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zandjyo committed Oct 17, 2024
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Expand Up @@ -41,12 +41,12 @@ <h2> Documents and appendices </h2>
<h3> September documentation:</h3>
<li><a href="https://afsc-assessments.github.io/EBS_PCOD/2024_ASSESSMENT/SEPTEMBER_MODELS/"> September Github page</a></li>
<h3> Main document:</h3>
<!-- <li><a href="EBSpcod.pdf">2023 EBS Pacific Cod Stock Assessment (.pdf) </a></li> -->
<li><a href="https://meetings.npfmc.org/CommentReview/DownloadFile?p=c0cfbe39-2f52-41e3-8062-1ea6df995cb4.pdf&fileName=BS_PCod_September%202024.pdf">2024 EBS Pacific Cod Stock Assessment (.pdf) </a></li>
<!-- <li><a href="">2024 EBS Pacific Cod Stock Assessment (.pdf) </a></li> -->
<li><a href="">2024 EBS Pacific Cod Stock Assessment (.pdf) (not yet available) </a></li>

<h3> Appendices:</h3>
<li><a href="https://meetings.npfmc.org/CommentReview/DownloadFile?p=c0cfbe39-2f52-41e3-8062-1ea6df995cb4.pdf&fileName=BS_PCod_September%202024.pdf"> Appendix 2.1: September documentation (.pdf)</a></li>
<li><a href="">Appendix 2.2: Eastern Bering Sea Pacific Cod ESP Report Card(.pdf) </a></li>
<li><a href="">Appendix 2.2: Eastern Bering Sea Pacific Cod ESP Report Card(.pdf)(not yet available </a></li>
<li><a href="APPENDICES/APPENDIX_2.3_2024_MODELS.zip" download>Appendix 2.3: 2024 Models SS Files (.zip) </a></li>
<li><a href="APPENDICES/Appendix_2.4_Data_and_results.xlsx" download>Appendix 2.4: All model data and results tables (.xlsx)</a></li>

Expand All @@ -57,45 +57,50 @@ <h2>Presentations </h2>
<p>
<ul>
<h3> Plan Team:</h3>
<li><a href="BSPCOD_NOV_Plan_Team_Presentation.pdf">2024 EBS Pacific Cod Stock Assessment Plan Team Presentation (.pdf)</a></li>
<li><a href="">2024 EBS Pacific Cod Stock Assessment Plan Team Presentation (.pdf) (not yet available)</a></li>
<h3> Science and Statistical Committee:</h3>
<li><a href="BSPCOD_DEC_SSC_Presentation.pdf">2024 EBS Pacific Cod Stock Assessment SSC Presentation (.pdf)</a></li>
<li><a href="">2024 EBS Pacific Cod Stock Assessment SSC Presentation (.pdf) (not yet available)</a></li>
</ul>
</p>

<h2>r4ss plots:</h2>
<p>Updated 1 October 2024 to reflect the draft models:
<p>Updated 16 October 2024 to reflect the draft models:
<ul>
<h3>2023 Model:</h3>
<h3>Models for 2024:</h3>
<li><a href="FIGURES/R4SS_FIGURES/MODEL23.1.0.d/plots">Model 23.1.0.d</a></li>

<h3>2024 Model:</h3>
<li><a href="FIGURES/R4SS_FIGURES/MODEL24.1/plots">Model 24.1</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL24.0/plots">Model 24.0</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL24.1/plots">Model 24.1</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL24.2/plots">Model 24.2</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL24.3/plots">Model 24.3</a></li>
<h3>Bridging models from 2023 to 2024:</h3>
<li><a href="FIGURES/R4SS_FIGURES/MODEL23.1.0.d_A_nochange/plots">2023 Model 23.1.0.d</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL23.1.0.d_B_new_data/plots">2023 Model 23.1.0.d with 2024 data</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL23.1.0.d_C_VAF_tuned/plots">2023 Model 23.1.0.d with 2024 data and Francis tuned</a></li>
<li><a href="FIGURES/R4SS_FIGURES/MODEL23.1.0.d/plots"">2024 Model 23.1.0.d with 2024 data and sigmas and Francis tuned</a></li>

</ul>
</p>
<h2> Associated PDF of other figures:</h2>
<p>Survey and fishing maps
<ul>
<li><a href="FIGURES/BT_SURVEY_MAPS/NBS_COD.pdf">Bottom trawl survey maps with NBS (pdf)</a></li>
<li><a href="FIGURES/BT_SURVEY_MAPS/EBS_COD.pdf">Bottom trawl survey maps EBS only (pdf)</a></li>
<li><a href="FIGURES/FISHING_MAPS/EBS_COD_FISHING_MAPS.pdf">Fishing maps (pdf)</a></li>
</ul>
</p>

<p> Model and ensemble figures
<p> Model figures
<ul>
<li><a href="FIGURES/OTHER/CATCH_TO_BIOMASS.pdf"> Catch to biomass figures(pdf)</a></li>
<li><a href="FIGURES/OTHER/BIOMASS_TRENDS.pdf"> Catch to biomass figures(pdf)</a></li>
<li><a href="FIGURES/OTHER/SSplotComparisons.pdf"> Model comparison figures(pdf)</a></li>
</ul>
</p>

<p>Projection figures
<ul>
<h3>2023 Models:</h3>
<li><a href="FIGURES/PROJECTIONS/PROJ_23.1.0.d.pdf">Model 23.1.0.d (pdf)</a></li>

<h3>2024 Models:</h3>
<li><a href="FIGURES/PROJECTIONS/PROJ_24.1.pdf">Model 24.1 (pdf)</a></li>
<li><a href="FIGURES/PROJECTIONS/Projections_23.1.0.d.pdf">Model 23.1.0.d (pdf)</a></li>
<li><a href="FIGURES/PROJECTIONS/Projections_24.0.pdf">Model 24.0 (pdf)</a></li>
<li><a href="FIGURES/PROJECTIONS/Projections_24.1.pdf">Model 24.1 (pdf)</a></li>
<li><a href="FIGURES/PROJECTIONS/Projections_24.3.pdf">Model 24.3 (pdf)</a></li>
</ul>
</p>

Expand All @@ -107,45 +112,31 @@ <h3>2024 Models:</h3>

<p>Diagnostic plots (ss3diags library)
<ul>
<h3>2023 Models:</h3>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M23.1.0.d.pdf">Model 23.1.0.d (pdf)</a></li>
<h3>ss3diags library:</h3>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M23.1.0.d.pdf">Model 23.1.0.d (pdf)</a></li>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M24.0.pdf">Model 24.0 (pdf)</a></li>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M24.1.pdf">Model 24.1 (pdf)</a></li>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M24.2.pdf">Model 24.2 (pdf)</a></li>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M24.3.pdf">Model 24.3 (pdf)</a></li>

<h3>2024 Models:</h3>
<li><a href="FIGURES/SS3DIAGS/SS3DIAGS_M24.1.pdf">Model 24.1 (pdf)</a></li>
<h3>One step ahead (OSA) residual plots</h3>
<li><a href="FIGURES/OSA_RESIDUALS/LENGTHS_OSA.pdf">Fishery and survey length composition residuals(pdf)</a></li>
<li><a href="FIGURES/OSA_RESIDUALS/SURVEY_AGES_OSA.pdf">Survey age composition residuals(pdf)</a></li>

<h3>JABBA All models:</h3>
<li><a href="FIGURES/SS3DIAGS/JABBA_ANALYSIS.pdf">JABBA figures(pdf)</a></li>
</ul>
</p>

<p>Other figures
<ul>
<h3>Profiles:</h3>
<li><a href="FIGURES/OTHER/M_Profile_Model23.1.0.d.pdf">Profiles over natural mortality for Model 23.1.0.d (pdf)</a></li>
<li><a href="FIGURES/OTHER/Q_Profile_Model23.10.d.pdf">Profiles over survey catchability for Model 23.10.d (pdf)</a></li>
<li><a href="FIGURES/OTHER/SigmaR_Profile_Model23.10.d.pdf">Profiles over sigma R for Model 23.10.d (pdf)</a></li>
<li><a href="FIGURES/OTHER/M_Profile_Model24.1.pdf">Profiles over natural mortality for Model 24.1 (pdf)</a></li>
<li><a href="FIGURES/OTHER/Q_Profile_Model24.1.pdf">Profiles over survey catchability for Model 24.1 (pdf)</a></li>
<li><a href="FIGURES/OTHER/SigmaR_Profile_Model24.1.pdf">Profiles over sigma R for Model 24.1 (pdf)</a></li>
<h3>Parameters and derived quantities figures:</h3>
<li><a href="FIGURES/OTHER/PARAMETERS.pdf">Model parameter figures(pdf)</a></li>
<li><a href="FIGURES/OTHER/DERIVED_QUANTS.pdf">Model derived quantities figures(pdf)</a></li>


<h3> Misc.:</h3>
<li><a href="FIGURES/OTHER/CATCH_FIGURES.pdf">Random catch figures (pdf)</a></li>
</ul>
</p>
<p>Alternative diagnostic plots (OSA plots)
<ul>
<h3>2023 Models:</h3>
<li><a href="FIGURES/OSA_RESIDUALS/L_EBS_COD_Model_23.1.0.a_FISHERY_Length_(cm).pdf"> Model 23.1.0.a Fishery Length (pdf)</a></li>
<li><a href="FIGURES/OSA_RESIDUALS/A_EBS_COD_Model_23.1.0.d_EBSSHELF_Age.pdf"> Model 23.1.0.d Survey Age (pdf)</a></li>
<li><a href="FIGURES/OSA_RESIDUALS/L_EBS_COD_Model_23.1.0.d_EBSSHELF_Length_(cm).pdf"> Model 23.1.0.d Survey Length (pdf)</a></li>


<h3>2024 Models:</h3>
<li><a href="FIGURES/OSA_RESIDUALS/A_EBS_COD_Model_24.1_EBSSHELF_Age.pdf"> Model 24.1 Survey Age (pdf)</a></li>
<li><a href="FIGURES/OSA_RESIDUALS/L_EBS_COD_Model_24.1_EBSSHELF_Length_(cm).pdf"> Model 24.1 Survey Length (pdf)</a></li>
<li><a href="FIGURES/OSA_RESIDUALS/L_EBS_COD_Model_24.1_FISHERY_Length_(cm).pdf"> Model 24.1 Fishery Length (pdf)</a></li>
<li><a href="FIGURES/OTHER/Length_weight_at_age.pdf">Length and weight at age figures (pdf)</a></li>
</ul>
</p>

</div>

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