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index.html

@@ -213,7 +213,7 @@ <h2 id="toc-title">On this page</h2>
   <ul class="collapse">
   <li><a href="#getting-started-using-the-stock-assessment-continuum-tool" id="toc-getting-started-using-the-stock-assessment-continuum-tool" class="nav-link" data-scroll-target="#getting-started-using-the-stock-assessment-continuum-tool">Getting Started Using the Stock Assessment Continuum Tool</a></li>
   <li><a href="#getting-started-using-the-input-files" id="toc-getting-started-using-the-input-files" class="nav-link" data-scroll-target="#getting-started-using-the-input-files">Getting Started Using the Input Files</a></li>
-  <li><a href="#viewing-stock-synthesis-output-with-r4ss" id="toc-viewing-stock-synthesis-output-with-r4ss" class="nav-link" data-scroll-target="#viewing-stock-synthesis-output-with-r4ss">Viewing Stock Synthesis Output with {r4ss}</a></li>
+  <li><a href="#interacting-with-stock-synthesis-and-viewing-output-using-r4ss" id="toc-interacting-with-stock-synthesis-and-viewing-output-using-r4ss" class="nav-link" data-scroll-target="#interacting-with-stock-synthesis-and-viewing-output-using-r4ss">Interacting with Stock Synthesis and Viewing Output Using {r4ss}</a></li>
   <li><a href="#user-example-models" id="toc-user-example-models" class="nav-link" data-scroll-target="#user-example-models">User Example Models</a></li>
   </ul></li>
   <li><a href="#asking-questions-about-stock-synthesis" id="toc-asking-questions-about-stock-synthesis" class="nav-link" data-scroll-target="#asking-questions-about-stock-synthesis">Asking questions about Stock Synthesis</a></li>
@@ -246,7 +246,7 @@ <h1 class="title">Stock Synthesis (SS3) Website</h1>
 <p>Welcome to the Stock Synthesis (SS3) Website!</p>
 <section id="introduction" class="level2">
 <h2 class="anchored" data-anchor-id="introduction">Introduction</h2>
-<p>Stock Synthesis (SS3) is an age- and size-structured stock assessment model in the class of models termed integrated analysis. Stock Synthesis has evolved over time to be able to model a wide range of fish population dynamics and body growth, and to utilize diverse types of data. The model is coded in C++ with parameter estimation enabled by automatic differention though AD Model Builder <a href="https://www.admb-project.org/">ADMB</a>.</p>
+<p>Stock Synthesis (SS3) is an age- and size-structured stock assessment model in the class of models termed integrated analysis. Stock Synthesis has evolved over time to be able to model a wide range of fish population dynamics and body growth, and to utilize diverse types of data. The model is coded in C++ with parameter estimation enabled by automatic differentiation though AD Model Builder <a href="https://www.admb-project.org/">ADMB</a>.</p>
 <p>SS3 is made up of:</p>
 <ul>
 <li>A population sub-model that simulates a stock’s:
@@ -277,14 +277,14 @@ <h2 class="anchored" data-anchor-id="getting-started-with-stock-synthesis">Getti
 </div>
 <section id="getting-started-using-the-stock-assessment-continuum-tool" class="level3">
 <h3 class="anchored" data-anchor-id="getting-started-using-the-stock-assessment-continuum-tool">Getting Started Using the Stock Assessment Continuum Tool</h3>
-<p>If you are just getting started with Stock Synthesis, we highly recommend downloading the <a href="https://github.com/shcaba/SS-DL-tool">Stock Assessment Continuum Tool</a>, a shiny app interface where users can provide data and life history information to create the Stock Synthesis input files, run the model, and produce plots and tables via the <a href="https://github.com/r4ss/r4ss">{r4ss}</a> package.</p>
+<p>If you are just getting started with Stock Synthesis, we highly recommend downloading the <a href="https://github.com/shcaba/SS-DL-tool">Stock Assessment Continuum Tool</a>, a shiny app interface where users can provide data and life history information to create the Stock Synthesis input files, run the model, and produce plots and tables via the <a href="https://github.com/r4ss/r4ss">{r4ss}</a> package. <img src="qmds/images/stock_assess_cont_tool.png" class="img-fluid"></p>
 </section>
 <section id="getting-started-using-the-input-files" class="level3">
 <h3 class="anchored" data-anchor-id="getting-started-using-the-input-files">Getting Started Using the Input Files</h3>
 <p>To learn more about how to build your own models in Stock Synthesis using the input files directly, see the <a href="https://nmfs-ost.github.io/ss3-doc/ss3_model_tips.html">Develop a Stock Synthesis model</a> guide.</p>
 </section>
-<section id="viewing-stock-synthesis-output-with-r4ss" class="level3">
-<h3 class="anchored" data-anchor-id="viewing-stock-synthesis-output-with-r4ss">Viewing Stock Synthesis Output with {r4ss}</h3>
+<section id="interacting-with-stock-synthesis-and-viewing-output-using-r4ss" class="level3">
+<h3 class="anchored" data-anchor-id="interacting-with-stock-synthesis-and-viewing-output-using-r4ss">Interacting with Stock Synthesis and Viewing Output Using {r4ss}</h3>
 <div class="quarto-figure quarto-figure-right" style="float: right;">
 <figure class="figure">
 <p><img src="qmds/images/r4ss_logo.png" class="img-fluid figure-img" width="210"></p>
@@ -308,9 +308,6 @@ <h2 class="anchored" data-anchor-id="contributing-to-stock-synthesis">Contributi
 </section>
 <section id="tools-for-working-with-stock-synthesis" class="level2">
 <h2 class="anchored" data-anchor-id="tools-for-working-with-stock-synthesis">Tools for working with Stock Synthesis</h2>
-<div class="rstudio-cloud">
-<p>this is a test</p>
-</div>
 <p>As Stock Synthesis usage has grown, so has the number of tools to work with it. These include <a href="https://github.com/topics/stock-synthesis">repositories on GitHub with the stock-synthesis topic</a> as well as:</p>
 <ul>
 <li><a href="https://github.com/r4ss/r4ss">r4ss</a>: Create plots of Stock Synthesis output and functions to work with Stock Synthesis in R.</li>

search.json

@@ -186,7 +186,7 @@
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     "title": "Stock Synthesis (SS3) Website",
     "section": "Introduction",
-    "text": "Introduction\nStock Synthesis (SS3) is an age- and size-structured stock assessment model in the class of models termed integrated analysis. Stock Synthesis has evolved over time to be able to model a wide range of fish population dynamics and body growth, and to utilize diverse types of data. The model is coded in C++ with parameter estimation enabled by automatic differention though AD Model Builder ADMB.\nSS3 is made up of:\n\nA population sub-model that simulates a stock’s:\n\nBiology (growth, maturity, fecundity),\nRecruitment,\nMovement,\nFishery selectivity\nNatural and fishing mortality, and\nResponsiveness to environmental and predation factors.\n\nAn observation sub-model that estimates expected values for various types of data,\nA statistical sub-model characterizes the data’s goodness of fit and obtains best-fitting parameters with associated variance, and\nA forecast sub-model projects needed management quantities."
+    "text": "Introduction\nStock Synthesis (SS3) is an age- and size-structured stock assessment model in the class of models termed integrated analysis. Stock Synthesis has evolved over time to be able to model a wide range of fish population dynamics and body growth, and to utilize diverse types of data. The model is coded in C++ with parameter estimation enabled by automatic differentiation though AD Model Builder ADMB.\nSS3 is made up of:\n\nA population sub-model that simulates a stock’s:\n\nBiology (growth, maturity, fecundity),\nRecruitment,\nMovement,\nFishery selectivity\nNatural and fishing mortality, and\nResponsiveness to environmental and predation factors.\n\nAn observation sub-model that estimates expected values for various types of data,\nA statistical sub-model characterizes the data’s goodness of fit and obtains best-fitting parameters with associated variance, and\nA forecast sub-model projects needed management quantities."
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@@ -200,7 +200,7 @@
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     "title": "Stock Synthesis (SS3) Website",
     "section": "Getting Started with Stock Synthesis",
-    "text": "Getting Started with Stock Synthesis\nTo getting started with Stock Synthesis, please see the presentation below and the Getting Started with Stock Synthesis Tutorial:\n\n\n\n\n\n\nGetting Started Using the Stock Assessment Continuum Tool\nIf you are just getting started with Stock Synthesis, we highly recommend downloading the Stock Assessment Continuum Tool, a shiny app interface where users can provide data and life history information to create the Stock Synthesis input files, run the model, and produce plots and tables via the {r4ss} package.\n\n\nGetting Started Using the Input Files\nTo learn more about how to build your own models in Stock Synthesis using the input files directly, see the Develop a Stock Synthesis model guide.\n\n\nViewing Stock Synthesis Output with {r4ss}\n\n\n\n\n\nThe {r4ss} package is a collection of R functions for interacting with Stock Synthesis. These functions include downloading the executable, changing model input, running the model, and creating an assortment of model plots and tables. More information about using r4ss is available in the “Introduction to r4ss” vignette as well as example plots created with {r4ss} (these plots were created usingthe Big Skate model found in the ss3-test-models repository).\n\n\nUser Example Models\nWe maintain a GitHub repository of example stock synthesis models for users. Information on what the key features of the user example models and how to download can be found here."
+    "text": "Getting Started with Stock Synthesis\nTo getting started with Stock Synthesis, please see the presentation below and the Getting Started with Stock Synthesis Tutorial:\n\n\n\n\n\n\nGetting Started Using the Stock Assessment Continuum Tool\nIf you are just getting started with Stock Synthesis, we highly recommend downloading the Stock Assessment Continuum Tool, a shiny app interface where users can provide data and life history information to create the Stock Synthesis input files, run the model, and produce plots and tables via the {r4ss} package. \n\n\nGetting Started Using the Input Files\nTo learn more about how to build your own models in Stock Synthesis using the input files directly, see the Develop a Stock Synthesis model guide.\n\n\nInteracting with Stock Synthesis and Viewing Output Using {r4ss}\n\n\n\n\n\nThe {r4ss} package is a collection of R functions for interacting with Stock Synthesis. These functions include downloading the executable, changing model input, running the model, and creating an assortment of model plots and tables. More information about using r4ss is available in the “Introduction to r4ss” vignette as well as example plots created with {r4ss} (these plots were created usingthe Big Skate model found in the ss3-test-models repository).\n\n\nUser Example Models\nWe maintain a GitHub repository of example stock synthesis models for users. Information on what the key features of the user example models and how to download can be found here."
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@@ -221,7 +221,7 @@
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     "title": "Stock Synthesis (SS3) Website",
     "section": "Tools for working with Stock Synthesis",
-    "text": "Tools for working with Stock Synthesis\n\nthis is a test\n\nAs Stock Synthesis usage has grown, so has the number of tools to work with it. These include repositories on GitHub with the stock-synthesis topic as well as:\n\nr4ss: Create plots of Stock Synthesis output and functions to work with Stock Synthesis in R.\nss3diags: Run advanced diagnostics for Stock Synthesis models.\nss3sim: Conduct simulation studies using Stock Synthesis.\nSSI: Stock Synthesis Interface, a GUI for developing models and running Stock Synthesis. Links to r4ss.\nSS3 Shiny helper app: Visualize common selectivity pattern options available within Stock Synthesis.\nSSMSE: Use Stock Synthesis operating models in Management Strategy Evaluation.\nsa4ss: Create accessible R markdown stock assessment documents with results from Stock Synthesis models. Note this tool is intended for use by analysts within the Northwest and Southwest Fisheries Science Centers currently.\nData limited tools - Options included Simple Stock Synthesis (SSS) and Extended Simple Stock Synthesis (XSSS), as well as SS-DL-tool, a shiny app that includes XSSS and SSS in its functionality.\n\nHave a tool to work with Stock Synthesis that should be mentioned here? Open an issue or pull request to let us know!"
+    "text": "Tools for working with Stock Synthesis\nAs Stock Synthesis usage has grown, so has the number of tools to work with it. These include repositories on GitHub with the stock-synthesis topic as well as:\n\nr4ss: Create plots of Stock Synthesis output and functions to work with Stock Synthesis in R.\nss3diags: Run advanced diagnostics for Stock Synthesis models.\nss3sim: Conduct simulation studies using Stock Synthesis.\nSSI: Stock Synthesis Interface, a GUI for developing models and running Stock Synthesis. Links to r4ss.\nSS3 Shiny helper app: Visualize common selectivity pattern options available within Stock Synthesis.\nSSMSE: Use Stock Synthesis operating models in Management Strategy Evaluation.\nsa4ss: Create accessible R markdown stock assessment documents with results from Stock Synthesis models. Note this tool is intended for use by analysts within the Northwest and Southwest Fisheries Science Centers currently.\nData limited tools - Options included Simple Stock Synthesis (SSS) and Extended Simple Stock Synthesis (XSSS), as well as SS-DL-tool, a shiny app that includes XSSS and SSS in its functionality.\n\nHave a tool to work with Stock Synthesis that should be mentioned here? Open an issue or pull request to let us know!"
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