-file-line html-div" data-testid="code-cell" data-line-number="391" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC392" class="react-file-line html-div" data-testid="code-cell" data-line-number="392" style="position:relative">  <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecast<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-c1">4</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC393" class="react-file-line html-div" data-testid="code-cell" data-line-number="393" style="position:relative">  <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>InputBasis<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-k">-</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC394" class="react-file-line html-div" data-testid="code-cell" data-line-number="394" style="position:relative">  <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>ForeCatch<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast_F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC395" class="react-file-line html-div" data-testid="code-cell" data-line-number="395" style="position:relative">  <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>FirstYear_for_caps_and_allocations<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> (<span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">+</span><span class="pl-c1">1</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC396" class="react-file-line html-div" data-testid="code-cell" data-line-number="396" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC397" class="react-file-line html-div" data-testid="code-cell" data-line-number="397" style="position:relative">  <span class="pl-smi">keepFitting</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">TRUE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC398" class="react-file-line html-div" data-testid="code-cell" data-line-number="398" style="position:relative">  <span class="pl-smi">loop</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC399" class="react-file-line html-div" data-testid="code-cell" data-line-number="399" style="position:relative">  <span class="pl-smi">subloop</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC400" class="react-file-line html-div" data-testid="code-cell" data-line-number="400" style="position:relative">  <span class="pl-smi">F_maxed</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">100000</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC401" class="react-file-line html-div" data-testid="code-cell" data-line-number="401" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC402" class="react-file-line html-div" data-testid="code-cell" data-line-number="402" style="position:relative">  <span class="pl-smi">F_adjust1</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">F_adjust2</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC403" class="react-file-line html-div" data-testid="code-cell" data-line-number="403" style="position:relative">  <span class="pl-smi">F_adjust3</span> <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">1</span>,<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC404" class="react-file-line html-div" data-testid="code-cell" data-line-number="404" style="position:relative">  <span class="pl-smi">search_step</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">MSY_step</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC405" class="react-file-line html-div" data-testid="code-cell" data-line-number="405" style="position:relative">  <span class="pl-smi">Fmult1</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Fmult2</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Fmult3</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Fmult4</span> <span class="pl-k">&lt;-</span> rep(<span class="pl-c1">1.01</span>,<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC406" class="react-file-line html-div" data-testid="code-cell" data-line-number="406" style="position:relative">  <span class="pl-smi">Fmult2a</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Fmult2b</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC407" class="react-file-line html-div" data-testid="code-cell" data-line-number="407" style="position:relative">  <span class="pl-smi">First_run</span><span class="pl-k">&lt;-</span><span class="pl-c1">TRUE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC408" class="react-file-line html-div" data-testid="code-cell" data-line-number="408" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC409" class="react-file-line html-div" data-testid="code-cell" data-line-number="409" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">Const_Catch</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC410" class="react-file-line html-div" data-testid="code-cell" data-line-number="410" style="position:relative">    <span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">fcast_rec_option</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">catch_rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC411" class="react-file-line html-div" data-testid="code-cell" data-line-number="411" style="position:relative">    SS_writepar_3.30(<span class="pl-v">parlist</span> <span class="pl-k">=</span> <span class="pl-smi">parlist</span>,<span class="pl-v">outfile</span><span class="pl-k">=</span><span class="pl-smi">par_name</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC412" class="react-file-line html-div" data-testid="code-cell" data-line-number="412" style="position:relative">    SS_writeforecast(<span class="pl-v">mylist</span><span class="pl-k">=</span><span class="pl-smi">forecast</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC413" class="react-file-line html-div" data-testid="code-cell" data-line-number="413" style="position:relative">    SS_writestarter(<span class="pl-v">mylist</span><span class="pl-k">=</span><span class="pl-smi">start</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC414" class="react-file-line html-div" data-testid="code-cell" data-line-number="414" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC415" class="react-file-line html-div" data-testid="code-cell" data-line-number="415" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">run_in_MSE</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC416" class="react-file-line html-div" data-testid="code-cell" data-line-number="416" style="position:relative">      <span class="pl-e">SSMSE</span><span class="pl-k">:::</span>run_EM(<span class="pl-v">EM_dir</span> <span class="pl-k">=</span> getwd(), <span class="pl-v">verbose</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>, <span class="pl-v">check_converged</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC417" class="react-file-line html-div" data-testid="code-cell" data-line-number="417" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC418" class="react-file-line html-div" data-testid="code-cell" data-line-number="418" style="position:relative">      shell(paste(<span class="pl-s"><span class="pl-pds">&quot;</span>cd /d <span class="pl-pds">&quot;</span></span>,getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span> &amp;&amp; <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">SS_exe</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> -nohess<span class="pl-pds">&quot;</span></span>,<span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC419" class="react-file-line html-div" data-testid="code-cell" data-line-number="419" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC420" class="react-file-line html-div" data-testid="code-cell" data-line-number="420" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Begin the search in the Benchmark phase</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC421" class="react-file-line html-div" data-testid="code-cell" data-line-number="421" style="position:relative">    <span class="pl-smi">fitting_Benchmark</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC422" class="react-file-line html-div" data-testid="code-cell" data-line-number="422" style="position:relative">    <span class="pl-smi">fitting_OFL</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC423" class="react-file-line html-div" data-testid="code-cell" data-line-number="423" style="position:relative">    <span class="pl-smi">fitting_ABC</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC424" class="react-file-line html-div" data-testid="code-cell" data-line-number="424" style="position:relative">    <span class="pl-smi">fitting_Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC425" class="react-file-line html-div" data-testid="code-cell" data-line-number="425" style="position:relative">    <span class="pl-smi">fitting_F0</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC426" class="react-file-line html-div" data-testid="code-cell" data-line-number="426" style="position:relative">    <span class="pl-smi">fitting_Fixed_Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">TRUE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC427" class="react-file-line html-div" data-testid="code-cell" data-line-number="427" style="position:relative">    <span class="pl-smi">CC_loop</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC428" class="react-file-line html-div" data-testid="code-cell" data-line-number="428" style="position:relative">    <span class="pl-smi">Catch_Target</span> <span class="pl-k">&lt;-</span> rep(<span class="pl-smi">Const_Catch</span>[<span class="pl-smi">CC_loop</span>],<span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Nforecastyrs<span class="pl-pds">&quot;</span></span>]])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC429" class="react-file-line html-div" data-testid="code-cell" data-line-number="429" style="position:relative">    <span class="pl-smi">Catch_trunc</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC430" class="react-file-line html-div" data-testid="code-cell" data-line-number="430" style="position:relative">    <span class="pl-smi">method</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>fixed_catch<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC431" class="react-file-line html-div" data-testid="code-cell" data-line-number="431" style="position:relative">  }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">Benchmark_complete</span> <span class="pl-k">==</span> <span class="pl-c1">FALSE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC432" class="react-file-line html-div" data-testid="code-cell" data-line-number="432" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Save all the modified files and then perform a base run of SS so that output is specified correctly with </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC433" class="react-file-line html-div" data-testid="code-cell" data-line-number="433" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>a forecast[[&quot;Nforecastyrs&quot;]] year projection series.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC434" class="react-file-line html-div" data-testid="code-cell" data-line-number="434" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC435" class="react-file-line html-div" data-testid="code-cell" data-line-number="435" style="position:relative">    SS_writepar_3.30(<span class="pl-v">parlist</span> <span class="pl-k">=</span> <span class="pl-smi">parlist</span>, <span class="pl-v">outfile</span> <span class="pl-k">=</span> <span class="pl-smi">par_name</span>, <span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC436" class="react-file-line html-div" data-testid="code-cell" data-line-number="436" style="position:relative">    SS_writeforecast(<span class="pl-v">mylist</span><span class="pl-k">=</span><span class="pl-smi">forecast</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC437" class="react-file-line html-div" data-testid="code-cell" data-line-number="437" style="position:relative">    SS_writestarter(<span class="pl-v">mylist</span><span class="pl-k">=</span><span class="pl-smi">start</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC438" class="react-file-line html-div" data-testid="code-cell" data-line-number="438" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC439" class="react-file-line html-div" data-testid="code-cell" data-line-number="439" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">run_in_MSE</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC440" class="react-file-line html-div" data-testid="code-cell" data-line-number="440" style="position:relative">      <span class="pl-e">SSMSE</span><span class="pl-k">:::</span>run_EM(<span class="pl-v">EM_dir</span> <span class="pl-k">=</span> getwd(), <span class="pl-v">verbose</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>, <span class="pl-v">check_converged</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC441" class="react-file-line html-div" data-testid="code-cell" data-line-number="441" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC442" class="react-file-line html-div" data-testid="code-cell" data-line-number="442" style="position:relative">      shell(paste(<span class="pl-s"><span class="pl-pds">&quot;</span>cd /d <span class="pl-pds">&quot;</span></span>,getwd(),<span class="pl-s"><span class="pl-pds">&quot;</span> &amp;&amp; <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">SS_exe</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> -nohess<span class="pl-pds">&quot;</span></span>,<span class="pl-v">sep</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span><span class="pl-pds">&quot;</span></span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC443" class="react-file-line html-div" data-testid="code-cell" data-line-number="443" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC444" class="react-file-line html-div" data-testid="code-cell" data-line-number="444" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Begin the search in the Benchmark phase</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC445" class="react-file-line html-div" data-testid="code-cell" data-line-number="445" style="position:relative">    <span class="pl-smi">fitting_Benchmark</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">TRUE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC446" class="react-file-line html-div" data-testid="code-cell" data-line-number="446" style="position:relative">    <span class="pl-smi">fitting_OFL</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC447" class="react-file-line html-div" data-testid="code-cell" data-line-number="447" style="position:relative">    <span class="pl-smi">fitting_ABC</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC448" class="react-file-line html-div" data-testid="code-cell" data-line-number="448" style="position:relative">    <span class="pl-smi">fitting_Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC449" class="react-file-line html-div" data-testid="code-cell" data-line-number="449" style="position:relative">    <span class="pl-smi">fitting_F0</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC450" class="react-file-line html-div" data-testid="code-cell" data-line-number="450" style="position:relative">    <span class="pl-smi">fitting_Fixed_Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC451" class="react-file-line html-div" data-testid="code-cell" data-line-number="451" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC452" class="react-file-line html-div" data-testid="code-cell" data-line-number="452" style="position:relative">    <span class="pl-smi">MSY.Fit</span> <span class="pl-k">&lt;-</span> <span class="pl-k">data.frame</span>(<span class="pl-v">catch</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>),<span class="pl-v">Ave.F</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>),<span class="pl-v">depletion</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>),<span class="pl-v">target.depletion</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC453" class="react-file-line html-div" data-testid="code-cell" data-line-number="453" style="position:relative">    <span class="pl-smi">method</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>Benchmark<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC454" class="react-file-line html-div" data-testid="code-cell" data-line-number="454" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC455" class="react-file-line html-div" data-testid="code-cell" data-line-number="455" style="position:relative">  }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC456" class="react-file-line html-div" data-testid="code-cell" data-line-number="456" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Save all the modified files and then set search to begin in OFL phase </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC457" class="react-file-line html-div" data-testid="code-cell" data-line-number="457" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC458" class="react-file-line html-div" data-testid="code-cell" data-line-number="458" style="position:relative">    <span class="pl-smi">start</span> <span class="pl-k">&lt;-</span> SS_readstarter()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC459" class="react-file-line html-div" data-testid="code-cell" data-line-number="459" style="position:relative">    <span class="pl-smi">dat</span> <span class="pl-k">&lt;-</span> SS_readdat(<span class="pl-v">file</span> <span class="pl-k">=</span> <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">datfile</span>, <span class="pl-v">version</span> <span class="pl-k">=</span> <span class="pl-c1">3.3</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC460" class="react-file-line html-div" data-testid="code-cell" data-line-number="460" style="position:relative">    <span class="pl-smi">ctl</span> <span class="pl-k">&lt;-</span> SS_readctl(<span class="pl-v">file</span> <span class="pl-k">=</span> <span class="pl-smi">start</span><span class="pl-k">$</span><span class="pl-smi">ctlfile</span>, <span class="pl-v">version</span> <span class="pl-k">=</span> <span class="pl-c1">3.3</span>, <span class="pl-v">use_datlist</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>, <span class="pl-v">datlist</span> <span class="pl-k">=</span> <span class="pl-smi">dat</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC461" class="react-file-line html-div" data-testid="code-cell" data-line-number="461" style="position:relative">    <span class="pl-smi">results</span> <span class="pl-k">&lt;-</span> SS_output(<span class="pl-v">dir</span> <span class="pl-k">=</span> getwd(), <span class="pl-v">covar</span> <span class="pl-k">=</span> <span class="pl-c1">FALSE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC462" class="react-file-line html-div" data-testid="code-cell" data-line-number="462" style="position:relative">    <span class="pl-smi">forecast</span> <span class="pl-k">&lt;-</span> SS_readforecast() </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC463" class="react-file-line html-div" data-testid="code-cell" data-line-number="463" style="position:relative">    <span class="pl-smi">parlist</span> <span class="pl-k">&lt;-</span> SS_readpar_3.30(<span class="pl-v">parfile</span> <span class="pl-k">=</span> <span class="pl-smi">par_name</span>, <span class="pl-v">datsource</span> <span class="pl-k">=</span> <span class="pl-smi">dat</span>, <span class="pl-v">ctlsource</span> <span class="pl-k">=</span> <span class="pl-smi">ctl</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC464" class="react-file-line html-div" data-testid="code-cell" data-line-number="464" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC465" class="react-file-line html-div" data-testid="code-cell" data-line-number="465" style="position:relative">    <span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">fcast_rec_option</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">catch_rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC466" class="react-file-line html-div" data-testid="code-cell" data-line-number="466" style="position:relative">    SS_writeforecast(<span class="pl-v">mylist</span><span class="pl-k">=</span><span class="pl-smi">forecast</span>,<span class="pl-v">overwrite</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC467" class="react-file-line html-div" data-testid="code-cell" data-line-number="467" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC468" class="react-file-line html-div" data-testid="code-cell" data-line-number="468" style="position:relative">    <span class="pl-smi">fitting_Benchmark</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC469" class="react-file-line html-div" data-testid="code-cell" data-line-number="469" style="position:relative">    <span class="pl-smi">fitting_OFL</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">TRUE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC470" class="react-file-line html-div" data-testid="code-cell" data-line-number="470" style="position:relative">	  <span class="pl-smi">fitting_ABC</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC471" class="react-file-line html-div" data-testid="code-cell" data-line-number="471" style="position:relative">    <span class="pl-smi">fitting_Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC472" class="react-file-line html-div" data-testid="code-cell" data-line-number="472" style="position:relative">    <span class="pl-smi">fitting_F0</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC473" class="react-file-line html-div" data-testid="code-cell" data-line-number="473" style="position:relative">    <span class="pl-smi">fitting_Fixed_Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC474" class="react-file-line html-div" data-testid="code-cell" data-line-number="474" style="position:relative">    <span class="pl-smi">method</span> <span class="pl-k">&lt;-</span> <span class="pl-s"><span class="pl-pds">&quot;</span>OFL<span class="pl-pds">&quot;</span></span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC475" class="react-file-line html-div" data-testid="code-cell" data-line-number="475" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC476" class="react-file-line html-div" data-testid="code-cell" data-line-number="476" style="position:relative">  </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC477" class="react-file-line html-div" data-testid="code-cell" data-line-number="477" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Set up plot window for production of search diagnostic plots depending on target specifications</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC478" class="react-file-line html-div" data-testid="code-cell" data-line-number="478" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>These plots were largely for diagnostic testing during code development but can allow you to see what</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC479" class="react-file-line html-div" data-testid="code-cell" data-line-number="479" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>is going wrong if a future bug does occur.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC480" class="react-file-line html-div" data-testid="code-cell" data-line-number="480" style="position:relative">  <span class="pl-k">if</span>(<span class="pl-smi">Make_plots</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC481" class="react-file-line html-div" data-testid="code-cell" data-line-number="481" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">Forecast_target</span><span class="pl-k">==</span><span class="pl-c1">2</span> <span class="pl-k">&amp;</span> <span class="pl-smi">fitting_Benchmark</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC482" class="react-file-line html-div" data-testid="code-cell" data-line-number="482" style="position:relative">      par(<span class="pl-v">mfrow</span><span class="pl-k">=</span>c(<span class="pl-c1">5</span>,<span class="pl-c1">2</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC483" class="react-file-line html-div" data-testid="code-cell" data-line-number="483" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC484" class="react-file-line html-div" data-testid="code-cell" data-line-number="484" style="position:relative">      par(<span class="pl-v">mfrow</span><span class="pl-k">=</span>c(<span class="pl-c1">4</span>,<span class="pl-c1">2</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC485" class="react-file-line html-div" data-testid="code-cell" data-line-number="485" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC486" class="react-file-line html-div" data-testid="code-cell" data-line-number="486" style="position:relative">  }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC487" class="react-file-line html-div" data-testid="code-cell" data-line-number="487" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>Now start a loop of projecting and modifying fixed F&#039;s until the desired </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC488" class="react-file-line html-div" data-testid="code-cell" data-line-number="488" style="position:relative">  <span class="pl-c"><span class="pl-c">#</span>landings projections are achieved</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC489" class="react-file-line html-div" data-testid="code-cell" data-line-number="489" style="position:relative">  <span class="pl-k">while</span>(<span class="pl-smi">keepFitting</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC490" class="react-file-line html-div" data-testid="code-cell" data-line-number="490" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Read in the SS results for landings and stock status to determine if desired</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC491" class="react-file-line html-div" data-testid="code-cell" data-line-number="491" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>targets have been achieved</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC492" class="react-file-line html-div" data-testid="code-cell" data-line-number="492" style="position:relative">    <span class="pl-smi">resultsFit</span> <span class="pl-k">&lt;-</span> SS_output(<span class="pl-v">dir</span><span class="pl-k">=</span>getwd(),<span class="pl-v">covar</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC493" class="react-file-line html-div" data-testid="code-cell" data-line-number="493" style="position:relative">    <span class="pl-smi">TimeFit</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">resultsFit</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>timeseries<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC494" class="react-file-line html-div" data-testid="code-cell" data-line-number="494" style="position:relative">    <span class="pl-smi">TimeFit</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit</span>[<span class="pl-smi">TimeFit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>]<span class="pl-k">&gt;</span><span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC495" class="react-file-line html-div" data-testid="code-cell" data-line-number="495" style="position:relative">    <span class="pl-smi">SPRfit</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">resultsFit</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>sprseries<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC496" class="react-file-line html-div" data-testid="code-cell" data-line-number="496" style="position:relative">    <span class="pl-smi">SPRfit</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span>[<span class="pl-smi">SPRfit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>]<span class="pl-k">&gt;</span><span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC497" class="react-file-line html-div" data-testid="code-cell" data-line-number="497" style="position:relative">    <span class="pl-smi">loop</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">loop</span> <span class="pl-k">+</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC498" class="react-file-line html-div" data-testid="code-cell" data-line-number="498" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">Make_plots</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC499" class="react-file-line html-div" data-testid="code-cell" data-line-number="499" style="position:relative">      par(<span class="pl-v">mar</span><span class="pl-k">=</span>c(<span class="pl-c1">4</span>,<span class="pl-c1">3</span>,<span class="pl-c1">3</span>,<span class="pl-c1">2</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC500" class="react-file-line html-div" data-testid="code-cell" data-line-number="500" style="position:relative">      plot(<span class="pl-smi">SPRfit</span>[<span class="pl-smi">SPRfit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>]<span class="pl-k">&gt;</span><span class="pl-k">=</span><span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],<span class="pl-s"><span class="pl-pds">&quot;</span>F_report<span class="pl-pds">&quot;</span></span>],<span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC501" class="react-file-line html-div" data-testid="code-cell" data-line-number="501" style="position:relative">      plot(<span class="pl-smi">SPRfit</span>[<span class="pl-smi">SPRfit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>]<span class="pl-k">&gt;</span><span class="pl-k">=</span><span class="pl-smi">dat</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>endyr<span class="pl-pds">&quot;</span></span>]],<span class="pl-s"><span class="pl-pds">&quot;</span>Deplete<span class="pl-pds">&quot;</span></span>],<span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Depletion<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC502" class="react-file-line html-div" data-testid="code-cell" data-line-number="502" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC503" class="react-file-line html-div" data-testid="code-cell" data-line-number="503" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC504" class="react-file-line html-div" data-testid="code-cell" data-line-number="504" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Identify the column numbers for Catch, F, SSB, Recruits, etc</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC505" class="react-file-line html-div" data-testid="code-cell" data-line-number="505" style="position:relative">    <span class="pl-smi">Catch_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC506" class="react-file-line html-div" data-testid="code-cell" data-line-number="506" style="position:relative">    <span class="pl-smi">Dead_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC507" class="react-file-line html-div" data-testid="code-cell" data-line-number="507" style="position:relative">    <span class="pl-smi">CatchN_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC508" class="react-file-line html-div" data-testid="code-cell" data-line-number="508" style="position:relative">    <span class="pl-smi">DeadN_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC509" class="react-file-line html-div" data-testid="code-cell" data-line-number="509" style="position:relative">    <span class="pl-smi">F_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC510" class="react-file-line html-div" data-testid="code-cell" data-line-number="510" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC511" class="react-file-line html-div" data-testid="code-cell" data-line-number="511" style="position:relative">      <span class="pl-smi">F_cols</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC512" class="react-file-line html-div" data-testid="code-cell" data-line-number="512" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC513" class="react-file-line html-div" data-testid="code-cell" data-line-number="513" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC514" class="react-file-line html-div" data-testid="code-cell" data-line-number="514" style="position:relative">    <span class="pl-smi">TimeFit2</span> <span class="pl-k">&lt;-</span> aggregate(<span class="pl-smi">TimeFit</span>[,sort(c(<span class="pl-c1">2</span>,<span class="pl-c1">4</span>,<span class="pl-c1">7</span>,<span class="pl-smi">Catch_cols</span>,<span class="pl-smi">Dead_cols</span>,<span class="pl-smi">CatchN_cols</span>,<span class="pl-smi">DeadN_cols</span>,<span class="pl-smi">F_cols</span>))],<span class="pl-v">by</span><span class="pl-k">=</span><span class="pl-k">list</span>(<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span>,<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Seas</span>),<span class="pl-v">FUN</span><span class="pl-k">=</span><span class="pl-smi">sum</span>,<span class="pl-v">na.rm</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)[,<span class="pl-k">-</span>c(<span class="pl-c1">3</span>,<span class="pl-c1">4</span>,<span class="pl-c1">5</span>)]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC515" class="react-file-line html-div" data-testid="code-cell" data-line-number="515" style="position:relative">    names(<span class="pl-smi">TimeFit2</span>)[c(<span class="pl-c1">1</span>,<span class="pl-c1">2</span>)] <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>, <span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC516" class="react-file-line html-div" data-testid="code-cell" data-line-number="516" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC517" class="react-file-line html-div" data-testid="code-cell" data-line-number="517" style="position:relative">    <span class="pl-smi">Catch_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC518" class="react-file-line html-div" data-testid="code-cell" data-line-number="518" style="position:relative">    <span class="pl-smi">Dead_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC519" class="react-file-line html-div" data-testid="code-cell" data-line-number="519" style="position:relative">    <span class="pl-smi">CatchN_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC520" class="react-file-line html-div" data-testid="code-cell" data-line-number="520" style="position:relative">    <span class="pl-smi">DeadN_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC521" class="react-file-line html-div" data-testid="code-cell" data-line-number="521" style="position:relative">    <span class="pl-smi">F_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC522" class="react-file-line html-div" data-testid="code-cell" data-line-number="522" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols2</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC523" class="react-file-line html-div" data-testid="code-cell" data-line-number="523" style="position:relative">      <span class="pl-smi">F_cols2</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit2</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC524" class="react-file-line html-div" data-testid="code-cell" data-line-number="524" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC525" class="react-file-line html-div" data-testid="code-cell" data-line-number="525" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC526" class="react-file-line html-div" data-testid="code-cell" data-line-number="526" style="position:relative">    <span class="pl-smi">TimeFit3</span> <span class="pl-k">&lt;-</span> aggregate(<span class="pl-smi">TimeFit</span>[,sort(c(<span class="pl-c1">2</span>,<span class="pl-c1">7</span>,<span class="pl-c1">8</span>,<span class="pl-smi">Catch_cols</span>,<span class="pl-smi">Dead_cols</span>,<span class="pl-smi">CatchN_cols</span>,<span class="pl-smi">DeadN_cols</span>,<span class="pl-smi">F_cols</span>))],<span class="pl-v">by</span><span class="pl-k">=</span><span class="pl-k">list</span>(<span class="pl-smi">TimeFit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span>),<span class="pl-v">FUN</span><span class="pl-k">=</span><span class="pl-smi">sum</span>,<span class="pl-v">na.rm</span><span class="pl-k">=</span><span class="pl-c1">TRUE</span>)[,<span class="pl-k">-</span><span class="pl-c1">2</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC527" class="react-file-line html-div" data-testid="code-cell" data-line-number="527" style="position:relative">    names(<span class="pl-smi">TimeFit3</span>)[c(<span class="pl-c1">1</span>)] <span class="pl-k">&lt;-</span> c(<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC528" class="react-file-line html-div" data-testid="code-cell" data-line-number="528" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC529" class="react-file-line html-div" data-testid="code-cell" data-line-number="529" style="position:relative">    <span class="pl-smi">Catch_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC530" class="react-file-line html-div" data-testid="code-cell" data-line-number="530" style="position:relative">    <span class="pl-smi">Dead_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC531" class="react-file-line html-div" data-testid="code-cell" data-line-number="531" style="position:relative">    <span class="pl-smi">CatchN_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC532" class="react-file-line html-div" data-testid="code-cell" data-line-number="532" style="position:relative">    <span class="pl-smi">DeadN_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC533" class="react-file-line html-div" data-testid="code-cell" data-line-number="533" style="position:relative">    <span class="pl-smi">F_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC534" class="react-file-line html-div" data-testid="code-cell" data-line-number="534" style="position:relative">    <span class="pl-k">if</span>(length(<span class="pl-smi">F_cols3</span>)<span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC535" class="react-file-line html-div" data-testid="code-cell" data-line-number="535" style="position:relative">      <span class="pl-smi">F_cols3</span> <span class="pl-k">&lt;-</span> grep(<span class="pl-s"><span class="pl-pds">&quot;</span>Hrate<span class="pl-pds">&quot;</span></span>, names(<span class="pl-smi">TimeFit3</span>), <span class="pl-v">fixed</span> <span class="pl-k">=</span> <span class="pl-c1">TRUE</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC536" class="react-file-line html-div" data-testid="code-cell" data-line-number="536" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC537" class="react-file-line html-div" data-testid="code-cell" data-line-number="537" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC538" class="react-file-line html-div" data-testid="code-cell" data-line-number="538" style="position:relative">    <span class="pl-smi">achieved.report</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[<span class="pl-c1">0</span>,<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-c1">8</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC539" class="react-file-line html-div" data-testid="code-cell" data-line-number="539" style="position:relative">    colnames(<span class="pl-smi">achieved.report</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC540" class="react-file-line html-div" data-testid="code-cell" data-line-number="540" style="position:relative">    <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span>length(<span class="pl-smi">F_cols2</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC541" class="react-file-line html-div" data-testid="code-cell" data-line-number="541" style="position:relative">      <span class="pl-smi">temp.data</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-c1">8</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC542" class="react-file-line html-div" data-testid="code-cell" data-line-number="542" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">3</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">i</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC543" class="react-file-line html-div" data-testid="code-cell" data-line-number="543" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">Catch_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC544" class="react-file-line html-div" data-testid="code-cell" data-line-number="544" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">5</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">Dead_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC545" class="react-file-line html-div" data-testid="code-cell" data-line-number="545" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">6</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">CatchN_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC546" class="react-file-line html-div" data-testid="code-cell" data-line-number="546" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">7</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">DeadN_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC547" class="react-file-line html-div" data-testid="code-cell" data-line-number="547" style="position:relative">      <span class="pl-smi">temp.data</span>[,<span class="pl-c1">8</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit2</span>[,<span class="pl-smi">F_cols2</span>[<span class="pl-smi">i</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC548" class="react-file-line html-div" data-testid="code-cell" data-line-number="548" style="position:relative">      colnames(<span class="pl-smi">temp.data</span>)<span class="pl-k">&lt;-</span>c(<span class="pl-s"><span class="pl-pds">&quot;</span>Year<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Seas<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>Fleet<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(B)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>retain(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>dead(N)<span class="pl-pds">&quot;</span></span>,<span class="pl-s"><span class="pl-pds">&quot;</span>F<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC549" class="react-file-line html-div" data-testid="code-cell" data-line-number="549" style="position:relative">      <span class="pl-smi">achieved.report</span> <span class="pl-k">&lt;-</span> rbind(<span class="pl-smi">achieved.report</span>,<span class="pl-smi">temp.data</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC550" class="react-file-line html-div" data-testid="code-cell" data-line-number="550" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC551" class="react-file-line html-div" data-testid="code-cell" data-line-number="551" style="position:relative">    <span class="pl-smi">achieved.report</span><span class="pl-k">&lt;-</span><span class="pl-smi">achieved.report</span>[order(<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Year</span>,<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Seas</span>,<span class="pl-smi">achieved.report</span><span class="pl-k">$</span><span class="pl-smi">Fleet</span>),]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC552" class="react-file-line html-div" data-testid="code-cell" data-line-number="552" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC553" class="react-file-line html-div" data-testid="code-cell" data-line-number="553" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">fitting_Rebuild</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC554" class="react-file-line html-div" data-testid="code-cell" data-line-number="554" style="position:relative">      <span class="pl-smi">terminal_year</span> <span class="pl-k">&lt;-</span> min(length(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span>[<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span><span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-smi">Rebuild_yr</span>])<span class="pl-k">+</span><span class="pl-c1">5</span>, <span class="pl-smi">Years_projection</span>) <span class="pl-c"><span class="pl-c">#</span>min to ensure report years beyond projection length not requested</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC555" class="react-file-line html-div" data-testid="code-cell" data-line-number="555" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC556" class="react-file-line html-div" data-testid="code-cell" data-line-number="556" style="position:relative">      <span class="pl-smi">terminal_year</span> <span class="pl-k">&lt;-</span> min(<span class="pl-smi">Years_report</span>, <span class="pl-smi">Years_projection</span>) <span class="pl-c"><span class="pl-c">#</span>min to ensure report years beyond projection length not requested</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC557" class="react-file-line html-div" data-testid="code-cell" data-line-number="557" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC558" class="react-file-line html-div" data-testid="code-cell" data-line-number="558" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC559" class="react-file-line html-div" data-testid="code-cell" data-line-number="559" style="position:relative">    <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[,<span class="pl-smi">Catch_cols3</span>,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC560" class="react-file-line html-div" data-testid="code-cell" data-line-number="560" style="position:relative">    <span class="pl-smi">Achieved.Catch.All</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[,<span class="pl-smi">Catch_cols3</span>,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC561" class="react-file-line html-div" data-testid="code-cell" data-line-number="561" style="position:relative">    <span class="pl-smi">Achieved.SSBratio</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]<span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC562" class="react-file-line html-div" data-testid="code-cell" data-line-number="562" style="position:relative">    <span class="pl-smi">Achieved.SPR</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]<span class="pl-k">/</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC563" class="react-file-line html-div" data-testid="code-cell" data-line-number="563" style="position:relative">    <span class="pl-smi">Achieved.SSB</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC564" class="react-file-line html-div" data-testid="code-cell" data-line-number="564" style="position:relative">    <span class="pl-smi">Achieved.Rec</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC565" class="react-file-line html-div" data-testid="code-cell" data-line-number="565" style="position:relative">    <span class="pl-smi">Achieved.F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC566" class="react-file-line html-div" data-testid="code-cell" data-line-number="566" style="position:relative">    <span class="pl-k">if</span>(is.null(<span class="pl-smi">Achieved.F</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC567" class="react-file-line html-div" data-testid="code-cell" data-line-number="567" style="position:relative">      <span class="pl-smi">Achieved.F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC568" class="react-file-line html-div" data-testid="code-cell" data-line-number="568" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC569" class="react-file-line html-div" data-testid="code-cell" data-line-number="569" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>If reading in results of a previous OFL run then set the F_OFL and F.ABC values before begining ABC/Rebuild loops</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC570" class="react-file-line html-div" data-testid="code-cell" data-line-number="570" style="position:relative">   </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC571" class="react-file-line html-div" data-testid="code-cell" data-line-number="571" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">Benchmark_complete</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span> <span class="pl-k">&amp;</span> <span class="pl-smi">First_run</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC572" class="react-file-line html-div" data-testid="code-cell" data-line-number="572" style="position:relative">      <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC573" class="react-file-line html-div" data-testid="code-cell" data-line-number="573" style="position:relative">      <span class="pl-k">if</span>(is.null(<span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC574" class="react-file-line html-div" data-testid="code-cell" data-line-number="574" style="position:relative">        <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC575" class="react-file-line html-div" data-testid="code-cell" data-line-number="575" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC576" class="react-file-line html-div" data-testid="code-cell" data-line-number="576" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span>median(<span class="pl-smi">F_report</span>[(length(<span class="pl-smi">F_report</span>)<span class="pl-k">-</span><span class="pl-c1">0.5</span><span class="pl-k">*</span><span class="pl-smi">Years_projection</span>)<span class="pl-k">:</span>length(<span class="pl-smi">F_report</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC577" class="react-file-line html-div" data-testid="code-cell" data-line-number="577" style="position:relative">      <span class="pl-smi">F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC578" class="react-file-line html-div" data-testid="code-cell" data-line-number="578" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">ABC_Fraction</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC579" class="react-file-line html-div" data-testid="code-cell" data-line-number="579" style="position:relative">        <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">ABC_Fraction</span><span class="pl-k">*</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC580" class="react-file-line html-div" data-testid="code-cell" data-line-number="580" style="position:relative">      }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC581" class="react-file-line html-div" data-testid="code-cell" data-line-number="581" style="position:relative">        <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC582" class="react-file-line html-div" data-testid="code-cell" data-line-number="582" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC583" class="react-file-line html-div" data-testid="code-cell" data-line-number="583" style="position:relative">      <span class="pl-smi">First_run</span><span class="pl-k">&lt;-</span><span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC584" class="react-file-line html-div" data-testid="code-cell" data-line-number="584" style="position:relative">      <span class="pl-smi">Depletion</span><span class="pl-k">&lt;-</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span><span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC585" class="react-file-line html-div" data-testid="code-cell" data-line-number="585" style="position:relative">      <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion</span>[(length(<span class="pl-smi">Depletion</span>)<span class="pl-k">-</span><span class="pl-c1">29</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC586" class="react-file-line html-div" data-testid="code-cell" data-line-number="586" style="position:relative">      <span class="pl-smi">Target.Rebuild</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion</span>[(length(<span class="pl-smi">Depletion</span>)<span class="pl-k">-</span><span class="pl-c1">29</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC587" class="react-file-line html-div" data-testid="code-cell" data-line-number="587" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC588" class="react-file-line html-div" data-testid="code-cell" data-line-number="588" style="position:relative">      <span class="pl-smi">Achieved.Catch.equil</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC589" class="react-file-line html-div" data-testid="code-cell" data-line-number="589" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC590" class="react-file-line html-div" data-testid="code-cell" data-line-number="590" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC591" class="react-file-line html-div" data-testid="code-cell" data-line-number="591" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Benchmark<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC592" class="react-file-line html-div" data-testid="code-cell" data-line-number="592" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC593" class="react-file-line html-div" data-testid="code-cell" data-line-number="593" style="position:relative">          <span class="pl-smi">Achieved.Catch.group.equil</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]]])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC594" class="react-file-line html-div" data-testid="code-cell" data-line-number="594" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Equil_Benchmark<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC595" class="react-file-line html-div" data-testid="code-cell" data-line-number="595" style="position:relative">          </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC596" class="react-file-line html-div" data-testid="code-cell" data-line-number="596" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC597" class="react-file-line html-div" data-testid="code-cell" data-line-number="597" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Benchmark<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC598" class="react-file-line html-div" data-testid="code-cell" data-line-number="598" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC599" class="react-file-line html-div" data-testid="code-cell" data-line-number="599" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC600" class="react-file-line html-div" data-testid="code-cell" data-line-number="600" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC601" class="react-file-line html-div" data-testid="code-cell" data-line-number="601" style="position:relative">      <span class="pl-smi">Achieved.SSBratio.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)])<span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC602" class="react-file-line html-div" data-testid="code-cell" data-line-number="602" style="position:relative">      <span class="pl-smi">Achieved.SPR.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)]<span class="pl-k">/</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)]) <span class="pl-c"><span class="pl-c">#</span>median(SPRfit$SPR[(length(SPRfit$SPR)-9):length(SPRfit$SPR)])</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC603" class="react-file-line html-div" data-testid="code-cell" data-line-number="603" style="position:relative">      <span class="pl-smi">Achieved.SSB.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC604" class="react-file-line html-div" data-testid="code-cell" data-line-number="604" style="position:relative">      <span class="pl-smi">Achieved.Rec.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC605" class="react-file-line html-div" data-testid="code-cell" data-line-number="605" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC606" class="react-file-line html-div" data-testid="code-cell" data-line-number="606" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC607" class="react-file-line html-div" data-testid="code-cell" data-line-number="607" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">F_OFL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC608" class="react-file-line html-div" data-testid="code-cell" data-line-number="608" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC609" class="react-file-line html-div" data-testid="code-cell" data-line-number="609" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC610" class="react-file-line html-div" data-testid="code-cell" data-line-number="610" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC611" class="react-file-line html-div" data-testid="code-cell" data-line-number="611" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC612" class="react-file-line html-div" data-testid="code-cell" data-line-number="612" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC613" class="react-file-line html-div" data-testid="code-cell" data-line-number="613" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC614" class="react-file-line html-div" data-testid="code-cell" data-line-number="614" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC615" class="react-file-line html-div" data-testid="code-cell" data-line-number="615" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC616" class="react-file-line html-div" data-testid="code-cell" data-line-number="616" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC617" class="react-file-line html-div" data-testid="code-cell" data-line-number="617" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC618" class="react-file-line html-div" data-testid="code-cell" data-line-number="618" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC619" class="react-file-line html-div" data-testid="code-cell" data-line-number="619" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC620" class="react-file-line html-div" data-testid="code-cell" data-line-number="620" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC621" class="react-file-line html-div" data-testid="code-cell" data-line-number="621" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC622" class="react-file-line html-div" data-testid="code-cell" data-line-number="622" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC623" class="react-file-line html-div" data-testid="code-cell" data-line-number="623" style="position:relative">    <span class="pl-k">if</span>(is.na(max(abs(<span class="pl-smi">achieved.report</span>[,<span class="pl-s"><span class="pl-pds">&#039;</span>F<span class="pl-pds">&#039;</span></span>]<span class="pl-k">-</span><span class="pl-smi">forecast_F</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>])[<span class="pl-smi">adjusted_F_OFL</span>]))){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC624" class="react-file-line html-div" data-testid="code-cell" data-line-number="624" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">fitting_Fixed_Catch</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC625" class="react-file-line html-div" data-testid="code-cell" data-line-number="625" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">Catch_trunc</span> <span class="pl-k">&gt;</span><span class="pl-k">=</span> (<span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">Nforecastyrs</span> <span class="pl-k">-</span> <span class="pl-c1">20</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC626" class="react-file-line html-div" data-testid="code-cell" data-line-number="626" style="position:relative">          <span class="pl-smi">Catch_trunc</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Catch_trunc</span> <span class="pl-k">+</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC627" class="react-file-line html-div" data-testid="code-cell" data-line-number="627" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC628" class="react-file-line html-div" data-testid="code-cell" data-line-number="628" style="position:relative">          <span class="pl-smi">Catch_trunc</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Catch_trunc</span> <span class="pl-k">+</span> <span class="pl-c1">5</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC629" class="react-file-line html-div" data-testid="code-cell" data-line-number="629" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC630" class="react-file-line html-div" data-testid="code-cell" data-line-number="630" style="position:relative">        <span class="pl-smi">Catch_Target</span>[(<span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">Nforecastyrs</span><span class="pl-k">-</span>c((<span class="pl-smi">Catch_trunc</span><span class="pl-k">-</span><span class="pl-c1">1</span>)<span class="pl-k">:</span><span class="pl-c1">0</span>))] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC631" class="react-file-line html-div" data-testid="code-cell" data-line-number="631" style="position:relative">        <span class="pl-smi">forecast_F</span>[(length(<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span>c((<span class="pl-smi">Catch_trunc</span><span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)<span class="pl-k">-</span><span class="pl-c1">1</span>)<span class="pl-k">:</span><span class="pl-c1">0</span>)),<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC632" class="react-file-line html-div" data-testid="code-cell" data-line-number="632" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC633" class="react-file-line html-div" data-testid="code-cell" data-line-number="633" style="position:relative">      <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">4</span>]<span class="pl-k">*</span><span class="pl-c1">0.5</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC634" class="react-file-line html-div" data-testid="code-cell" data-line-number="634" style="position:relative">      <span class="pl-smi">loop</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">loop</span> <span class="pl-k">-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC635" class="react-file-line html-div" data-testid="code-cell" data-line-number="635" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC636" class="react-file-line html-div" data-testid="code-cell" data-line-number="636" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC637" class="react-file-line html-div" data-testid="code-cell" data-line-number="637" style="position:relative">    <span class="pl-k">if</span>(max(abs(<span class="pl-smi">achieved.report</span>[,<span class="pl-s"><span class="pl-pds">&#039;</span>F<span class="pl-pds">&#039;</span></span>]<span class="pl-k">-</span><span class="pl-smi">forecast_F</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Catch or F<span class="pl-pds">&quot;</span></span>])[<span class="pl-smi">adjusted_F_OFL</span>])<span class="pl-k">&gt;</span><span class="pl-c1">0.1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC638" class="react-file-line html-div" data-testid="code-cell" data-line-number="638" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">fitting_Fixed_Catch</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC639" class="react-file-line html-div" data-testid="code-cell" data-line-number="639" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">Catch_trunc</span> <span class="pl-k">&gt;</span><span class="pl-k">=</span> (<span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">Nforecastyrs</span> <span class="pl-k">-</span> <span class="pl-c1">20</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC640" class="react-file-line html-div" data-testid="code-cell" data-line-number="640" style="position:relative">          <span class="pl-smi">Catch_trunc</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Catch_trunc</span> <span class="pl-k">+</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC641" class="react-file-line html-div" data-testid="code-cell" data-line-number="641" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC642" class="react-file-line html-div" data-testid="code-cell" data-line-number="642" style="position:relative">          <span class="pl-smi">Catch_trunc</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Catch_trunc</span> <span class="pl-k">+</span> <span class="pl-c1">5</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC643" class="react-file-line html-div" data-testid="code-cell" data-line-number="643" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC644" class="react-file-line html-div" data-testid="code-cell" data-line-number="644" style="position:relative">        <span class="pl-smi">Catch_Target</span>[(<span class="pl-smi">forecast</span><span class="pl-k">$</span><span class="pl-smi">Nforecastyrs</span><span class="pl-k">-</span>c((<span class="pl-smi">Catch_trunc</span><span class="pl-k">-</span><span class="pl-c1">1</span>)<span class="pl-k">:</span><span class="pl-c1">0</span>))] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC645" class="react-file-line html-div" data-testid="code-cell" data-line-number="645" style="position:relative">        <span class="pl-smi">forecast_F</span>[(length(<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span>c((<span class="pl-smi">Catch_trunc</span><span class="pl-k">*</span>length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)<span class="pl-k">-</span><span class="pl-c1">1</span>)<span class="pl-k">:</span><span class="pl-c1">0</span>)),<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC646" class="react-file-line html-div" data-testid="code-cell" data-line-number="646" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC647" class="react-file-line html-div" data-testid="code-cell" data-line-number="647" style="position:relative">      <span class="pl-smi">F_maxed</span> <span class="pl-k">&lt;-</span> max(<span class="pl-smi">achieved.report</span>[,<span class="pl-s"><span class="pl-pds">&#039;</span>F<span class="pl-pds">&#039;</span></span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC648" class="react-file-line html-div" data-testid="code-cell" data-line-number="648" style="position:relative">      <span class="pl-smi">forecast_F</span>[,<span class="pl-c1">4</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span>[,<span class="pl-s"><span class="pl-pds">&#039;</span>F<span class="pl-pds">&#039;</span></span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC649" class="react-file-line html-div" data-testid="code-cell" data-line-number="649" style="position:relative">      <span class="pl-smi">loop</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">loop</span> <span class="pl-k">-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC650" class="react-file-line html-div" data-testid="code-cell" data-line-number="650" style="position:relative">    }<span class="pl-k">else</span> {</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC651" class="react-file-line html-div" data-testid="code-cell" data-line-number="651" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">fitting_Benchmark</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC652" class="react-file-line html-div" data-testid="code-cell" data-line-number="652" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC653" class="react-file-line html-div" data-testid="code-cell" data-line-number="653" style="position:relative">      <span class="pl-c"><span class="pl-c">#</span>Calculate the average F at equilibrium that all F&#039;s will be scaled to in order</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC654" class="react-file-line html-div" data-testid="code-cell" data-line-number="654" style="position:relative">      <span class="pl-c"><span class="pl-c">#</span>to achieve equal F in every year. As depletion approaches the target value this </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC655" class="react-file-line html-div" data-testid="code-cell" data-line-number="655" style="position:relative">      <span class="pl-c"><span class="pl-c">#</span>F will approach F(OFL).</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC656" class="react-file-line html-div" data-testid="code-cell" data-line-number="656" style="position:relative">       </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC657" class="react-file-line html-div" data-testid="code-cell" data-line-number="657" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC658" class="react-file-line html-div" data-testid="code-cell" data-line-number="658" style="position:relative">      <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC659" class="react-file-line html-div" data-testid="code-cell" data-line-number="659" style="position:relative">      <span class="pl-k">if</span>(is.null(<span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC660" class="react-file-line html-div" data-testid="code-cell" data-line-number="660" style="position:relative">        <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC661" class="react-file-line html-div" data-testid="code-cell" data-line-number="661" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC662" class="react-file-line html-div" data-testid="code-cell" data-line-number="662" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span>median(<span class="pl-smi">F_report</span>[(length(<span class="pl-smi">F_report</span>)<span class="pl-k">-</span><span class="pl-c1">0.5</span><span class="pl-k">*</span><span class="pl-smi">Years_projection</span>)<span class="pl-k">:</span>length(<span class="pl-smi">F_report</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC663" class="react-file-line html-div" data-testid="code-cell" data-line-number="663" style="position:relative">      <span class="pl-smi">F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC664" class="react-file-line html-div" data-testid="code-cell" data-line-number="664" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">ABC_Fraction</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC665" class="react-file-line html-div" data-testid="code-cell" data-line-number="665" style="position:relative">        <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">ABC_Fraction</span><span class="pl-k">*</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC666" class="react-file-line html-div" data-testid="code-cell" data-line-number="666" style="position:relative">      }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC667" class="react-file-line html-div" data-testid="code-cell" data-line-number="667" style="position:relative">        <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC668" class="react-file-line html-div" data-testid="code-cell" data-line-number="668" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC669" class="react-file-line html-div" data-testid="code-cell" data-line-number="669" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC670" class="react-file-line html-div" data-testid="code-cell" data-line-number="670" style="position:relative">      <span class="pl-smi">Achieved.Catch.equil</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC671" class="react-file-line html-div" data-testid="code-cell" data-line-number="671" style="position:relative">      <span class="pl-smi">Achieved.SSBratio.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)])<span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC672" class="react-file-line html-div" data-testid="code-cell" data-line-number="672" style="position:relative">      <span class="pl-smi">Achieved.SPR.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)]<span class="pl-k">/</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)]) <span class="pl-c"><span class="pl-c">#</span>median(SPRfit$SPR[(length(SPRfit$SPR)-9):length(SPRfit$SPR)])</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC673" class="react-file-line html-div" data-testid="code-cell" data-line-number="673" style="position:relative">      <span class="pl-smi">Achieved.SSB.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC674" class="react-file-line html-div" data-testid="code-cell" data-line-number="674" style="position:relative">      <span class="pl-smi">Achieved.Rec.equil</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>[(length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">Recruit_0</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC675" class="react-file-line html-div" data-testid="code-cell" data-line-number="675" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC676" class="react-file-line html-div" data-testid="code-cell" data-line-number="676" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC677" class="react-file-line html-div" data-testid="code-cell" data-line-number="677" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC678" class="react-file-line html-div" data-testid="code-cell" data-line-number="678" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC679" class="react-file-line html-div" data-testid="code-cell" data-line-number="679" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Benchmark<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC680" class="react-file-line html-div" data-testid="code-cell" data-line-number="680" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Equil_Benchmark<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC681" class="react-file-line html-div" data-testid="code-cell" data-line-number="681" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC682" class="react-file-line html-div" data-testid="code-cell" data-line-number="682" style="position:relative">          <span class="pl-smi">Achieved.Catch.group.equil</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]]])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC683" class="react-file-line html-div" data-testid="code-cell" data-line-number="683" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Equil_Benchmark<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC684" class="react-file-line html-div" data-testid="code-cell" data-line-number="684" style="position:relative">          </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC685" class="react-file-line html-div" data-testid="code-cell" data-line-number="685" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC686" class="react-file-line html-div" data-testid="code-cell" data-line-number="686" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Benchmark<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC687" class="react-file-line html-div" data-testid="code-cell" data-line-number="687" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC688" class="react-file-line html-div" data-testid="code-cell" data-line-number="688" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC689" class="react-file-line html-div" data-testid="code-cell" data-line-number="689" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC690" class="react-file-line html-div" data-testid="code-cell" data-line-number="690" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC691" class="react-file-line html-div" data-testid="code-cell" data-line-number="691" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">F_OFL</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC692" class="react-file-line html-div" data-testid="code-cell" data-line-number="692" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC693" class="react-file-line html-div" data-testid="code-cell" data-line-number="693" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC694" class="react-file-line html-div" data-testid="code-cell" data-line-number="694" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC695" class="react-file-line html-div" data-testid="code-cell" data-line-number="695" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_equil_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec.equil</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC696" class="react-file-line html-div" data-testid="code-cell" data-line-number="696" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC697" class="react-file-line html-div" data-testid="code-cell" data-line-number="697" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC698" class="react-file-line html-div" data-testid="code-cell" data-line-number="698" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC699" class="react-file-line html-div" data-testid="code-cell" data-line-number="699" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC700" class="react-file-line html-div" data-testid="code-cell" data-line-number="700" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC701" class="react-file-line html-div" data-testid="code-cell" data-line-number="701" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC702" class="react-file-line html-div" data-testid="code-cell" data-line-number="702" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC703" class="react-file-line html-div" data-testid="code-cell" data-line-number="703" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC704" class="react-file-line html-div" data-testid="code-cell" data-line-number="704" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_Benchmark<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC705" class="react-file-line html-div" data-testid="code-cell" data-line-number="705" style="position:relative">      <span class="pl-c"><span class="pl-c">#</span>Calculate depletion target adjustment scale depending on the specified target (SPR ratio, SSB ratio, or true MSY)   </span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC706" class="react-file-line html-div" data-testid="code-cell" data-line-number="706" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">Forecast_target</span><span class="pl-k">==</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC707" class="react-file-line html-div" data-testid="code-cell" data-line-number="707" style="position:relative">        <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC708" class="react-file-line html-div" data-testid="code-cell" data-line-number="708" style="position:relative">        <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPRtarget<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC709" class="react-file-line html-div" data-testid="code-cell" data-line-number="709" style="position:relative">        <span class="pl-smi">Depletion</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC710" class="react-file-line html-div" data-testid="code-cell" data-line-number="710" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC711" class="react-file-line html-div" data-testid="code-cell" data-line-number="711" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion</span>[(length(<span class="pl-smi">Depletion</span>)<span class="pl-k">-</span><span class="pl-c1">29</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC712" class="react-file-line html-div" data-testid="code-cell" data-line-number="712" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC713" class="react-file-line html-div" data-testid="code-cell" data-line-number="713" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> min(<span class="pl-smi">Achieved.Depletion</span>,max(<span class="pl-smi">Target.Depletion</span>,<span class="pl-c1">0.9</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC714" class="react-file-line html-div" data-testid="code-cell" data-line-number="714" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC715" class="react-file-line html-div" data-testid="code-cell" data-line-number="715" style="position:relative">        <span class="pl-smi">DepletionScale</span> <span class="pl-k">&lt;-</span> (<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)<span class="pl-k">/</span>(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Achieved.Depletion</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC716" class="react-file-line html-div" data-testid="code-cell" data-line-number="716" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC717" class="react-file-line html-div" data-testid="code-cell" data-line-number="717" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">FScale</span><span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC718" class="react-file-line html-div" data-testid="code-cell" data-line-number="718" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-c1">1.0001</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC719" class="react-file-line html-div" data-testid="code-cell" data-line-number="719" style="position:relative">            <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC720" class="react-file-line html-div" data-testid="code-cell" data-line-number="720" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC721" class="react-file-line html-div" data-testid="code-cell" data-line-number="721" style="position:relative">            <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.0001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC722" class="react-file-line html-div" data-testid="code-cell" data-line-number="722" style="position:relative">            <span class="pl-smi">F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC723" class="react-file-line html-div" data-testid="code-cell" data-line-number="723" style="position:relative">            <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">ABC_Fraction</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC724" class="react-file-line html-div" data-testid="code-cell" data-line-number="724" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">ABC_Fraction</span><span class="pl-k">*</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC725" class="react-file-line html-div" data-testid="code-cell" data-line-number="725" style="position:relative">            }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC726" class="react-file-line html-div" data-testid="code-cell" data-line-number="726" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC727" class="react-file-line html-div" data-testid="code-cell" data-line-number="727" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC728" class="react-file-line html-div" data-testid="code-cell" data-line-number="728" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC729" class="react-file-line html-div" data-testid="code-cell" data-line-number="729" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC730" class="react-file-line html-div" data-testid="code-cell" data-line-number="730" style="position:relative">          <span class="pl-smi">DepletionScale</span> <span class="pl-k">&lt;-</span> (<span class="pl-k">-</span>log(<span class="pl-c1">1</span><span class="pl-k">-</span>((<span class="pl-c1">1</span><span class="pl-k">-</span>exp(<span class="pl-k">-</span><span class="pl-smi">FScale</span>))<span class="pl-k">*</span><span class="pl-smi">DepletionScale</span>))<span class="pl-k">/</span><span class="pl-smi">FScale</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC731" class="react-file-line html-div" data-testid="code-cell" data-line-number="731" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC732" class="react-file-line html-div" data-testid="code-cell" data-line-number="732" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC733" class="react-file-line html-div" data-testid="code-cell" data-line-number="733" style="position:relative">        <span class="pl-smi">Depletion_R</span><span class="pl-k">&lt;-</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span><span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC734" class="react-file-line html-div" data-testid="code-cell" data-line-number="734" style="position:relative">        <span class="pl-smi">Target.Rebuild</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion_R</span>[(length(<span class="pl-smi">Depletion_R</span>)<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion_R</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC735" class="react-file-line html-div" data-testid="code-cell" data-line-number="735" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC736" class="react-file-line html-div" data-testid="code-cell" data-line-number="736" style="position:relative">      }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">Forecast_target</span><span class="pl-k">==</span><span class="pl-c1">2</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC737" class="react-file-line html-div" data-testid="code-cell" data-line-number="737" style="position:relative">        <span class="pl-smi">Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span><span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC738" class="react-file-line html-div" data-testid="code-cell" data-line-number="738" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion</span>[(length(<span class="pl-smi">Depletion</span>)<span class="pl-k">-</span><span class="pl-c1">29</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC739" class="react-file-line html-div" data-testid="code-cell" data-line-number="739" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> min(<span class="pl-smi">Achieved.Depletion</span>,<span class="pl-smi">.9</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC740" class="react-file-line html-div" data-testid="code-cell" data-line-number="740" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">First_run</span> <span class="pl-k">==</span> <span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC741" class="react-file-line html-div" data-testid="code-cell" data-line-number="741" style="position:relative">          <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Btarget<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC742" class="react-file-line html-div" data-testid="code-cell" data-line-number="742" style="position:relative">          <span class="pl-smi">First_run</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">FALSE</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC743" class="react-file-line html-div" data-testid="code-cell" data-line-number="743" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC744" class="react-file-line html-div" data-testid="code-cell" data-line-number="744" style="position:relative">        <span class="pl-smi">Target.Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Target.Depletion</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC745" class="react-file-line html-div" data-testid="code-cell" data-line-number="745" style="position:relative">        <span class="pl-smi">Achieved.SSB</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Depletion</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC746" class="react-file-line html-div" data-testid="code-cell" data-line-number="746" style="position:relative">        <span class="pl-k">if</span>(max(abs(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Fmult3</span>))<span class="pl-k">&gt;</span><span class="pl-smi">Allocation.Threshold</span> <span class="pl-k">|</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC747" class="react-file-line html-div" data-testid="code-cell" data-line-number="747" style="position:relative">		       max(abs(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Fmult2</span>))<span class="pl-k">&gt;</span><span class="pl-smi">Annual.F.Threshold</span> <span class="pl-k">|</span> </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC748" class="react-file-line html-div" data-testid="code-cell" data-line-number="748" style="position:relative">		       max(abs(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Fmult1</span>))<span class="pl-k">&gt;</span><span class="pl-smi">Depletion.Threshold</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC749" class="react-file-line html-div" data-testid="code-cell" data-line-number="749" style="position:relative">          <span class="pl-smi">loop</span><span class="pl-k">&lt;-</span><span class="pl-smi">loop</span><span class="pl-k">-</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC750" class="react-file-line html-div" data-testid="code-cell" data-line-number="750" style="position:relative">          <span class="pl-smi">subloop</span><span class="pl-k">&lt;-</span><span class="pl-smi">subloop</span><span class="pl-k">+</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC751" class="react-file-line html-div" data-testid="code-cell" data-line-number="751" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">F_max</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC752" class="react-file-line html-div" data-testid="code-cell" data-line-number="752" style="position:relative">            <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC753" class="react-file-line html-div" data-testid="code-cell" data-line-number="753" style="position:relative">			                  sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-s"><span class="pl-pds">&quot;</span>Recruit_0<span class="pl-pds">&quot;</span></span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC754" class="react-file-line html-div" data-testid="code-cell" data-line-number="754" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC755" class="react-file-line html-div" data-testid="code-cell" data-line-number="755" style="position:relative">            <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC756" class="react-file-line html-div" data-testid="code-cell" data-line-number="756" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC757" class="react-file-line html-div" data-testid="code-cell" data-line-number="757" style="position:relative">          <span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,] <span class="pl-k">&lt;-</span> c(<span class="pl-smi">Achieved.Catch</span>,<span class="pl-smi">FScale</span>,<span class="pl-smi">Achieved.Depletion</span>,<span class="pl-smi">Target.Depletion</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC758" class="react-file-line html-div" data-testid="code-cell" data-line-number="758" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC759" class="react-file-line html-div" data-testid="code-cell" data-line-number="759" style="position:relative">          <span class="pl-smi">subloop</span><span class="pl-k">&lt;-</span><span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC760" class="react-file-line html-div" data-testid="code-cell" data-line-number="760" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">F_max</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC761" class="react-file-line html-div" data-testid="code-cell" data-line-number="761" style="position:relative">            <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC762" class="react-file-line html-div" data-testid="code-cell" data-line-number="762" style="position:relative">			                  sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-s"><span class="pl-pds">&quot;</span>Recruit_0<span class="pl-pds">&quot;</span></span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC763" class="react-file-line html-div" data-testid="code-cell" data-line-number="763" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC764" class="react-file-line html-div" data-testid="code-cell" data-line-number="764" style="position:relative">            <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> sum(<span class="pl-smi">TimeFit3</span>[(length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>])<span class="pl-k">-</span><span class="pl-c1">9</span>)<span class="pl-k">:</span>length(<span class="pl-smi">TimeFit3</span>[,<span class="pl-c1">1</span>]),<span class="pl-smi">Catch_cols3</span>])<span class="pl-k">/</span><span class="pl-c1">10</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC765" class="react-file-line html-div" data-testid="code-cell" data-line-number="765" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC766" class="react-file-line html-div" data-testid="code-cell" data-line-number="766" style="position:relative">          <span class="pl-smi">MSY.Fit</span> <span class="pl-k">&lt;-</span> rbind(<span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,],<span class="pl-smi">MSY.Fit</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC767" class="react-file-line html-div" data-testid="code-cell" data-line-number="767" style="position:relative">          <span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,] <span class="pl-k">&lt;-</span> c(<span class="pl-smi">Achieved.Catch</span>,<span class="pl-smi">FScale</span>,<span class="pl-smi">Achieved.Depletion</span>,<span class="pl-smi">Target.Depletion</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC768" class="react-file-line html-div" data-testid="code-cell" data-line-number="768" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">loop</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC769" class="react-file-line html-div" data-testid="code-cell" data-line-number="769" style="position:relative">            <span class="pl-k">if</span>(<span class="pl-smi">Achieved.Catch</span><span class="pl-k">&lt;</span><span class="pl-smi">Last_Achieved_Catch</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC770" class="react-file-line html-div" data-testid="code-cell" data-line-number="770" style="position:relative">              <span class="pl-smi">search_step</span> <span class="pl-k">&lt;-</span> <span class="pl-k">-</span><span class="pl-c1">0.5</span><span class="pl-k">*</span><span class="pl-smi">search_step</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC771" class="react-file-line html-div" data-testid="code-cell" data-line-number="771" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC772" class="react-file-line html-div" data-testid="code-cell" data-line-number="772" style="position:relative">          </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC773" class="react-file-line html-div" data-testid="code-cell" data-line-number="773" style="position:relative">            <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Target.Depletion</span><span class="pl-k">+</span><span class="pl-smi">search_step</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC774" class="react-file-line html-div" data-testid="code-cell" data-line-number="774" style="position:relative">            </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC775" class="react-file-line html-div" data-testid="code-cell" data-line-number="775" style="position:relative">            <span class="pl-smi">min_diff</span> <span class="pl-k">&lt;-</span> which(abs(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-c1">4</span>]<span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)<span class="pl-k">&lt;</span><span class="pl-c1">0.001</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC776" class="react-file-line html-div" data-testid="code-cell" data-line-number="776" style="position:relative">            <span class="pl-k">if</span>(length(<span class="pl-smi">min_diff</span>)<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC777" class="react-file-line html-div" data-testid="code-cell" data-line-number="777" style="position:relative">              <span class="pl-smi">Old.Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">MSY.Fit</span>[<span class="pl-smi">min_diff</span>[<span class="pl-c1">1</span>],<span class="pl-c1">1</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC778" class="react-file-line html-div" data-testid="code-cell" data-line-number="778" style="position:relative">              <span class="pl-k">if</span>(<span class="pl-smi">Old.Catch</span><span class="pl-k">&lt;</span><span class="pl-smi">Achieved.Catch</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC779" class="react-file-line html-div" data-testid="code-cell" data-line-number="779" style="position:relative">                <span class="pl-smi">search_step</span> <span class="pl-k">&lt;-</span> <span class="pl-k">-</span><span class="pl-c1">0.5</span><span class="pl-k">*</span><span class="pl-smi">search_step</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC780" class="react-file-line html-div" data-testid="code-cell" data-line-number="780" style="position:relative">              }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC781" class="react-file-line html-div" data-testid="code-cell" data-line-number="781" style="position:relative">              <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Target.Depletion</span><span class="pl-k">+</span><span class="pl-smi">search_step</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC782" class="react-file-line html-div" data-testid="code-cell" data-line-number="782" style="position:relative">              <span class="pl-smi">Achieved.Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Old.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC783" class="react-file-line html-div" data-testid="code-cell" data-line-number="783" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC784" class="react-file-line html-div" data-testid="code-cell" data-line-number="784" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC785" class="react-file-line html-div" data-testid="code-cell" data-line-number="785" style="position:relative">            <span class="pl-smi">steps</span> <span class="pl-k">&lt;-</span> seq(<span class="pl-c1">0.1</span>,<span class="pl-c1">0.9</span>,<span class="pl-c1">0.1</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC786" class="react-file-line html-div" data-testid="code-cell" data-line-number="786" style="position:relative">            <span class="pl-smi">New.Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">steps</span>[which(abs(<span class="pl-smi">steps</span><span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)<span class="pl-k">==</span>min(abs(<span class="pl-smi">steps</span><span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)))[<span class="pl-c1">1</span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC787" class="react-file-line html-div" data-testid="code-cell" data-line-number="787" style="position:relative">            <span class="pl-k">if</span>(<span class="pl-smi">New.Target.Depletion</span><span class="pl-k">&lt;</span><span class="pl-smi">Target.Depletion</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC788" class="react-file-line html-div" data-testid="code-cell" data-line-number="788" style="position:relative">              <span class="pl-smi">search_step</span> <span class="pl-k">&lt;-</span> <span class="pl-k">-</span><span class="pl-c1">1</span><span class="pl-k">*</span><span class="pl-smi">search_step</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC789" class="react-file-line html-div" data-testid="code-cell" data-line-number="789" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC790" class="react-file-line html-div" data-testid="code-cell" data-line-number="790" style="position:relative">            <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">New.Target.Depletion</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC791" class="react-file-line html-div" data-testid="code-cell" data-line-number="791" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC792" class="react-file-line html-div" data-testid="code-cell" data-line-number="792" style="position:relative">          <span class="pl-smi">Last_Achieved_Catch</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC793" class="react-file-line html-div" data-testid="code-cell" data-line-number="793" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC794" class="react-file-line html-div" data-testid="code-cell" data-line-number="794" style="position:relative">        <span class="pl-smi">DepletionScale</span> <span class="pl-k">&lt;-</span> (<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)<span class="pl-k">/</span>(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Achieved.Depletion</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC795" class="react-file-line html-div" data-testid="code-cell" data-line-number="795" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC796" class="react-file-line html-div" data-testid="code-cell" data-line-number="796" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">FScale</span><span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC797" class="react-file-line html-div" data-testid="code-cell" data-line-number="797" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-c1">1.0001</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC798" class="react-file-line html-div" data-testid="code-cell" data-line-number="798" style="position:relative">            <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC799" class="react-file-line html-div" data-testid="code-cell" data-line-number="799" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC800" class="react-file-line html-div" data-testid="code-cell" data-line-number="800" style="position:relative">            <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.0001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC801" class="react-file-line html-div" data-testid="code-cell" data-line-number="801" style="position:relative">            <span class="pl-smi">F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC802" class="react-file-line html-div" data-testid="code-cell" data-line-number="802" style="position:relative">            <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">ABC_Fraction</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC803" class="react-file-line html-div" data-testid="code-cell" data-line-number="803" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">ABC_Fraction</span><span class="pl-k">*</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC804" class="react-file-line html-div" data-testid="code-cell" data-line-number="804" style="position:relative">            }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC805" class="react-file-line html-div" data-testid="code-cell" data-line-number="805" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC806" class="react-file-line html-div" data-testid="code-cell" data-line-number="806" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC807" class="react-file-line html-div" data-testid="code-cell" data-line-number="807" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC808" class="react-file-line html-div" data-testid="code-cell" data-line-number="808" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC809" class="react-file-line html-div" data-testid="code-cell" data-line-number="809" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC810" class="react-file-line html-div" data-testid="code-cell" data-line-number="810" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">Make_plots</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC811" class="react-file-line html-div" data-testid="code-cell" data-line-number="811" style="position:relative">          par(<span class="pl-v">mar</span><span class="pl-k">=</span>c(<span class="pl-c1">4</span>,<span class="pl-c1">3</span>,<span class="pl-c1">3</span>,<span class="pl-c1">2</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC812" class="react-file-line html-div" data-testid="code-cell" data-line-number="812" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">F_max</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC813" class="react-file-line html-div" data-testid="code-cell" data-line-number="813" style="position:relative">            plot(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">TimeFit3</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>],<span class="pl-v">y</span><span class="pl-k">=</span>apply(<span class="pl-smi">TimeFit3</span>[,<span class="pl-smi">Catch_cols3</span>,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)<span class="pl-k">/</span><span class="pl-smi">TimeFit3</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Recruit_0<span class="pl-pds">&quot;</span></span>],</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC814" class="react-file-line html-div" data-testid="code-cell" data-line-number="814" style="position:relative">  		       <span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Total Yield Per Recruit<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>.<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">subloop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC815" class="react-file-line html-div" data-testid="code-cell" data-line-number="815" style="position:relative">            plot(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>depletion<span class="pl-pds">&quot;</span></span>],<span class="pl-v">y</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>catch<span class="pl-pds">&quot;</span></span>],<span class="pl-v">xlim</span><span class="pl-k">=</span>c(<span class="pl-c1">0.9</span><span class="pl-k">*</span>min(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-c1">3</span><span class="pl-k">:</span><span class="pl-c1">4</span>]),<span class="pl-c1">1.1</span><span class="pl-k">*</span>max(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-c1">3</span><span class="pl-k">:</span><span class="pl-c1">4</span>])),</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC816" class="react-file-line html-div" data-testid="code-cell" data-line-number="816" style="position:relative">  		       <span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Esimated depletion<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Total Yield Per Recruit<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>.<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">subloop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC817" class="react-file-line html-div" data-testid="code-cell" data-line-number="817" style="position:relative">            lines(<span class="pl-v">x</span><span class="pl-k">=</span>c(<span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,c(<span class="pl-c1">4</span>,<span class="pl-c1">4</span>)]),<span class="pl-v">y</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>,<span class="pl-c1">2</span><span class="pl-k">*</span>max(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>catch<span class="pl-pds">&quot;</span></span>])),<span class="pl-v">col</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>dark red<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC818" class="react-file-line html-div" data-testid="code-cell" data-line-number="818" style="position:relative">            points(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,<span class="pl-c1">3</span>],<span class="pl-v">y</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,<span class="pl-c1">1</span>],<span class="pl-v">pch</span><span class="pl-k">=</span><span class="pl-c1">16</span>,<span class="pl-v">col</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>dark blue<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC819" class="react-file-line html-div" data-testid="code-cell" data-line-number="819" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC820" class="react-file-line html-div" data-testid="code-cell" data-line-number="820" style="position:relative">            plot(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">TimeFit3</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>Yr<span class="pl-pds">&quot;</span></span>],<span class="pl-v">y</span><span class="pl-k">=</span>apply(<span class="pl-smi">TimeFit3</span>[,<span class="pl-smi">Catch_cols3</span>,<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>),</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC821" class="react-file-line html-div" data-testid="code-cell" data-line-number="821" style="position:relative">  		       <span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>year<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Total Yield<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>.<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">subloop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC822" class="react-file-line html-div" data-testid="code-cell" data-line-number="822" style="position:relative">            plot(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>depletion<span class="pl-pds">&quot;</span></span>],<span class="pl-v">y</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>catch<span class="pl-pds">&quot;</span></span>],<span class="pl-v">xlim</span><span class="pl-k">=</span>c(<span class="pl-c1">0.9</span><span class="pl-k">*</span>min(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-c1">3</span><span class="pl-k">:</span><span class="pl-c1">4</span>]),<span class="pl-c1">1.1</span><span class="pl-k">*</span>max(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-c1">3</span><span class="pl-k">:</span><span class="pl-c1">4</span>])),</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC823" class="react-file-line html-div" data-testid="code-cell" data-line-number="823" style="position:relative">  		       <span class="pl-v">xlab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Esimated depletion<span class="pl-pds">&quot;</span></span>,<span class="pl-v">ylab</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>Total Yield<span class="pl-pds">&quot;</span></span>,<span class="pl-v">main</span> <span class="pl-k">=</span> paste0(<span class="pl-smi">method</span>,<span class="pl-s"><span class="pl-pds">&quot;</span> loop = <span class="pl-pds">&quot;</span></span>,<span class="pl-smi">loop</span>,<span class="pl-s"><span class="pl-pds">&quot;</span>.<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">subloop</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC824" class="react-file-line html-div" data-testid="code-cell" data-line-number="824" style="position:relative">            lines(<span class="pl-v">x</span><span class="pl-k">=</span>c(<span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,c(<span class="pl-c1">4</span>,<span class="pl-c1">4</span>)]),<span class="pl-v">y</span><span class="pl-k">=</span>c(<span class="pl-c1">0</span>,<span class="pl-c1">2</span><span class="pl-k">*</span>max(<span class="pl-smi">MSY.Fit</span>[,<span class="pl-s"><span class="pl-pds">&quot;</span>catch<span class="pl-pds">&quot;</span></span>])),<span class="pl-v">col</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>dark red<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC825" class="react-file-line html-div" data-testid="code-cell" data-line-number="825" style="position:relative">            points(<span class="pl-v">x</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,<span class="pl-c1">3</span>],<span class="pl-v">y</span><span class="pl-k">=</span><span class="pl-smi">MSY.Fit</span>[<span class="pl-c1">1</span>,<span class="pl-c1">1</span>],<span class="pl-v">pch</span><span class="pl-k">=</span><span class="pl-c1">16</span>,<span class="pl-v">col</span><span class="pl-k">=</span><span class="pl-s"><span class="pl-pds">&quot;</span>dark blue<span class="pl-pds">&quot;</span></span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC826" class="react-file-line html-div" data-testid="code-cell" data-line-number="826" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC827" class="react-file-line html-div" data-testid="code-cell" data-line-number="827" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC828" class="react-file-line html-div" data-testid="code-cell" data-line-number="828" style="position:relative">      }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">Forecast_target</span><span class="pl-k">==</span><span class="pl-c1">3</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC829" class="react-file-line html-div" data-testid="code-cell" data-line-number="829" style="position:relative">        <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC830" class="react-file-line html-div" data-testid="code-cell" data-line-number="830" style="position:relative">        <span class="pl-smi">Target.Depletion</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Btarget<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC831" class="react-file-line html-div" data-testid="code-cell" data-line-number="831" style="position:relative">        <span class="pl-smi">Target.Rebuild</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">forecast</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Btarget<span class="pl-pds">&quot;</span></span>]]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC832" class="react-file-line html-div" data-testid="code-cell" data-line-number="832" style="position:relative">        <span class="pl-smi">Depletion</span><span class="pl-k">&lt;-</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span><span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC833" class="react-file-line html-div" data-testid="code-cell" data-line-number="833" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> median(<span class="pl-smi">Depletion</span>[(length(<span class="pl-smi">Depletion</span>)<span class="pl-k">-</span><span class="pl-c1">29</span>)<span class="pl-k">:</span>length(<span class="pl-smi">Depletion</span>)])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC834" class="react-file-line html-div" data-testid="code-cell" data-line-number="834" style="position:relative">        <span class="pl-smi">Achieved.Depletion</span> <span class="pl-k">&lt;-</span> min(<span class="pl-smi">Achieved.Depletion</span>,max(<span class="pl-c1">0.9</span>,<span class="pl-smi">Target.Depletion</span>))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC835" class="react-file-line html-div" data-testid="code-cell" data-line-number="835" style="position:relative">        <span class="pl-smi">DepletionScale</span> <span class="pl-k">&lt;-</span> (<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Target.Depletion</span>)<span class="pl-k">/</span>(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Achieved.Depletion</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC836" class="react-file-line html-div" data-testid="code-cell" data-line-number="836" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC837" class="react-file-line html-div" data-testid="code-cell" data-line-number="837" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">FScale</span><span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC838" class="react-file-line html-div" data-testid="code-cell" data-line-number="838" style="position:relative">          <span class="pl-k">if</span>(<span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;</span><span class="pl-k">=</span><span class="pl-c1">1.0001</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC839" class="react-file-line html-div" data-testid="code-cell" data-line-number="839" style="position:relative">            <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC840" class="react-file-line html-div" data-testid="code-cell" data-line-number="840" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC841" class="react-file-line html-div" data-testid="code-cell" data-line-number="841" style="position:relative">            <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.0001</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC842" class="react-file-line html-div" data-testid="code-cell" data-line-number="842" style="position:relative">            <span class="pl-smi">F_OFL</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC843" class="react-file-line html-div" data-testid="code-cell" data-line-number="843" style="position:relative">            <span class="pl-k">if</span>(<span class="pl-k">!</span>is.null(<span class="pl-smi">ABC_Fraction</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC844" class="react-file-line html-div" data-testid="code-cell" data-line-number="844" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">ABC_Fraction</span><span class="pl-k">*</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC845" class="react-file-line html-div" data-testid="code-cell" data-line-number="845" style="position:relative">            }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC846" class="react-file-line html-div" data-testid="code-cell" data-line-number="846" style="position:relative">              <span class="pl-c1">F</span><span class="pl-smi">.ABC</span><span class="pl-k">&lt;-</span><span class="pl-smi">FScale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC847" class="react-file-line html-div" data-testid="code-cell" data-line-number="847" style="position:relative">            }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC848" class="react-file-line html-div" data-testid="code-cell" data-line-number="848" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC849" class="react-file-line html-div" data-testid="code-cell" data-line-number="849" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC850" class="react-file-line html-div" data-testid="code-cell" data-line-number="850" style="position:relative">          <span class="pl-smi">DepletionScale</span> <span class="pl-k">&lt;-</span> (<span class="pl-k">-</span>log(<span class="pl-c1">1</span><span class="pl-k">-</span>((<span class="pl-c1">1</span><span class="pl-k">-</span>exp(<span class="pl-k">-</span><span class="pl-smi">FScale</span>))<span class="pl-k">*</span><span class="pl-smi">DepletionScale</span>))<span class="pl-k">/</span><span class="pl-smi">FScale</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC851" class="react-file-line html-div" data-testid="code-cell" data-line-number="851" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC852" class="react-file-line html-div" data-testid="code-cell" data-line-number="852" style="position:relative">        </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC853" class="react-file-line html-div" data-testid="code-cell" data-line-number="853" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC854" class="react-file-line html-div" data-testid="code-cell" data-line-number="854" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">fitting_OFL</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC855" class="react-file-line html-div" data-testid="code-cell" data-line-number="855" style="position:relative">      <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span> <span class="pl-c"><span class="pl-c">#</span>Set search step to small value so it doesn&#039;t trigger continued loops this value is only needed during the Benchmark MSY search</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC856" class="react-file-line html-div" data-testid="code-cell" data-line-number="856" style="position:relative">      <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span> <span class="pl-c"><span class="pl-c">#</span>Set depletion scale to 1 so it doesn&#039;t trigger continued loops now that Benchmark search is complete</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC857" class="react-file-line html-div" data-testid="code-cell" data-line-number="857" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-smi">F_OFL</span> <span class="pl-c"><span class="pl-c">#</span>Set the F target to F.OFL for rescaling annual F values</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC858" class="react-file-line html-div" data-testid="code-cell" data-line-number="858" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC859" class="react-file-line html-div" data-testid="code-cell" data-line-number="859" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC860" class="react-file-line html-div" data-testid="code-cell" data-line-number="860" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_OFL<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC861" class="react-file-line html-div" data-testid="code-cell" data-line-number="861" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC862" class="react-file-line html-div" data-testid="code-cell" data-line-number="862" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC863" class="react-file-line html-div" data-testid="code-cell" data-line-number="863" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_OFL<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC864" class="react-file-line html-div" data-testid="code-cell" data-line-number="864" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC865" class="react-file-line html-div" data-testid="code-cell" data-line-number="865" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC866" class="react-file-line html-div" data-testid="code-cell" data-line-number="866" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC867" class="react-file-line html-div" data-testid="code-cell" data-line-number="867" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC868" class="react-file-line html-div" data-testid="code-cell" data-line-number="868" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC869" class="react-file-line html-div" data-testid="code-cell" data-line-number="869" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC870" class="react-file-line html-div" data-testid="code-cell" data-line-number="870" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC871" class="react-file-line html-div" data-testid="code-cell" data-line-number="871" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC872" class="react-file-line html-div" data-testid="code-cell" data-line-number="872" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC873" class="react-file-line html-div" data-testid="code-cell" data-line-number="873" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_OFL<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC874" class="react-file-line html-div" data-testid="code-cell" data-line-number="874" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC875" class="react-file-line html-div" data-testid="code-cell" data-line-number="875" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">fitting_ABC</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC876" class="react-file-line html-div" data-testid="code-cell" data-line-number="876" style="position:relative">      <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span> <span class="pl-c"><span class="pl-c">#</span>Set search step to small value so it doesn&#039;t trigger continued loops this value is only needed during the Benchmark MSY search</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC877" class="react-file-line html-div" data-testid="code-cell" data-line-number="877" style="position:relative">      <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span> <span class="pl-c"><span class="pl-c">#</span>Set depletion scale to 1 so it doesn&#039;t trigger continued loops now that Benchmark search is complete</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC878" class="react-file-line html-div" data-testid="code-cell" data-line-number="878" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">F</span><span class="pl-smi">.ABC</span> <span class="pl-c"><span class="pl-c">#</span>Set the F target to F.ABC for rescaling annual F values</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC879" class="react-file-line html-div" data-testid="code-cell" data-line-number="879" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC880" class="react-file-line html-div" data-testid="code-cell" data-line-number="880" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC881" class="react-file-line html-div" data-testid="code-cell" data-line-number="881" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_ABC<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC882" class="react-file-line html-div" data-testid="code-cell" data-line-number="882" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC883" class="react-file-line html-div" data-testid="code-cell" data-line-number="883" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC884" class="react-file-line html-div" data-testid="code-cell" data-line-number="884" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_ABC<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC885" class="react-file-line html-div" data-testid="code-cell" data-line-number="885" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC886" class="react-file-line html-div" data-testid="code-cell" data-line-number="886" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC887" class="react-file-line html-div" data-testid="code-cell" data-line-number="887" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC888" class="react-file-line html-div" data-testid="code-cell" data-line-number="888" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC889" class="react-file-line html-div" data-testid="code-cell" data-line-number="889" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC890" class="react-file-line html-div" data-testid="code-cell" data-line-number="890" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC891" class="react-file-line html-div" data-testid="code-cell" data-line-number="891" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC892" class="react-file-line html-div" data-testid="code-cell" data-line-number="892" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC893" class="react-file-line html-div" data-testid="code-cell" data-line-number="893" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC894" class="react-file-line html-div" data-testid="code-cell" data-line-number="894" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_ABC<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC895" class="react-file-line html-div" data-testid="code-cell" data-line-number="895" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">fitting_F0</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC896" class="react-file-line html-div" data-testid="code-cell" data-line-number="896" style="position:relative">      <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span> <span class="pl-c"><span class="pl-c">#</span>Set search step to small value so it doesn&#039;t trigger continued loops this value is only needed during the Benchmark MSY search</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC897" class="react-file-line html-div" data-testid="code-cell" data-line-number="897" style="position:relative">      <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span> <span class="pl-c"><span class="pl-c">#</span>Set depletion scale to 1 so it doesn&#039;t trigger continued loops now that Benchmark search is complete</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC898" class="react-file-line html-div" data-testid="code-cell" data-line-number="898" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">0</span> <span class="pl-c"><span class="pl-c">#</span>Set the F target to 0 for rescaling annual F values</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC899" class="react-file-line html-div" data-testid="code-cell" data-line-number="899" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC900" class="react-file-line html-div" data-testid="code-cell" data-line-number="900" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC901" class="react-file-line html-div" data-testid="code-cell" data-line-number="901" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_F0<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC902" class="react-file-line html-div" data-testid="code-cell" data-line-number="902" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC903" class="react-file-line html-div" data-testid="code-cell" data-line-number="903" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC904" class="react-file-line html-div" data-testid="code-cell" data-line-number="904" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_F0<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC905" class="react-file-line html-div" data-testid="code-cell" data-line-number="905" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC906" class="react-file-line html-div" data-testid="code-cell" data-line-number="906" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC907" class="react-file-line html-div" data-testid="code-cell" data-line-number="907" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC908" class="react-file-line html-div" data-testid="code-cell" data-line-number="908" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC909" class="react-file-line html-div" data-testid="code-cell" data-line-number="909" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC910" class="react-file-line html-div" data-testid="code-cell" data-line-number="910" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC911" class="react-file-line html-div" data-testid="code-cell" data-line-number="911" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC912" class="react-file-line html-div" data-testid="code-cell" data-line-number="912" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC913" class="react-file-line html-div" data-testid="code-cell" data-line-number="913" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC914" class="react-file-line html-div" data-testid="code-cell" data-line-number="914" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_F0<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC915" class="react-file-line html-div" data-testid="code-cell" data-line-number="915" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">fitting_Rebuild</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC916" class="react-file-line html-div" data-testid="code-cell" data-line-number="916" style="position:relative">      <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span> <span class="pl-c"><span class="pl-c">#</span>Set search step to small value so it doesn&#039;t trigger continued loops this value is only needed during the Benchmark MSY search</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC917" class="react-file-line html-div" data-testid="code-cell" data-line-number="917" style="position:relative">      <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span> <span class="pl-c"><span class="pl-c">#</span>Set depletion scale to 1 so it doesn&#039;t trigger continued loops now that Benchmark search is complete</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC918" class="react-file-line html-div" data-testid="code-cell" data-line-number="918" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-smi">F_OFL</span> <span class="pl-c"><span class="pl-c">#</span>Set the F target to F_OFL for rescaling annual F values in years after the rebuild period.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC919" class="react-file-line html-div" data-testid="code-cell" data-line-number="919" style="position:relative">      <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC920" class="react-file-line html-div" data-testid="code-cell" data-line-number="920" style="position:relative">      <span class="pl-k">if</span>(is.null(<span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC921" class="react-file-line html-div" data-testid="code-cell" data-line-number="921" style="position:relative">        <span class="pl-smi">F_report</span><span class="pl-k">&lt;-</span><span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC922" class="react-file-line html-div" data-testid="code-cell" data-line-number="922" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC923" class="react-file-line html-div" data-testid="code-cell" data-line-number="923" style="position:relative">      <span class="pl-smi">F_Rebuild_Scale</span><span class="pl-k">&lt;-</span><span class="pl-smi">F_report</span>[<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span><span class="pl-k">==</span><span class="pl-smi">Rebuild_yr</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC924" class="react-file-line html-div" data-testid="code-cell" data-line-number="924" style="position:relative">      <span class="pl-smi">Depletion</span><span class="pl-k">&lt;-</span><span class="pl-smi">TimeFit3</span><span class="pl-k">$</span><span class="pl-smi">SpawnBio</span><span class="pl-k">/</span><span class="pl-smi">Virgin_bio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC925" class="react-file-line html-div" data-testid="code-cell" data-line-number="925" style="position:relative">      <span class="pl-smi">Achieved.Rebuild</span> <span class="pl-k">&lt;-</span> mean(<span class="pl-smi">Depletion</span>[<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">Yr</span><span class="pl-k">==</span><span class="pl-smi">Rebuild_yr</span>])</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC926" class="react-file-line html-div" data-testid="code-cell" data-line-number="926" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC927" class="react-file-line html-div" data-testid="code-cell" data-line-number="927" style="position:relative">      <span class="pl-smi">Rebuild.Scale</span> <span class="pl-k">&lt;-</span> (<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Target.Rebuild</span>)<span class="pl-k">/</span>(<span class="pl-c1">1</span><span class="pl-k">-</span><span class="pl-smi">Achieved.Rebuild</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC928" class="react-file-line html-div" data-testid="code-cell" data-line-number="928" style="position:relative">      <span class="pl-smi">Rebuild.Ratio</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">Rebuild.Scale</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC929" class="react-file-line html-div" data-testid="code-cell" data-line-number="929" style="position:relative">      <span class="pl-smi">Rebuild.Scale</span> <span class="pl-k">&lt;-</span> min(<span class="pl-k">-</span>log(<span class="pl-c1">1</span><span class="pl-k">-</span>((<span class="pl-c1">1</span><span class="pl-k">-</span>exp(<span class="pl-k">-</span><span class="pl-smi">F_Rebuild_Scale</span>))<span class="pl-k">*</span><span class="pl-smi">Rebuild.Scale</span>)),<span class="pl-smi">FScale</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC930" class="react-file-line html-div" data-testid="code-cell" data-line-number="930" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">Rebuild.Scale</span> <span class="pl-k">&lt;</span> <span class="pl-c1">0.00001</span> <span class="pl-k">&amp;</span> <span class="pl-smi">Rebuild.Ratio</span> <span class="pl-k">&lt;</span> <span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC931" class="react-file-line html-div" data-testid="code-cell" data-line-number="931" style="position:relative">        <span class="pl-smi">Rebuild.Scale</span> <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC932" class="react-file-line html-div" data-testid="code-cell" data-line-number="932" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC933" class="react-file-line html-div" data-testid="code-cell" data-line-number="933" style="position:relative">      <span class="pl-k">if</span>(<span class="pl-smi">n_groups</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC934" class="react-file-line html-div" data-testid="code-cell" data-line-number="934" style="position:relative">        <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Rebuild<span class="pl-pds">&quot;</span></span>]]<span class="pl-k">&lt;-</span><span class="pl-k">list</span>()</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC935" class="react-file-line html-div" data-testid="code-cell" data-line-number="935" style="position:relative">        <span class="pl-k">for</span>(<span class="pl-smi">i</span> <span class="pl-k">in</span> <span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">n_groups</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC936" class="react-file-line html-div" data-testid="code-cell" data-line-number="936" style="position:relative">          <span class="pl-smi">Achieved.Catch.group</span> <span class="pl-k">&lt;-</span> apply(<span class="pl-smi">TimeFit3</span>[<span class="pl-c1">1</span><span class="pl-k">:</span><span class="pl-smi">terminal_year</span>,<span class="pl-smi">Catch_cols3</span>[<span class="pl-smi">fleets_by_group</span>[[<span class="pl-smi">i</span>]]],<span class="pl-v">drop</span><span class="pl-k">=</span><span class="pl-c1">FALSE</span>],<span class="pl-c1">1</span>,<span class="pl-smi">sum</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC937" class="react-file-line html-div" data-testid="code-cell" data-line-number="937" style="position:relative">          <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Group_Catch_Rebuild<span class="pl-pds">&quot;</span></span>]][[<span class="pl-smi">i</span>]]<span class="pl-k">&lt;-</span><span class="pl-smi">Achieved.Catch.group</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC938" class="react-file-line html-div" data-testid="code-cell" data-line-number="938" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC939" class="react-file-line html-div" data-testid="code-cell" data-line-number="939" style="position:relative">      }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC940" class="react-file-line html-div" data-testid="code-cell" data-line-number="940" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC941" class="react-file-line html-div" data-testid="code-cell" data-line-number="941" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC942" class="react-file-line html-div" data-testid="code-cell" data-line-number="942" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>F_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC943" class="react-file-line html-div" data-testid="code-cell" data-line-number="943" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC944" class="react-file-line html-div" data-testid="code-cell" data-line-number="944" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC945" class="react-file-line html-div" data-testid="code-cell" data-line-number="945" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC946" class="react-file-line html-div" data-testid="code-cell" data-line-number="946" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC947" class="react-file-line html-div" data-testid="code-cell" data-line-number="947" style="position:relative">      <span class="pl-smi">projection_results</span>[[<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_Rebuild<span class="pl-pds">&quot;</span></span>]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC948" class="react-file-line html-div" data-testid="code-cell" data-line-number="948" style="position:relative">    }<span class="pl-k">else</span> <span class="pl-k">if</span> (<span class="pl-smi">fitting_Fixed_Catch</span><span class="pl-k">==</span><span class="pl-c1">TRUE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC949" class="react-file-line html-div" data-testid="code-cell" data-line-number="949" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC950" class="react-file-line html-div" data-testid="code-cell" data-line-number="950" style="position:relative">      <span class="pl-smi">search_step</span><span class="pl-k">&lt;-</span><span class="pl-c1">0.00001</span> <span class="pl-c"><span class="pl-c">#</span>Set search step to small value so it doesn&#039;t trigger continued loops this value is only needed during the Benchmark MSY search</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC951" class="react-file-line html-div" data-testid="code-cell" data-line-number="951" style="position:relative">      <span class="pl-smi">DepletionScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">1</span> <span class="pl-c"><span class="pl-c">#</span>Set depletion scale to 1 so it doesn&#039;t trigger continued loops now that Benchmark search is complete</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC952" class="react-file-line html-div" data-testid="code-cell" data-line-number="952" style="position:relative">      <span class="pl-smi">FScale</span><span class="pl-k">&lt;-</span><span class="pl-c1">0</span> <span class="pl-c"><span class="pl-c">#</span>Set the F target to F_OFL for rescaling annual F values in years after the rebuild period.</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC953" class="react-file-line html-div" data-testid="code-cell" data-line-number="953" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC954" class="react-file-line html-div" data-testid="code-cell" data-line-number="954" style="position:relative">      <span class="pl-smi">Fmult4</span> <span class="pl-k">&lt;-</span> rep(<span class="pl-smi">Catch_Target</span><span class="pl-k">/</span><span class="pl-smi">Achieved.Catch.All</span>,<span class="pl-v">each</span><span class="pl-k">=</span>(length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC955" class="react-file-line html-div" data-testid="code-cell" data-line-number="955" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC956" class="react-file-line html-div" data-testid="code-cell" data-line-number="956" style="position:relative">      <span class="pl-smi">Fmult4</span> <span class="pl-k">&lt;-</span> ifelse(<span class="pl-smi">forecast_F</span>[,<span class="pl-c1">4</span>]<span class="pl-k">&gt;</span><span class="pl-k">=</span><span class="pl-c1">1.5</span>,ifelse(<span class="pl-smi">Fmult4</span><span class="pl-k">&gt;</span><span class="pl-c1">1</span>,<span class="pl-c1">1</span>,<span class="pl-smi">Fmult4</span>),<span class="pl-smi">Fmult4</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC957" class="react-file-line html-div" data-testid="code-cell" data-line-number="957" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC958" class="react-file-line html-div" data-testid="code-cell" data-line-number="958" style="position:relative">      <span class="pl-smi">Fmult4</span>[is.na(<span class="pl-smi">Fmult4</span>)] <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC959" class="react-file-line html-div" data-testid="code-cell" data-line-number="959" style="position:relative">      </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC960" class="react-file-line html-div" data-testid="code-cell" data-line-number="960" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>Catch_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Catch</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC961" class="react-file-line html-div" data-testid="code-cell" data-line-number="961" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>F_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC962" class="react-file-line html-div" data-testid="code-cell" data-line-number="962" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>Depletion_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSBratio</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC963" class="react-file-line html-div" data-testid="code-cell" data-line-number="963" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>SSB_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SSB</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC964" class="react-file-line html-div" data-testid="code-cell" data-line-number="964" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>SPR_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.SPR</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC965" class="react-file-line html-div" data-testid="code-cell" data-line-number="965" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>Recruitment_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">Achieved.Rec</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC966" class="react-file-line html-div" data-testid="code-cell" data-line-number="966" style="position:relative">      <span class="pl-smi">projection_results</span>[[paste0(<span class="pl-s"><span class="pl-pds">&quot;</span>Forecatch_FixedCatch_<span class="pl-pds">&quot;</span></span>,<span class="pl-smi">CC_loop</span>)]] <span class="pl-k">&lt;-</span> <span class="pl-smi">achieved.report</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC967" class="react-file-line html-div" data-testid="code-cell" data-line-number="967" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC968" class="react-file-line html-div" data-testid="code-cell" data-line-number="968" style="position:relative">    </div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC969" class="react-file-line html-div" data-testid="code-cell" data-line-number="969" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Fmult2 calculations define the multiplier for adjusting annual F values</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC970" class="react-file-line html-div" data-testid="code-cell" data-line-number="970" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>Zero catch years are identified first to prevent divide by zero errors in the scaling and</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC971" class="react-file-line html-div" data-testid="code-cell" data-line-number="971" style="position:relative">    <span class="pl-c"><span class="pl-c">#</span>to tell the search algorithm that the target has been achieved</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC972" class="react-file-line html-div" data-testid="code-cell" data-line-number="972" style="position:relative">
</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC973" class="react-file-line html-div" data-testid="code-cell" data-line-number="973" style="position:relative">    <span class="pl-k">if</span>(is.null(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC974" class="react-file-line html-div" data-testid="code-cell" data-line-number="974" style="position:relative">      <span class="pl-smi">zero_catch</span> <span class="pl-k">&lt;-</span> which(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))]<span class="pl-k">==</span><span class="pl-c1">0</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC975" class="react-file-line html-div" data-testid="code-cell" data-line-number="975" style="position:relative">    }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC976" class="react-file-line html-div" data-testid="code-cell" data-line-number="976" style="position:relative">      <span class="pl-smi">zero_catch</span> <span class="pl-k">&lt;-</span> which(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))]<span class="pl-k">==</span><span class="pl-c1">0</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC977" class="react-file-line html-div" data-testid="code-cell" data-line-number="977" style="position:relative">    }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC978" class="react-file-line html-div" data-testid="code-cell" data-line-number="978" style="position:relative">    <span class="pl-k">if</span>(<span class="pl-smi">fitting_Fixed_Catch</span><span class="pl-k">==</span><span class="pl-c1">FALSE</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC979" class="react-file-line html-div" data-testid="code-cell" data-line-number="979" style="position:relative">      <span class="pl-k">if</span>(length(<span class="pl-smi">zero_catch</span>)<span class="pl-k">&gt;</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC980" class="react-file-line html-div" data-testid="code-cell" data-line-number="980" style="position:relative">        <span class="pl-k">if</span>(<span class="pl-smi">FScale</span><span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC981" class="react-file-line html-div" data-testid="code-cell" data-line-number="981" style="position:relative">          <span class="pl-smi">Fmult2</span>[<span class="pl-smi">zero_catch</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">1</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC982" class="react-file-line html-div" data-testid="code-cell" data-line-number="982" style="position:relative">          <span class="pl-smi">Fmult2</span>[<span class="pl-k">-</span><span class="pl-smi">zero_catch</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC983" class="react-file-line html-div" data-testid="code-cell" data-line-number="983" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC984" class="react-file-line html-div" data-testid="code-cell" data-line-number="984" style="position:relative">          <span class="pl-smi">Fmult2</span>[<span class="pl-smi">zero_catch</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">2</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC985" class="react-file-line html-div" data-testid="code-cell" data-line-number="985" style="position:relative">          <span class="pl-k">if</span>(is.null(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC986" class="react-file-line html-div" data-testid="code-cell" data-line-number="986" style="position:relative">            <span class="pl-smi">temp_F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))][<span class="pl-k">-</span><span class="pl-smi">zero_catch</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC987" class="react-file-line html-div" data-testid="code-cell" data-line-number="987" style="position:relative">          }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC988" class="react-file-line html-div" data-testid="code-cell" data-line-number="988" style="position:relative">            <span class="pl-smi">temp_F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))][<span class="pl-k">-</span><span class="pl-smi">zero_catch</span>]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC989" class="react-file-line html-div" data-testid="code-cell" data-line-number="989" style="position:relative">          }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC990" class="react-file-line html-div" data-testid="code-cell" data-line-number="990" style="position:relative">          <span class="pl-smi">temp_F</span>[<span class="pl-smi">temp_F</span><span class="pl-k">&gt;</span><span class="pl-c1">1.5</span>] <span class="pl-k">&lt;-</span> <span class="pl-c1">1.5</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC991" class="react-file-line html-div" data-testid="code-cell" data-line-number="991" style="position:relative">          <span class="pl-smi">temp_F</span>[<span class="pl-smi">temp_F</span><span class="pl-k">&lt;</span>(min(<span class="pl-c1">0.001</span>,<span class="pl-smi">FScale</span>))] <span class="pl-k">&lt;-</span> min(<span class="pl-c1">0.001</span>,<span class="pl-smi">FScale</span>)</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC992" class="react-file-line html-div" data-testid="code-cell" data-line-number="992" style="position:relative">          <span class="pl-smi">Fmult2</span>[<span class="pl-k">-</span><span class="pl-smi">zero_catch</span>] <span class="pl-k">&lt;-</span> <span class="pl-smi">FScale</span><span class="pl-k">/</span><span class="pl-smi">temp_F</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC993" class="react-file-line html-div" data-testid="code-cell" data-line-number="993" style="position:relative">        }</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC994" class="react-file-line html-div" data-testid="code-cell" data-line-number="994" style="position:relative">      }<span class="pl-k">else</span> <span class="pl-k">if</span>(<span class="pl-smi">FScale</span><span class="pl-k">==</span><span class="pl-c1">0</span>){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC995" class="react-file-line html-div" data-testid="code-cell" data-line-number="995" style="position:relative">        <span class="pl-smi">Fmult2</span>[] <span class="pl-k">&lt;-</span> <span class="pl-c1">0</span></div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC996" class="react-file-line html-div" data-testid="code-cell" data-line-number="996" style="position:relative">      }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC997" class="react-file-line html-div" data-testid="code-cell" data-line-number="997" style="position:relative">        <span class="pl-k">if</span>(is.null(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>)){</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC998" class="react-file-line html-div" data-testid="code-cell" data-line-number="998" style="position:relative">          <span class="pl-smi">temp_F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_std</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))]</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC999" class="react-file-line html-div" data-testid="code-cell" data-line-number="999" style="position:relative">        }<span class="pl-k">else</span>{</div></div></div><div class="child-of-line-45  react-code-text react-code-line-contents" style="min-height:auto"><div><div id="LC1000" class="react-file-line html-div" data-testid="code-cell" data-line-number="1000" style="position:relative">          <span class="pl-smi">temp_F</span> <span class="pl-k">&lt;-</span> <span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>[sort(rep(seq_along(<span class="pl-smi">SPRfit</span><span class="pl-k">$</span><span class="pl-smi">F_report</span>),length(<span class="pl-smi">seasons</span>)<span class="pl-k">*</span>length(<span class="pl-smi">F_cols</span>)))]</div></div></div></div></div><div class="Box-sc-g0xbh4-0 gkZUDI"><a class="prc-Link-Link-85e08" href="https://github.com/SEFSC/SFD-AllocationForecasting/raw/refs/heads/main/Allocation_forecasting.R">View remainder of file in raw view</a></div></div><div id="copilot-button-container"></div></div><div id="highlighted-line-menu-container"></div></div></div><button hidden="" data-testid="hotkey-button" data-hotkey-scope="read-only-cursor-text-area"></button><button hidden=""></button></section></div></div></div> <!-- --> <!-- --> </div></div></div><div class="Box-sc-g0xbh4-0"></div></div></div></div></div><div id="find-result-marks-container" class="Box-sc-g0xbh4-0 cCoXib"></div><button hidden="" data-testid="" data-hotkey-scope="read-only-cursor-text-area"></button><button hidden=""></button></div> <!-- --> <!-- --> <script type="application/json" id="__PRIMER_DATA_:R0:__">{"resolvedServerColorMode":"day"}</script></div>
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    <clipboard-copy aria-label="Copy" class="ClipboardButton btn js-clipboard-copy m-2 p-0" data-copy-feedback="Copied!" data-tooltip-direction="w">
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon m-2">
    <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none m-2">
    <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path>
</svg>
    </clipboard-copy>
  </div>
</template>
<template id="snippet-clipboard-copy-button-unpositioned">
  <div class="zeroclipboard-container">
    <clipboard-copy aria-label="Copy" class="ClipboardButton btn btn-invisible js-clipboard-copy m-2 p-0 d-flex flex-justify-center flex-items-center" data-copy-feedback="Copied!" data-tooltip-direction="w">
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-copy js-clipboard-copy-icon">
    <path d="M0 6.75C0 5.784.784 5 1.75 5h1.5a.75.75 0 0 1 0 1.5h-1.5a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-1.5a.75.75 0 0 1 1.5 0v1.5A1.75 1.75 0 0 1 9.25 16h-7.5A1.75 1.75 0 0 1 0 14.25Z"></path><path d="M5 1.75C5 .784 5.784 0 6.75 0h7.5C15.216 0 16 .784 16 1.75v7.5A1.75 1.75 0 0 1 14.25 11h-7.5A1.75 1.75 0 0 1 5 9.25Zm1.75-.25a.25.25 0 0 0-.25.25v7.5c0 .138.112.25.25.25h7.5a.25.25 0 0 0 .25-.25v-7.5a.25.25 0 0 0-.25-.25Z"></path>
</svg>
      <svg aria-hidden="true" height="16" viewBox="0 0 16 16" version="1.1" width="16" data-view-component="true" class="octicon octicon-check js-clipboard-check-icon color-fg-success d-none">
    <path d="M13.78 4.22a.75.75 0 0 1 0 1.06l-7.25 7.25a.75.75 0 0 1-1.06 0L2.22 9.28a.751.751 0 0 1 .018-1.042.751.751 0 0 1 1.042-.018L6 10.94l6.72-6.72a.75.75 0 0 1 1.06 0Z"></path>
</svg>
    </clipboard-copy>
  </div>
</template>




    </div>

    <div id="js-global-screen-reader-notice" class="sr-only mt-n1" aria-live="polite" aria-atomic="true" ></div>
    <div id="js-global-screen-reader-notice-assertive" class="sr-only mt-n1" aria-live="assertive" aria-atomic="true"></div>
  </body>
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