diff --git a/404.html b/404.html
index 68f480b..a27a2c6 100644
--- a/404.html
+++ b/404.html
@@ -31,7 +31,7 @@
     
     <a class="navbar-brand me-2" href="https://pifscstockassessments.github.io/ss3diags/index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CODE_OF_CONDUCT.html b/CODE_OF_CONDUCT.html
index 1bc1f34..aae12c5 100644
--- a/CODE_OF_CONDUCT.html
+++ b/CODE_OF_CONDUCT.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
index 5f19ebd..657d6a5 100644
--- a/CONTRIBUTING.html
+++ b/CONTRIBUTING.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/Jitter.html b/articles/Jitter.html
index 70ddc30..ef57a61 100644
--- a/articles/Jitter.html
+++ b/articles/Jitter.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -137,7 +137,7 @@ <h2 id="model-inputs">Model inputs<a class="anchor" aria-label="anchor" href="#m
 <code>r4ss</code> function <code><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe()</a></code>.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">r4ss</span><span class="fu">::</span><span class="fu"><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe</a></span><span class="op">(</span>dir <span class="op">=</span> <span class="va">dir_jitter</span>, version <span class="op">=</span> <span class="st">"v3.30.21"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmp6Xyarr/jitter/ss3</span></span></code></pre></div>
+<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmp2ZDhQV/jitter/ss3</span></span></code></pre></div>
 <p>We will run the model in <code>dir_jitter</code> first to produce the
 necessary output files. It is recommended to do jitter runs in a
 subdirectory of your model run. This will keep all of the output files
@@ -206,13 +206,13 @@ <h2 id="jitter">Jitter<a class="anchor" aria-label="anchor" href="#jitter"></a>
 <span><span class="co">#&gt;      replist18    replist19    replist20    replist21    replist22    replist23</span></span>
 <span><span class="co">#&gt; 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02</span></span>
 <span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10</span></span>
-<span><span class="co">#&gt; 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01</span></span>
+<span><span class="co">#&gt; 3  1.74852e-01  1.74852e-01  1.74853e-01  1.74852e-01  1.74852e-01  1.74852e-01</span></span>
 <span><span class="co">#&gt; 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00</span></span>
 <span><span class="co">#&gt; 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02</span></span>
 <span><span class="co">#&gt; 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02</span></span>
 <span><span class="co">#&gt;      replist24    replist25    replist26    replist27    replist28    replist29</span></span>
 <span><span class="co">#&gt; 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02</span></span>
-<span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10</span></span>
+<span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33480e-10  1.33479e-10</span></span>
 <span><span class="co">#&gt; 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01</span></span>
 <span><span class="co">#&gt; 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00</span></span>
 <span><span class="co">#&gt; 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02</span></span>
@@ -226,7 +226,7 @@ <h2 id="jitter">Jitter<a class="anchor" aria-label="anchor" href="#jitter"></a>
 <span><span class="co">#&gt; 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02</span></span>
 <span><span class="co">#&gt;      replist36    replist37    replist38    replist39    replist40    replist41</span></span>
 <span><span class="co">#&gt; 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02</span></span>
-<span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10</span></span>
+<span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33480e-10  1.33479e-10</span></span>
 <span><span class="co">#&gt; 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01</span></span>
 <span><span class="co">#&gt; 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00</span></span>
 <span><span class="co">#&gt; 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02</span></span>
@@ -241,7 +241,7 @@ <h2 id="jitter">Jitter<a class="anchor" aria-label="anchor" href="#jitter"></a>
 <span><span class="co">#&gt;      replist48    replist49    replist50       Label</span></span>
 <span><span class="co">#&gt; 1  7.54302e+02  7.54302e+02  7.54302e+02       TOTAL</span></span>
 <span><span class="co">#&gt; 2  1.33479e-10  1.33479e-10  1.33479e-10       Catch</span></span>
-<span><span class="co">#&gt; 3  1.74852e-01  1.74852e-01  1.74852e-01 Equil_catch</span></span>
+<span><span class="co">#&gt; 3  1.74853e-01  1.74852e-01  1.74852e-01 Equil_catch</span></span>
 <span><span class="co">#&gt; 4 -7.11813e+00 -7.11813e+00 -7.11813e+00      Survey</span></span>
 <span><span class="co">#&gt; 5  3.66756e+02  3.66756e+02  3.66756e+02 Length_comp</span></span>
 <span><span class="co">#&gt; 6  2.31845e+02  2.31845e+02  2.31845e+02    Age_comp</span></span>
diff --git a/articles/Retrospective-Analysis.html b/articles/Retrospective-Analysis.html
index b7e7f9b..c8d816d 100644
--- a/articles/Retrospective-Analysis.html
+++ b/articles/Retrospective-Analysis.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -134,7 +134,7 @@ <h2 id="model-inputs">Model inputs<a class="anchor" aria-label="anchor" href="#m
 <code>r4ss</code> function <code><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe()</a></code>.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">r4ss</span><span class="fu">::</span><span class="fu"><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe</a></span><span class="op">(</span>dir <span class="op">=</span> <span class="va">dir_retro</span>, version <span class="op">=</span> <span class="st">"v3.30.21"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpUqXETR/retrospectives/ss3</span></span></code></pre></div>
+<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpWMaip6/retrospectives/ss3</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="retrospective-analysis">Retrospective Analysis<a class="anchor" aria-label="anchor" href="#retrospective-analysis"></a>
diff --git a/articles/aspm.html b/articles/aspm.html
index 81f0d54..ec4641c 100644
--- a/articles/aspm.html
+++ b/articles/aspm.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -134,7 +134,7 @@ <h2 id="model-inputs">Model inputs<a class="anchor" aria-label="anchor" href="#m
 <code>r4ss</code> function <code><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe()</a></code>.</p>
 <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">r4ss</span><span class="fu">::</span><span class="fu"><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe</a></span><span class="op">(</span>dir <span class="op">=</span> <span class="va">dir_tmp</span>, version <span class="op">=</span> <span class="st">"v3.30.21"</span><span class="op">)</span></span></code></pre></div>
-<pre><code><span><span class="co">## The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmpb2T15m/ss3</span></span></code></pre>
+<pre><code><span><span class="co">## The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpOZxxeY/ss3</span></span></code></pre>
 </div>
 <div class="section level2">
 <h2 id="aspm">ASPM<a class="anchor" aria-label="anchor" href="#aspm"></a>
diff --git a/articles/hcxval.html b/articles/hcxval.html
index 4762ed7..34d076c 100644
--- a/articles/hcxval.html
+++ b/articles/hcxval.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/index.html b/articles/index.html
index 4217cfc..e2c3493 100644
--- a/articles/index.html
+++ b/articles/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/likelihood.html b/articles/likelihood.html
index eb2f6d7..948dba9 100644
--- a/articles/likelihood.html
+++ b/articles/likelihood.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -135,7 +135,7 @@ <h2 id="model-inputs">Model inputs<a class="anchor" aria-label="anchor" href="#m
 <code>r4ss</code> function <code><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe()</a></code>.</p>
 <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
 <code class="sourceCode R"><span><span class="fu">r4ss</span><span class="fu">::</span><span class="fu"><a href="https://r4ss.github.io/r4ss/reference/get_ss3_exe.html" class="external-link">get_ss3_exe</a></span><span class="op">(</span>dir <span class="op">=</span> <span class="va">dir_tmp</span>, version <span class="op">=</span> <span class="st">"v3.30.21"</span><span class="op">)</span></span>
-<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpakzV4r/ss3</span></span></code></pre></div>
+<span><span class="co">#&gt; The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpnhVp2Y/ss3</span></span></code></pre></div>
 </div>
 <div class="section level2">
 <h2 id="running-a-profile-on-r0">Running a Profile on R<sub>0</sub><a class="anchor" aria-label="anchor" href="#running-a-profile-on-r0"></a>
diff --git a/articles/residuals.html b/articles/residuals.html
index 2251506..c65b157 100644
--- a/articles/residuals.html
+++ b/articles/residuals.html
@@ -33,7 +33,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/articles/residuals_files/figure-html/unnamed-chunk-6-1.png b/articles/residuals_files/figure-html/unnamed-chunk-6-1.png
index fedb098..712ab11 100644
Binary files a/articles/residuals_files/figure-html/unnamed-chunk-6-1.png and b/articles/residuals_files/figure-html/unnamed-chunk-6-1.png differ
diff --git a/authors.html b/authors.html
index 7ad3c4a..2116ec5 100644
--- a/authors.html
+++ b/authors.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -89,13 +89,13 @@ <h2 id="citation">Citation</h2>
 
       <p>Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E (2024).
 <em>ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments</em>.
-R package version 2.1.1, <a href="https://github.com/PIFSCstockassessments/ss3diags" class="external-link">https://github.com/PIFSCstockassessments/ss3diags</a>. 
+R package version 2.2.0, <a href="https://github.com/PIFSCstockassessments/ss3diags" class="external-link">https://github.com/PIFSCstockassessments/ss3diags</a>. 
 </p>
       <pre>@Manual{,
   title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments},
   author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher},
   year = {2024},
-  note = {R package version 2.1.1},
+  note = {R package version 2.2.0},
   url = {https://github.com/PIFSCstockassessments/ss3diags},
 }</pre>
     </div>
diff --git a/index.html b/index.html
index f434341..6886240 100644
--- a/index.html
+++ b/index.html
@@ -37,7 +37,7 @@
     
     <a class="navbar-brand me-2" href="index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/news/index.html b/news/index.html
index 55fd9aa..52ebe50 100644
--- a/news/index.html
+++ b/news/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@@ -55,6 +55,28 @@
       <small>Source: <a href="https://github.com/PIFSCstockassessments/ss3diags/blob/HEAD/NEWS.md" class="external-link"><code>NEWS.md</code></a></small>
     </div>
 
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2.2.0" id="ss3diags-220">ss3diags 2.2.0<a class="anchor" aria-label="anchor" href="#ss3diags-220"></a></h2>
+<ul><li>Add vignettes tutorials for implementing and interpreting diagnostic analyses (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/78" class="external-link">#78</a>, <a href="https://github.com/PIFSCstockassessments/ss3diags/issues/75" class="external-link">#75</a>, <a href="https://github.com/PIFSCstockassessments/ss3diags/issues/73" class="external-link">#73</a>, and <a href="https://github.com/PIFSCstockassessments/ss3diags/issues/68" class="external-link">#68</a>). The vignettes replaced the “Cookbook recipe” R scripts with updated code.</li>
+<li>Removed Rdata files (ss3diags::simple, ss3diags::retroSimple, and ss3diags::mcmcSimple). These objects are now automatically produced in the vignettes.</li>
+<li>Removed deprecated data objects from function arguments (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/100" class="external-link">#100</a>).</li>
+<li>Created generic functions to re-use common parameter documentation via roxygen tag <a href="https://github.com/inheritParams" class="external-link">@inheritParams</a> (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/66" class="external-link">#66</a> and <a href="https://github.com/PIFSCstockassessments/ss3diags/issues/2" class="external-link">#2</a>).</li>
+<li>Update r4ss dependency.</li>
+<li>Replacing installation of SS3 in container during R-CMD-Check GitHub Action workflow to use r4ss::get_ss_exe() (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/97" class="external-link">#97</a>).</li>
+</ul></div>
+    <div class="section level2">
+<h2 class="pkg-version" data-toc-text="2.1.1" id="ss3diags-211">ss3diags 2.1.1<a class="anchor" aria-label="anchor" href="#ss3diags-211"></a></h2>
+<ul><li>Added new logo. Thanks <a href="https://github.com/pdimens" class="external-link">@pdimens</a> (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/76" class="external-link">#76</a>, <a href="https://github.com/PIFSCstockassessments/ss3diags/issues/77" class="external-link">#77</a>)</li>
+<li>Added options to <code>SSdeltaMVLN</code> for Variance-Coveriance approximation and bias correction. Thanks <a href="https://github.com/N-DucharmeBarth-NOAA" class="external-link">@N-DucharmeBarth-NOAA</a> (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/64" class="external-link">#64</a>)</li>
+<li>Updated r4ss dependency (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/84" class="external-link">#84</a>)
+<ul><li>Dependency resolves r4ss function name conflicts w/ dplyr and kableExtra libraries (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/83" class="external-link">#83</a>). Side effect of nmfs-fish-tools/ghactions4r#69</li>
+</ul></li>
+<li>Removed <code>dplyr</code> from NAMESPACE. Removed roxygen import calls from <code><a href="../reference/SSplotJABBAres.html">SSplotJABBAres()</a></code> and <code><a href="../reference/SSrmse.html">SSrmse()</a></code>, and appended <strong>dplyr</strong> function calls with the double colon operator (<code>dplyr::</code>) (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/82" class="external-link">#82</a>)</li>
+<li>Updated default <strong>summaryoutput</strong> used in <code>SSplotModelComp()</code> for <code>ss3diags::retroSimple</code> and default <strong>ss3rep</strong> used in <code>SSplotRunsTest()</code> for <code>ss3diags::simple</code>
+</li>
+<li>Updated ss3diags citation.</li>
+<li>Minor documentation link fixes.</li>
+</ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="2.1.0" id="ss3diags-210">ss3diags 2.1.0<a class="anchor" aria-label="anchor" href="#ss3diags-210"></a></h2>
 <ul><li>RMSE calculations are modularized as a standalone function that can be called independently from <code><a href="../reference/SSplotJABBAres.html">SSplotJABBAres()</a></code> as <code><a href="../reference/SSrmse.html">SSrmse()</a></code>. (<a href="https://github.com/PIFSCstockassessments/ss3diags/issues/50" class="external-link">#50</a>)</li>
diff --git a/pkgdown.yml b/pkgdown.yml
index 803622e..061eae9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -8,7 +8,7 @@ articles:
   hcxval: hcxval.html
   likelihood: likelihood.html
   residuals: residuals.html
-last_built: 2024-02-16T20:40Z
+last_built: 2024-02-16T21:28Z
 urls:
   reference: https://pifscstockassessments.github.io/ss3diags/reference
   article: https://pifscstockassessments.github.io/ss3diags/articles
diff --git a/reference/SScompsTA1.8.html b/reference/SScompsTA1.8.html
index 9c1400a..6149d2a 100644
--- a/reference/SScompsTA1.8.html
+++ b/reference/SScompsTA1.8.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSdeltaMVLN.html b/reference/SSdeltaMVLN.html
index 991662f..e53a9c0 100644
--- a/reference/SSdeltaMVLN.html
+++ b/reference/SSdeltaMVLN.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSdeltaMVLN_old.html b/reference/SSdeltaMVLN_old.html
index 3d47c66..a286a20 100644
--- a/reference/SSdeltaMVLN_old.html
+++ b/reference/SSdeltaMVLN_old.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSdiagsMCMC.html b/reference/SSdiagsMCMC.html
index 5695475..775900c 100644
--- a/reference/SSdiagsMCMC.html
+++ b/reference/SSdiagsMCMC.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSdiagsMCMC_ancient.html b/reference/SSdiagsMCMC_ancient.html
index 936b406..4bef435 100644
--- a/reference/SSdiagsMCMC_ancient.html
+++ b/reference/SSdiagsMCMC_ancient.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SShcbias.html b/reference/SShcbias.html
index 65d558d..88a19a6 100644
--- a/reference/SShcbias.html
+++ b/reference/SShcbias.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSmase.html b/reference/SSmase.html
index 53c51d0..2174959 100644
--- a/reference/SSmase.html
+++ b/reference/SSmase.html
@@ -16,7 +16,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotEnsemble.html b/reference/SSplotEnsemble.html
index 4628a16..c59d54a 100644
--- a/reference/SSplotEnsemble.html
+++ b/reference/SSplotEnsemble.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotGeneric.html b/reference/SSplotGeneric.html
index d8852a3..11c542f 100644
--- a/reference/SSplotGeneric.html
+++ b/reference/SSplotGeneric.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotGenericLegend.html b/reference/SSplotGenericLegend.html
index 0ff4497..0d2a66c 100644
--- a/reference/SSplotGenericLegend.html
+++ b/reference/SSplotGenericLegend.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotGenericPar.html b/reference/SSplotGenericPar.html
index 190cc20..255dcfe 100644
--- a/reference/SSplotGenericPar.html
+++ b/reference/SSplotGenericPar.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotGenericUncertainty.html b/reference/SSplotGenericUncertainty.html
index b8f7376..20eb0bc 100644
--- a/reference/SSplotGenericUncertainty.html
+++ b/reference/SSplotGenericUncertainty.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotHCxval.html b/reference/SSplotHCxval.html
index 668b98b..e31b751 100644
--- a/reference/SSplotHCxval.html
+++ b/reference/SSplotHCxval.html
@@ -20,7 +20,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotJABBAres.html b/reference/SSplotJABBAres.html
index 709af01..1fee3f6 100644
--- a/reference/SSplotJABBAres.html
+++ b/reference/SSplotJABBAres.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotKobe.html b/reference/SSplotKobe.html
index 2de7b71..5ca8ca2 100644
--- a/reference/SSplotKobe.html
+++ b/reference/SSplotKobe.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotModelcomp.html b/reference/SSplotModelcomp.html
index 167dc19..74d3bdb 100644
--- a/reference/SSplotModelcomp.html
+++ b/reference/SSplotModelcomp.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotRetro.html b/reference/SSplotRetro.html
index 85d1ef5..eb90da2 100644
--- a/reference/SSplotRetro.html
+++ b/reference/SSplotRetro.html
@@ -12,7 +12,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSplotRunstest.html b/reference/SSplotRunstest.html
index 70e47ba..242ce5b 100644
--- a/reference/SSplotRunstest.html
+++ b/reference/SSplotRunstest.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSreadMCMC.html b/reference/SSreadMCMC.html
index 72d7bba..8492dc1 100644
--- a/reference/SSreadMCMC.html
+++ b/reference/SSreadMCMC.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSretroComps.html b/reference/SSretroComps.html
index 6b8381f..24638e6 100644
--- a/reference/SSretroComps.html
+++ b/reference/SSretroComps.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSrmse.html b/reference/SSrmse.html
index e1428e1..5c432ad 100644
--- a/reference/SSrmse.html
+++ b/reference/SSrmse.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSrunstest.html b/reference/SSrunstest.html
index 84e5f54..c83443a 100644
--- a/reference/SSrunstest.html
+++ b/reference/SSrunstest.html
@@ -18,7 +18,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/SSsettingsBratioF.html b/reference/SSsettingsBratioF.html
index de452b5..68d1737 100644
--- a/reference/SSsettingsBratioF.html
+++ b/reference/SSsettingsBratioF.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ensemble_plot_index.html b/reference/ensemble_plot_index.html
index b65fa53..519dd35 100644
--- a/reference/ensemble_plot_index.html
+++ b/reference/ensemble_plot_index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/index.html b/reference/index.html
index 029d6b2..345c663 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -10,7 +10,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/reference/ssruns_sig3.html b/reference/ssruns_sig3.html
index d9751fe..2d99411 100644
--- a/reference/ssruns_sig3.html
+++ b/reference/ssruns_sig3.html
@@ -14,7 +14,7 @@
     
     <a class="navbar-brand me-2" href="../index.html">ss3diags</a>
 
-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.2.0</small>
 
     
     <button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
diff --git a/search.json b/search.json
index 97d6002..202cce3 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://pifscstockassessments.github.io/ss3diags/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Code of Conduct","title":"Code of Conduct","text":"follow NFMS Fisheries Toolbox Code Conduct. NFMS Fisheries Toolbox Code Conduct adapted Contributor Covenant, version 1.4, available https://www.contributor-covenant.org/version/1/4/code--conduct.html answers common questions code conduct, see https://www.contributor-covenant.org/faq","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to ss3diags","title":"Contributing to ss3diags","text":"Thank interest contributing! strive follow NMFS Fisheries Toolbox Contribution Guide. Note guidelines, rules, open collaborations ways may work better . Please feel free reach us opening issue repository emailing project maintatainer megumi.oshima@noaa.gov. project everyone participating governed NMFS Fisheries Toolbox Code Conduct. participating, expected uphold code. Please report unacceptable behavior fisheries.toolbox@noaa.gov. Note maintainers ss3diags access email account, unacceptable behavior maintainers can also reported .","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Jitter Analysis","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running retrospective (case dir_jitter). easy way get latest release stock synthesis use r4ss function get_ss3_exe(). run model dir_jitter first produce necessary output files. recommended jitter runs subdirectory model run. keep output files separate diagnostic tests may run.","code":"install_github(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_jitter <- file.path(tempdir(check = TRUE), \"jitter\") dir.create(dir_jitter, showWarnings = FALSE, recursive = TRUE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_jitter) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_jitter, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmp6Xyarr/jitter/ss3 r4ss::run(dir = dir_jitter, exe = \"ss3\", verbose = FALSE) #> [1] \"ran model\""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"jitter","dir":"Articles","previous_headings":"","what":"Jitter","title":"Jitter Analysis","text":"example, run 50 jitters. jitter() function automates entire process need give arguments run produce total likelihoods run. Full documentation jitter() function can found r4ss website. analyze output 50 runs, use r4ss::SSgetoutput() r4ss::SSsummarize() shown . key sections may want check compare across models , likelihoods, derived quantities, estimated parameters. may also want check models converged. can check maximum gradients make sure small (< 0.0001). can also compare estimated spawning biomass, extreme values (+2x <0.5x base spawning biomass) suggests model didn’t converge.","code":"Njitter <- 50 jit.likes <- r4ss::jitter(   dir = dir_jitter,   Njitter = Njitter,   init_values_src = 1,   jitter_fraction = 0.1,   exe = \"ss3\",   printlikes = FALSE,   verbose = FALSE ) jit_mods <- SSgetoutput(   keyvec = 0:Njitter, # 0 to include reference run (Report0.sso)   getcomp = FALSE,   dirvec = dir_jitter,   getcovar = FALSE,   verbose = FALSE ) jit_summary <- SSsummarize(jit_mods, verbose = FALSE) head(jit_summary$likelihoods) #>       replist0     replist1     replist2     replist3     replist4     replist5 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>       replist6     replist7     replist8     replist9    replist10    replist11 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist12    replist13    replist14    replist15    replist16    replist17 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist18    replist19    replist20    replist21    replist22    replist23 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist24    replist25    replist26    replist27    replist28    replist29 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist30    replist31    replist32    replist33    replist34    replist35 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist36    replist37    replist38    replist39    replist40    replist41 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist42    replist43    replist44    replist45    replist46    replist47 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist48    replist49    replist50       Label #> 1  7.54302e+02  7.54302e+02  7.54302e+02       TOTAL #> 2  1.33479e-10  1.33479e-10  1.33479e-10       Catch #> 3  1.74852e-01  1.74852e-01  1.74852e-01 Equil_catch #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00      Survey #> 5  3.66756e+02  3.66756e+02  3.66756e+02 Length_comp #> 6  2.31845e+02  2.31845e+02  2.31845e+02    Age_comp head(jit_summary$quants) #>   replist0 replist1 replist2 replist3 replist4 replist5 replist6 replist7 #> 1  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8 #> 2  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4 #> 3  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4 #> 4  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1 #> 5  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1 #> 6  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5 #>   replist8 replist9 replist10 replist11 replist12 replist13 replist14 replist15 #> 1  54773.8  54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2  26071.4  26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3  26071.4  26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4  24096.1  24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5  22126.1  22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6  20143.5  20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist16 replist17 replist18 replist19 replist20 replist21 replist22 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist23 replist24 replist25 replist26 replist27 replist28 replist29 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist30 replist31 replist32 replist33 replist34 replist35 replist36 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist37 replist38 replist39 replist40 replist41 replist42 replist43 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist44 replist45 replist46 replist47 replist48 replist49 replist50 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>         Label   Yr #> 1  SSB_Virgin   NA #> 2 SSB_Initial   NA #> 3    SSB_2011 2011 #> 4    SSB_2012 2012 #> 5    SSB_2013 2013 #> 6    SSB_2014 2014 head(jit_summary$pars) #>    replist0  replist1  replist2  replist3  replist4  replist5  replist6 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>    replist7  replist8  replist9 replist10 replist11 replist12 replist13 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist14 replist15 replist16 replist17 replist18 replist19 replist20 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist21 replist22 replist23 replist24 replist25 replist26 replist27 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist28 replist29 replist30 replist31 replist32 replist33 replist34 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist35 replist36 replist37 replist38 replist39 replist40 replist41 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist42 replist43 replist44 replist45 replist46 replist47 replist48 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist49 replist50                 Label Yr recdev #> 1  0.100000  0.100000 NatM_uniform_Fem_GP_1 NA  FALSE #> 2 22.769000 22.769000    L_at_Amin_Fem_GP_1 NA  FALSE #> 3 71.807200 71.807200    L_at_Amax_Fem_GP_1 NA  FALSE #> 4  0.142165  0.142165    VonBert_K_Fem_GP_1 NA  FALSE #> 5  0.100000  0.100000     CV_young_Fem_GP_1 NA  FALSE #> 6  0.100000  0.100000       CV_old_Fem_GP_1 NA  FALSE # Maximum gradient converged_grad <- which(jit_summary$maxgrad < 0.0001)  converged_ssb <- jit_summary$SpawnBio %>%   mutate(across(c(1:(Njitter + 1)),     .fns = ~ . / replist0   )) %>% # for each column, divide SSB by SSB from the reference run (replist)   select(-Label) %>%   pivot_longer(col = c(1:(Njitter + 1)), names_to = \"jitter\", values_to = \"SSB\") %>%   pivot_wider(names_from = Yr, values_from = SSB) %>%   mutate(rownumber = seq(1, nrow(.))) %>%   tibble::column_to_rownames(\"jitter\") %>%   filter_at(vars(1:(ncol(.) - 1)), all_vars((.) < 2 & (.) > 0.5)) %>% # keep only rows where SSB is a reasonable value   select(rownumber) %>%   pull(rownumber) converged_mods <- intersect(converged_grad, converged_ssb) # getting which models are in both groups converged_jitters <- jit_mods[converged_grad] converged_sum <- SSsummarize(converged_jitters, verbose = FALSE)"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Jitter Analysis","text":"compare likelihoods runs, plot shown . built functions (writing vignette) r4ss ss3diags generate likelihood plot, therefore provide code tidyverse syntax (using ggplot2) visualize results.  figure plots total likelihood jitter run red line indicates total likelihood value reference run. runs points red line, use converged parameter values run lowest likelihood value starting values base model. can also use r4ss::SSplotComparisons() compare spawning biomass trajectories jitter runs see impact different parameter values estimated quantities.","code":"converged_sum$likelihoods %>%   filter(str_detect(Label, \"TOTAL\")) %>%   select(-Label) %>%   pivot_longer(cols = everything(), names_to = \"jitter\", values_to = \"likelihood\") %>%   separate(jitter, into = c(\"replist\", \"jitter\"), sep = \"(?<=[A-Za-z])(?=[0-9])\") %>%   mutate(jitter = as.numeric(jitter)) %>%   ggplot(aes(x = jitter, y = likelihood)) +   geom_point(size = 3) +   geom_hline(aes(yintercept = likelihood[1]), color = \"red\") +   theme_classic() +   labs(     y = \"Total Likelihood\",     x = \"Jitter runs at a converged solution\"   ) SSplotComparisons(converged_sum,   subplots = 2,   ylimAdj = 1,   new = FALSE ) #> showing uncertainty for all models #> subplot 2: spawning biomass with uncertainty intervals"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Retrospective Analysis","text":"run stock synthesis model, 4 input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running retrospective (case dir_retro). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_retro <- file.path(tempdir(check = TRUE), \"retrospectives\") dir.create(dir_retro, showWarnings = FALSE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_retro) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_retro, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpUqXETR/retrospectives/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"retrospective-analysis","dir":"Articles","previous_headings":"","what":"Retrospective Analysis","title":"Retrospective Analysis","text":"4 input files SS executable file, can run retrospective analysis shown . running five one-year peels, run, one five years data removed reference model model re-run total five times (.e. peel 1 removes last year data, peel 2 removes last 2 years data, etc.) . number year peels can adjusted years argument. SS executable file using named something “ss3” (e.g. ss_opt_win.exe), need specify argument exe = \"ss_opt_win\". Full documentation retro() function can found r4ss website.","code":"r4ss::retro(dir = dir_retro, exe = \"ss3\", years = 0:-5, verbose = FALSE) #> Warning in base::sink(type = \"output\", split = FALSE): no sink to remove"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Retrospective Analysis","text":"visualize outputted results inspect retrospective patterns, need load report files R use SSplotRetro() function ss3diags. easiest way load multiple report files using r4ss::SSgetoutput() r4ss::SSsummarize() functions. default sub-directories peel, 0 5, labeled retro0 retro-5.  default settings plot spawning stock biomass time series peel, reference run (.e. original, full time series model) “Ref” line successive peel colored lines labeled terminal year value. solid line ends terminal year followed dashed line extending circle representing one year forecast estimate. Displaying projected SSB value helps assessing forecast bias. note, forecasts done automatically using r4ss::retro() based settings forecast.ss. grey shaded area represents 95% confidence intervals uncertainty around spawning biomass time series. Displayed center plot combined Mohn’s \\(\\rho\\) retrospective runs, parentheses forecast Mohn’s \\(\\rho\\).","code":"retro_mods <- r4ss::SSgetoutput(dirvec = file.path(dir_retro, \"retrospectives\", paste0(\"retro\", seq(0, -5, by = -1))), verbose = F) retroSummary <- r4ss::SSsummarize(retro_mods, verbose = F) SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE) #> Mohn's Rho stats, including one step ahead forecasts: #>   type     peel         Rho  ForecastRho #> 1  SSB     2021 -0.20753686 -0.221050163 #> 2  SSB     2020 -0.19601072 -0.227304734 #> 3  SSB     2019 -0.29238505 -0.338600758 #> 4  SSB     2018 -0.00474920 -0.007462034 #> 5  SSB     2017  0.08716428  0.098849082 #> 6  SSB Combined -0.12270351 -0.139113722"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Visualizing Output","what":"Customizing the Plot","title":"Retrospective Analysis","text":"Retro plots can customized many ways, common features may want specify : removing uncertainty intervals adjusting years shown x-axis turning 1-year ahead forecasting displaying combined \\(\\rho\\) value plot Examples changes shown , incrementally making adjustment.  Additionally, fishing mortality can plotted instead spawning biomass replacing subplots = \"SSB\" subplots = \"F\"","code":"r4ss::sspar(mfrow = c(2, 2), plot.cex = 0.8) retro1 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE) #> Mohn's Rho stats, including one step ahead forecasts: retro2 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022)) #> Mohn's Rho stats, including one step ahead forecasts: retro3 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022), forecast = FALSE) #> Mohn's Rho stats, including one step ahead forecasts: retro4 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022), forecast = FALSE, showrho = FALSE, forecastrho = FALSE) #> Mohn's Rho stats, including one step ahead forecasts:"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"summary-table","dir":"Articles","previous_headings":"Visualizing Output","what":"Summary Table","title":"Retrospective Analysis","text":"addition retrospective plots, summary statistics table can produced using SShcbias(). table includes type estimate (SSB F) year removed “peel” Mohn’s \\(\\rho\\) forecast bias year overall (“Combined”). Mohn’s \\(\\rho\\) measure severity bias retrospective patterns forecast bias estimate bias forecasted quantities years data removed. rule thumb proposed Hurtado-Ferror et al. (2014) Mohn’s \\(\\rho\\) values long-lived species, \\(\\rho\\) value fall -0.15 0.20.","code":"SShcbias(retroSummary) #> Mohn's Rho stats, including one step ahead forecasts: #>    type     peel         Rho   ForcastRho #> 1   SSB     2021 -0.20753686 -0.221050163 #> 2   SSB     2020 -0.19601072 -0.227304734 #> 3   SSB     2019 -0.29238505 -0.338600758 #> 4   SSB     2018 -0.00474920 -0.007462034 #> 5   SSB     2017  0.08716428  0.098849082 #> 6   SSB Combined -0.12270351 -0.139113722 #> 7     F     2021  0.28425747  0.285936183 #> 8     F     2020  0.30941305  0.349748774 #> 9     F     2019  0.52629045  0.632574831 #> 10    F     2018  0.01822898  0.022822958 #> 11    F     2017 -0.04896989 -0.053882358 #> 12    F Combined  0.21784401  0.247440078"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"ASPM","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running ASPM (case dir_aspm). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_tmp <- tempdir(check = TRUE) dir_aspm <- file.path(dir_tmp, \"aspm\") dir.create(dir_aspm, showWarnings = FALSE, recursive = TRUE) list.files(files_path) ## [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_tmp) ## [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_tmp, version = \"v3.30.21\") ## The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmpb2T15m/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"aspm","dir":"Articles","previous_headings":"","what":"ASPM","title":"ASPM","text":"4 input files, need determine components need turned run ASPM. ASPM depend index abundance catch data, composition data, recruitment deviations, etc. need turned . provide example includes multiple types data recruitment deviations, however, exact steps necessary individual model may vary depending complexity components included. Therefore steps may fully comprehensive model sure check components may need change. , show use r4ss functions make necessary changes control.ss ss.par files.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"generate-files","dir":"Articles","previous_headings":"ASPM","what":"Generate files","title":"ASPM","text":"order get ss.par file, need run model . also produce new data control file use input files. run model dir_tmp copy new files dir_aspm.","code":"r4ss::run(dir = dir_tmp, verbose = FALSE, exe = \"ss3\") ## [1] \"ran model\" files <- c(\"data_echo.ss_new\", \"control.ss_new\", \"starter.ss\", \"forecast.ss\", \"ss.par\", \"ss3\") file.copy(from = file.path(dir_tmp, files), to = dir_aspm) ## [1] TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"recruitment-deviations","dir":"Articles","previous_headings":"ASPM","what":"Recruitment Deviations","title":"ASPM","text":"Set recruitment devations ss.par 0.","code":"par <- SS_readpar_3.30(   parfile = file.path(dir_aspm, \"ss.par\"),   datsource = file.path(dir_aspm, \"data_echo.ss_new\"),   ctlsource = file.path(dir_aspm, \"control.ss_new\"),   verbose = FALSE ) par$recdev1 ##       year      recdev ##  [1,] 2011 -0.06005247 ##  [2,] 2012 -0.01284866 ##  [3,] 2013  0.13478706 ##  [4,] 2014  0.11410144 ##  [5,] 2015 -0.08325396 ##  [6,] 2016  0.14556845 ##  [7,] 2017 -0.12973978 ##  [8,] 2018 -0.18308123 ##  [9,] 2019  0.02442762 ## [10,] 2020 -0.08979813 ## [11,] 2021 -0.07812317 ## [12,] 2022  0.21801284 par$recdev_forecast ##       year recdev ##  [1,] 2023      0 ##  [2,] 2024      0 ##  [3,] 2025      0 ##  [4,] 2026      0 ##  [5,] 2027      0 ##  [6,] 2028      0 ##  [7,] 2029      0 ##  [8,] 2030      0 ##  [9,] 2031      0 ## [10,] 2032      0 par$recdev1[, \"recdev\"] <- 0  # Would run if forecasts recdevs were not already 0 # par$recdev_forecast[,\"recdev\"] <- 0 SS_writepar_3.30(   parlist = par,   outfile = file.path(dir_aspm, \"ss.par\"),   overwrite = T, verbose = FALSE ) ## $headerlines ## [1] \"# Number of parameters = 32 Objective function value = 754.301687441726  Maximum gradient component = 8.77017492766611e-07\" ## [2] \"# dummy_parm:\"                                                                                                              ## [3] \"1.00000000000\"                                                                                                              ##  ## $MG_parms ##                            INIT       ESTIM ## NatM_p_1_Fem_GP_1    0.10000000  0.10000000 ## L_at_Amin_Fem_GP_1  22.76900000 22.76899194 ## L_at_Amax_Fem_GP_1  71.80720000 71.80721125 ## VonBert_K_Fem_GP_1   0.14216500  0.14216482 ## CV_young_Fem_GP_1    0.10000000  0.10000000 ## CV_old_Fem_GP_1      0.10000000  0.10000000 ## Wtlen_1_Fem_GP_1     0.00000244  0.00000244 ## Wtlen_2_Fem_GP_1     3.34694000  3.34694000 ## Mat50%_Fem_GP_1     55.00000000 55.00000000 ## Mat_slope_Fem_GP_1  -0.25000000 -0.25000000 ## Eggs_alpha_Fem_GP_1  1.00000000  1.00000000 ## Eggs_beta_Fem_GP_1   0.00000000  0.00000000 ## NatM_p_1_Mal_GP_1    0.00000000  0.00000000 ## L_at_Amin_Mal_GP_1   0.00000000  0.00000000 ## L_at_Amax_Mal_GP_1   0.00000000  0.00000000 ## VonBert_K_Mal_GP_1   0.00000000  0.00000000 ## CV_young_Mal_GP_1    0.00000000  0.00000000 ## CV_old_Mal_GP_1      0.00000000  0.00000000 ## Wtlen_1_Mal_GP_1     0.00000244  0.00000244 ## Wtlen_2_Mal_GP_1     3.34694000  3.34694000 ## CohortGrowDev        1.00000000  1.00000000 ## FracFemale_GP_1      0.50000000  0.50000000 ##  ## $SR_parms ##               INIT    ESTIM ## SR_LN(R0)   8.9274 8.927395 ## SR_BH_steep 0.8000 0.800000 ## SR_sigmaR   0.6000 0.600000 ## SR_regime   0.0000 0.000000 ## SR_autocorr 0.0000 0.000000 ##  ## $recdev1 ##       year recdev ##  [1,] 2011      0 ##  [2,] 2012      0 ##  [3,] 2013      0 ##  [4,] 2014      0 ##  [5,] 2015      0 ##  [6,] 2016      0 ##  [7,] 2017      0 ##  [8,] 2018      0 ##  [9,] 2019      0 ## [10,] 2020      0 ## [11,] 2021      0 ## [12,] 2022      0 ##  ## $recdev_forecast ##       year recdev ##  [1,] 2023      0 ##  [2,] 2024      0 ##  [3,] 2025      0 ##  [4,] 2026      0 ##  [5,] 2027      0 ##  [6,] 2028      0 ##  [7,] 2029      0 ##  [8,] 2030      0 ##  [9,] 2031      0 ## [10,] 2032      0 ##  ## $init_F ## [1] 0.1 ##  ## $Q_parms ##                           INIT      ESTIM ## LnQ_base_SURVEY1(2)   0.476759  0.4767585 ## Q_extraSD_SURVEY1(2)  0.000000  0.0000000 ## LnQ_base_SURVEY2(3)  -6.304070 -6.3040672 ##  ## $S_parms ##                            INIT     ESTIM ## SizeSel_P_1_FISHERY(1) 56.51380 56.513807 ## SizeSel_P_2_FISHERY(1) 20.17930 20.179340 ## SizeSel_P_1_SURVEY1(2) 36.02330 36.023325 ## SizeSel_P_2_SURVEY1(2)  5.33502  5.335021 ## AgeSel_P_1_SURVEY2(3)   0.00000  0.000000 ## AgeSel_P_2_SURVEY2(3)   0.00000  0.000000"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"starter-file","dir":"Articles","previous_headings":"ASPM","what":"Starter File","title":"ASPM","text":"Change starter file read ss.par (init_values_src = 1) use new data control files.","code":"starter <- SS_readstarter(file = file.path(dir_aspm, \"starter.ss\"), verbose = FALSE) starter$datfile <- \"data_echo.ss_new\" starter$ctlfile <- \"control.ss_new\" starter$init_values_src <- 1 SS_writestarter(starter,   dir = dir_aspm,   overwrite = TRUE,   verbose = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"control-file","dir":"Articles","previous_headings":"ASPM","what":"Control File","title":"ASPM","text":"estimation phases following parameters may need changed: length selectivity age selectivity size selectivity steepness sigmaR recruitment deviations Additionally, likelihood components may need turned well. can using lambda options control file. examples include: length-composition data age-composition data size-composition data initial F","code":"control <- SS_readctl_3.30(   file = file.path(dir_aspm, \"control.ss_new\"),   datlist = file.path(dir_aspm, \"data_echo.ss_new\"),   verbose = FALSE )  control$SR_parms ##               LO HI   INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link ## SR_LN(R0)    6.0 12 8.9274  10.3  10.0       0     1            0        0 ## SR_BH_steep  0.2  1 0.8000   0.8   1.0       0    -4            0        0 ## SR_sigmaR    0.0  2 0.6000   0.8   0.8       0    -4            0        0 ## SR_regime   -5.0  5 0.0000   0.0   1.0       0    -4            0        0 ## SR_autocorr  0.0  0 0.0000   0.0   0.0       0   -99            0        0 ##             dev_minyr dev_maxyr dev_PH Block Block_Fxn ## SR_LN(R0)           0         0      0     0         0 ## SR_BH_steep         0         0      0     0         0 ## SR_sigmaR           0         0      0     0         0 ## SR_regime           0         0      0     0         0 ## SR_autocorr         0         0      0     0         0 # Would need to run if PHASES were positive for \"steep\" and \"sigmaR\" # control$SR_parms[c(2,3),\"PHASE\"] <- c(-4,-4) control$age_selex_parms ##                       LO HI INIT PRIOR PR_SD PR_type PHASE env_var&link ## AgeSel_P_1_SURVEY2(3)  0 20    0     5    99       0   -99            0 ## AgeSel_P_2_SURVEY2(3)  0 20    0     6    99       0   -99            0 ##                       dev_link dev_minyr dev_maxyr dev_PH Block Block_Fxn ## AgeSel_P_1_SURVEY2(3)        0         0         0      0     0         0 ## AgeSel_P_2_SURVEY2(3)        0         0         0      0     0         0 # would need to run if PHASES were positive for age selectivity # control$age_selex_parms[,\"PHASE\"] <- control$age_selex_parms[,\"PHASE\"] * -1 control$size_selex_parms[, \"PHASE\"] <- control$size_selex_parms[, \"PHASE\"] * -1 control$recdev_early_phase <- -4 control$recdev_phase <- -2  new_lambdas <- data.frame(   like_comp = c(4, 4, 5, 5, 7, 7, 9, 9, 9, 10),   fleet = c(1, 2, 1, 2, 1, 2, 1, 2, 3, 1),   phase = rep(1, 10),   value = rep(0, 10),   sizefreq_method = rep(1, 10) ) new_lambdas ##    like_comp fleet phase value sizefreq_method ## 1          4     1     1     0               1 ## 2          4     2     1     0               1 ## 3          5     1     1     0               1 ## 4          5     2     1     0               1 ## 5          7     1     1     0               1 ## 6          7     2     1     0               1 ## 7          9     1     1     0               1 ## 8          9     2     1     0               1 ## 9          9     3     1     0               1 ## 10        10     1     1     0               1 control$lambdas <- new_lambdas control$N_lambdas <- nrow(new_lambdas) SS_writectl_3.30(control,   outfile = file.path(dir_aspm, \"control.ss_new\"),   overwrite = TRUE, verbose = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"run-aspm","dir":"Articles","previous_headings":"ASPM","what":"Run ASPM","title":"ASPM","text":"","code":"r4ss::run(dir = dir_aspm, exe = \"ss3\", skipfinished = FALSE, verbose = FALSE) ## [1] \"ran model\""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"visualize-results","dir":"Articles","previous_headings":"ASPM","what":"Visualize Results","title":"ASPM","text":"compare ASPM model age-structured model, can use SSplotComparisons(). Comparing spawning biomass F estimates two models fits indices abundance can help understand enough information indices inform production function.","code":"mods <- SSgetoutput(dirvec = c(   dir_tmp,   dir_aspm ), verbose = FALSE)  mods_sum <- SSsummarize(mods, verbose = FALSE)  SSplotComparisons(mods_sum,   legendlabels = c(\"Ref\", \"ASPM\"),   subplots = c(2, 8, 14), new = F ) ## showing uncertainty for all models ## subplot 2: spawning biomass with uncertainty intervals ## subplot 8: F value with uncertainty ## subplot 14: index fits on a log scale"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Hindcast Cross-Validation","text":"HCxval implemented using ss3diags::SSplotHCxval(), produces novel HCxval diagnostic plot computes MASE scores indices abundance, mean lengths, mean ages observations falling within hindcast evaluation period.  plots , see , fleets, model fairly good prediction skills index abundance data (compared random walk). plots, white points white dashed line observed data included model truncated time series. larger colored points observed data retrospective peel (.e. data removed peel). smaller colored points dashed lines show model predicted values. “Ref” line model run complete time series data. grey shaded areas represent uncertainty data, darker portion indicating portion included model lighter portion indicating ones removed projected. MASE scores displayed MASE adjusted MASE parentheses.","code":"r4ss::sspar(mfrow = c(1, 2)) SSplotHCxval(retroSummary, subplots = \"cpue\", add = TRUE) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with only 1 of 5  prediction residuals for Index SURVEY1  #>  #>  Warning:  Unequal spacing of naive predictions residuals may influence the interpretation of MASE #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index SURVEY2 #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR  MAE.base  MASE.adj n.eval #> 1 SURVEY1      1 0.5026435 0.08879379 0.1766536 0.5026435      1 #> 2 SURVEY2      1 0.6149530 0.37737925 0.6136717 0.6149530      5"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"composition-data","dir":"Articles","previous_headings":"Visualizing Output","what":"Composition Data","title":"Hindcast Cross-Validation","text":"visualize mean length mean age, need add additional step. forecast length- age-composition information stored “ghost files” SS report.sso file, need use ss3diags::SSretroComps() extract summarize information creating plots.","code":"retroSummary_comps <- SSretroComps(retro_mods)  r4ss::sspar(mfrow = c(1, 2)) hcl <- SSplotHCxval(retroSummary_comps, subplots = \"len\", add = TRUE, ylim = c(40, 75)) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #>  Computing MASE with only 1 of 5  prediction residuals for Index SURVEY1  #>  #>  Warning:  Unequal spacing of naive predictions residuals may influence the interpretation of MASE #>  #> MASE stats by Index:"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Visualizing Output","what":"Customizing the Plot","title":"Hindcast Cross-Validation","text":"HCxval plots can customized many ways, common features may want specify : displaying specific fleet removing uncertainty intervals adjusting x- y-axis displaying adjusted MASE value plot Examples changes shown , incrementally making adjustment.","code":"r4ss::sspar(mfrow = c(2, 2)) SSplotHCxval(retroSummary_comps, subplots = \"len\", add = TRUE, indexselect = 1) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE, ylim = c(45, 70) ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE, ylim = c(45, 70), show.mase.adj = F ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"summary-table","dir":"Articles","previous_headings":"","what":"Summary Table","title":"Hindcast Cross-Validation","text":"addition HCxval plots, summary statistics table can produced using ss3diags::SSmase(). table includes: Index - fleet Season MASE - MASE score MAE.PR - mean absolute error prediction residuals MASE.base - naive prediction MASE.adj - adjusted MASE score n.eval - number points prediction skill calculated Adjusted MASE gets invoked cases inter-annual variation observed values small (default MAE < 0.1 naive predictions log(y[t+1])-log(y[t])). reasoning prediction residuals must already accurate fall threshold. adjusted MASE essential keep naive prediction MAE denominator MASE maximum. show effect changing adjustment threshold default MAE.base.adj = 0.1 larger value MAE.base.adj = 0.15 MASE ratio mean absolute error prediction residuals MAE.PR residuals naive predictions MAE.base MASE.adj","code":"mase1 <- SSmase(retroSummary_comps, quant = \"len\", MAE.base.adj = 0.1) mase1 #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 #> 2 SURVEY1      1 0.6526074 0.05142002 0.07879167 0.5142002      1 #> 3   joint        0.4628955 0.01719056 0.03713702 0.1719056      6 SSmase(retroSummary_comps, quant = \"len\", MAE.base.adj = 0.15) #>     Index Season      MASE     MAE.PR   MAE.base   MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.06896444      5 #> 2 SURVEY1      1 0.6526074 0.05142002 0.07879167 0.34280015      1 #> 3   joint        0.4628955 0.01719056 0.03713702 0.11460372      6 mase1$MAE.PR / mase1$MAE.base #> [1] 0.3591138 0.6526074 0.4628955 mase1$MASE #> [1] 0.3591138 0.6526074 0.4628955 mase1$MAE.PR / pmax(mase1$MAE.base, 0.1) #> [1] 0.1034467 0.5142002 0.1719056 mase1$MASE.adj #> [1] 0.1034467 0.5142002 0.1719056"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Likelihood Profile","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running profile (case dir_profile). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_tmp <- tempdir(check = TRUE) dir_profile <- file.path(dir_tmp, \"profile\") dir.create(dir_profile, showWarnings = FALSE, recursive = TRUE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_tmp) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_tmp, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpakzV4r/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"running-a-profile-on-r0","dir":"Articles","previous_headings":"","what":"Running a Profile on R0","title":"Likelihood Profile","text":"four input files SS executable file, can run likelihood profile shown . first step run model like profile . dir_tmp copy necessary files dir_profile. ’s best run profile subdirectory main model run keep output files separate diagnostic tests may run. input files dir_profile directory, need create vector values profile across. range increments choose depend model resolution want analyze likelihood profile. example use fairly coarse resolution speed total run time. also need modify starter file changing name control file read making sure likelihood calculated non-estimated quantities. run profile, use r4ss::profile() need specify partial string name parameter profiling (case “SR_LN” match “SR_LN(R0)”), vector values profile across. newctlfile control file adjusted values profilevec can named anything prefer, just needs match put starter file “ctlfile”. Full documentation profile() function can found r4ss website.","code":"r4ss::run(dir = dir_tmp, exe = \"ss3\", verbose = FALSE) #> [1] \"ran model\" files <- c(\"data.ss\", \"control.ss_new\", \"starter.ss\", \"forecast.ss\", \"ss.par\", \"ss3\") file.copy(from = file.path(dir_tmp, files), to = dir_profile) #> [1] TRUE TRUE TRUE TRUE TRUE TRUE CTL <- SS_readctl_3.30(file = file.path(dir_profile, \"control.ss_new\"), datlist = file.path(dir_profile, \"data.ss\"))  CTL$SR_parms #>               LO HI   INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link #> SR_LN(R0)    6.0 12 8.9274  10.3  10.0       0     1            0        0 #> SR_BH_steep  0.2  1 0.8000   0.8   1.0       0    -4            0        0 #> SR_sigmaR    0.0  2 0.6000   0.8   0.8       0    -4            0        0 #> SR_regime   -5.0  5 0.0000   0.0   1.0       0    -4            0        0 #> SR_autocorr  0.0  0 0.0000   0.0   0.0       0   -99            0        0 #>             dev_minyr dev_maxyr dev_PH Block Block_Fxn #> SR_LN(R0)           0         0      0     0         0 #> SR_BH_steep         0         0      0     0         0 #> SR_sigmaR           0         0      0     0         0 #> SR_regime           0         0      0     0         0 #> SR_autocorr         0         0      0     0         0 # getting the estimated r0 value r0 <- CTL$SR_parms$INIT[1] # creating a vector that is +/- 1 unit away from the estimated value in increments of 0.2 r0_vec <- seq(r0 - 1, r0 + 1, by = 0.2) r0_vec #>  [1] 7.9274 8.1274 8.3274 8.5274 8.7274 8.9274 9.1274 9.3274 9.5274 9.7274 #> [11] 9.9274 START <- SS_readstarter(file = file.path(dir_profile, \"starter.ss\"), verbose = FALSE) START$prior_like <- 1 START$ctlfile <- \"control_modified.ss\" SS_writestarter(START, dir = dir_profile, overwrite = TRUE, verbose = F) profile(   dir = dir_profile,   newctlfile = \"control_modified.ss\",   string = \"SR_LN\",   profilevec = r0_vec,   exe = \"ss3\",   verbose = FALSE ) #> running profile i=1/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.9274  7.9274        1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=2/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  7.9274  8.1274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=3/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.1274  8.3274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=4/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.3274  8.5274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=5/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.5274  8.7274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=6/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.7274  8.9274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=7/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.9274  9.1274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=8/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.1274  9.3274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=9/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.3274  9.5274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=10/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.5274  9.7274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=11/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.7274  9.9274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #>     Value converged[whichruns]    TOTAL       Catch Equil_catch    Survey #> 1  7.9274                 TRUE 1067.570 4.40715e-01   16.620400  6.065520 #> 2  8.1274                 TRUE  940.077 2.29735e-01   12.985200  1.965820 #> 3  8.3274                 TRUE  844.236 1.08857e-01    9.799480 -2.132340 #> 4  8.5274                 TRUE  790.513 9.17170e-06    3.930790 -5.726270 #> 5  8.7274                 TRUE  762.562 6.48948e-08    0.271032 -7.140910 #> 6  8.9274                 TRUE  754.302 1.33458e-10    0.174869 -7.118110 #> 7  9.1274                 TRUE  758.927 2.10816e-13    1.337060 -6.106700 #> 8  9.3274                 TRUE  767.708 1.90347e-13    3.424990 -4.917570 #> 9  9.5274                 TRUE  777.243 1.15331e-13    6.433440 -3.857200 #> 10 9.7274                 TRUE  787.189 6.73658e-14   10.382600 -2.563580 #> 11 9.9274                 TRUE  798.152 4.05051e-14   15.279300 -0.380771 #>    Length_comp Age_comp Size_at_age Recruitment InitEQ_Regime #> 1      453.198  341.340     230.715   19.181500   0.00000e+00 #> 2      418.750  291.595     201.557   12.989400   0.00000e+00 #> 3      393.384  257.968     179.068    6.036600   0.00000e+00 #> 4      379.721  243.456     167.416    1.713560   1.54502e-30 #> 5      370.420  234.970     163.525    0.515980   1.54502e-30 #> 6      366.756  231.845     162.399    0.244060   1.54502e-30 #> 7      367.497  233.210     162.675    0.312441   0.00000e+00 #> 8      369.543  235.957     163.170    0.529082   0.00000e+00 #> 9      371.605  238.622     163.598    0.839498   1.54502e-30 #> 10     373.376  240.872     163.942    1.178030   0.00000e+00 #> 11     374.815  242.718     164.208    1.510550   0.00000e+00 #>    Forecast_Recruitment Parm_priors Parm_softbounds Parm_devs Crash_Pen #> 1                     0           0      0.00756177         0         0 #> 2                     0           0      0.00433602         0         0 #> 3                     0           0      0.00337783         0         0 #> 4                     0           0      0.00197985         0         0 #> 5                     0           0      0.00143663         0         0 #> 6                     0           0      0.00141332         0         0 #> 7                     0           0      0.00150262         0         0 #> 8                     0           0      0.00159065         0         0 #> 9                     0           0      0.00166199         0         0 #> 10                    0           0      0.00171844         0         0 #> 11                    0           0      0.00176282         0         0"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Likelihood Profile","text":"profile finished running, can visualize results determine conflict data sources. data sources reach negative log-likelihood (NLL) minimum R0 value, indicates good agreement . However, likely, one reach NLL minimum different R0 values global R0 value. sign conflict data sources may require consider data weighting.  profile plot shows changes log-likelihood across selected range values contributing data components. adjustable minimum contribution threshold component must meet appear figure (data source model show plot, contribution total likelihood may large enough). steepness trajectory indicates informative () data source . example, age data plot much steeper left side minimum R0 value index data, suggests age composition data informative model. can also plot data-type fleet-specific profiles using r4ss::PinerPlot(). plotting profile length composition data fleet likelihood survey data fleet. allow us see conflicts sources main drivers.","code":"profile_mods <- SSgetoutput(dirvec = dir_profile, keyvec = 1:length(r0_vec), verbose = FALSE) profile_mods_sum <- SSsummarize(profile_mods, verbose = FALSE) SSplotProfile(profile_mods_sum,   profile.string = \"SR_LN\",   profile.label = \"SR_LN(R0)\" ) #> Parameter matching profile.string=SR_LN: SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274 #> Likelihood components showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>                      frac_change include                            label #> TOTAL                     1.0000    TRUE                            Total #> Catch                     0.0014   FALSE                            Catch #> Equil_catch               0.0525    TRUE                Equilibrium catch #> Survey                    0.0422    TRUE                       Index data #> Length_comp               0.2759    TRUE                      Length data #> Age_comp                  0.3495    TRUE                         Age data #> Size_at_age               0.2181    TRUE                 Size-at-age data #> Recruitment               0.0605    TRUE                      Recruitment #> InitEQ_Regime             0.0000   FALSE Initital equilibrium recruitment #> Forecast_Recruitment      0.0000   FALSE             Forecast recruitment #> Parm_priors               0.0000   FALSE                           Priors #> Parm_softbounds           0.0000   FALSE                      Soft bounds #> Parm_devs                 0.0000   FALSE             Parameter deviations #> Crash_Pen                 0.0000   FALSE                    Crash penalty sspar(mfrow = c(1, 2)) PinerPlot(profile_mods_sum,   component = \"Length_like\",   main = \"Length\" ) #> Parameter matching profile.string = 'R0': 'SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274, #> Fleet-specific likelihoods showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>         frac_change include #> FISHERY      0.6825    TRUE #> SURVEY1      0.3208    TRUE #> SURVEY2      0.0000   FALSE PinerPlot(profile_mods_sum,   component = \"Surv_like\",   main = \"Survey\" ) #> Parameter matching profile.string = 'R0': 'SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274, #> Fleet-specific likelihoods showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>         frac_change include #> FISHERY      0.0000   FALSE #> SURVEY1      0.3218    TRUE #> SURVEY2      0.9202    TRUE"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"runs-test","dir":"Articles","previous_headings":"","what":"Runs Test","title":"Residual Analyses","text":"runs test nonparametric hypothesis test randomness data sequence calculates 2-sided p-value estimate number runs (.e., sequences values sign) reference value. runs test can diagnose model misspecification using residuals fits index composition data (Carvalho et al. 2017) testing non-random patterns residuals. addition, three-sigma limits can considered useful identifying potential outliers data point three standard deviations away expected residual process average unlikely given random process error observed residual distribution. example using “simple_small” SS model included within r4ss package. can read report file model output using r4ss::SS_output() function shown .  output SSplotRunstest() includes plot residuals fleet table results runs test ‘three-sigma limit’ values. plots , shaded area represents ‘three-sigma limit’, three residual standard deviations zero. individual residual points fall outside three-sigma limit, colored red. Green shaded area indicates residuals randomly distributed (p-value >= 0.05) whereas red shaded area indicates residuals randomly distributed. Failing runs test (p-value < 0.05) can indicative misspecification conflict indices composition data.","code":"library(r4ss)  files_path <- system.file(\"extdata\", \"simple_small\", package = \"r4ss\") report <- SS_output(dir = files_path, verbose = FALSE, printstats = FALSE) sspar(mfrow = c(1, 2)) SSplotRunstest(report, add = TRUE) #> Running Runs Test Diagnostics w/ plots forIndex #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Index: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1  0.159 Passed -0.7301441 0.7301441 cpue #> 2 SURVEY2  0.887 Passed -1.1052361 1.1052361 cpue"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Runs Test","what":"Customizing the Plot","title":"Residual Analyses","text":"Runs test plots can customized needed. common features may want specify : plotting data types (default Index Abundance) plotting specific fleet(s) adjusting y-axis range Examples changes shown , incrementally making adjustment. plot data types, can specified subplots argument, options include “cpue”, “len”, “age”, “size”, “con”. “con” conditional size--age data “size” generalized size composition data. Fleets can specified using indexselect() function, takes vector fleet numbers plot.  Note small adjustment automatically added ylim provide extra white space. third plot, even though set y-axis range -0.5 0.5, y-axis goes -0.6 0.6. want extra space, set ylimAdj = 1 done 4th plot.","code":"sspar(mfrow = c(2, 2)) SSplotRunstest(report, subplots = \"len\", indexselect = 1, add = TRUE) #> Running Runs Test Diagnostics w/ plots forMean length #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean length: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 FISHERY  0.126 Passed -0.0613176 0.0613176  len SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE, ylim = c(-0.5, 0.5)) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE, ylim = c(-0.5, 0.5), ylimAdj = 1) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"summary-table","dir":"Articles","previous_headings":"Runs Test","what":"Summary Table","title":"Residual Analyses","text":"addition residual plots, SSplotRunstest() produces summary table runs test output values, including: p-value runs test test passed failed (indicated green red shading plot) upper lower limits 3-sigma interval type data tested (CPUE, length-composition, age-composition, conditional age--length) produce summary table skip plot, e.g. faciliate automated processing, use SSrunstest().","code":"rcpue <- SSrunstest(report, quants = \"cpue\") #> Running Runs Test Diagnosics for Index #> Computing Residual Runs Tests #> Residual Runs Test stats by Index: rlen <- SSrunstest(report, quants = \"len\") #> Running Runs Test Diagnosics for Mean length #> Computing Residual Runs Tests #> Residual Runs Test stats by Mean length: rbind(rcpue, rlen) #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1  0.159 Passed -0.7301441 0.7301441 cpue #> 2 SURVEY2  0.887 Passed -1.1052361 1.1052361 cpue #> 3 FISHERY  0.126 Passed -0.0613176 0.0613176  len #> 4 SURVEY1  0.841 Passed -0.1725225 0.1725225  len"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"rmse","dir":"Articles","previous_headings":"","what":"RMSE","title":"Residual Analyses","text":"RMSE root mean square error useful evaluating far predictions fall observed data. ss3diags::SSplotJABBAres() function allows visualize full time series residuals fleets indicated data (index abundance composition). example , plot residuals index abundance, mean age (age-composition), mean length (length composition) fleets.  plots , point represents difference observed expected value (residual) color-coded correspond specific fleet. solid, color-coded vertical lines horizontal dashed line (y = 0) show distance 0 residual value. Box plots summarize spread residual values across fleets within year thick solid black line loess smoother fit residual points. Total RMSE displayed top right corner. assessing plot, important see patterns trends residuals, large overall RMSE , whether data different fleets generally agrees conflicts . retrieve just RMSE residual values without generating plot, SSrmse() produces named list 2 objects, RMSE residuals. can accessed shown . function useful automating analyses.","code":"sspar(mfrow = c(2, 2)) SSplotJABBAres(report, subplots = \"cpue\", add = TRUE) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 SURVEY1       21.6     4 #> 2 SURVEY2       27.7    12 #> 3 Combined      26.3    16 SSplotJABBAres(report, subplots = \"age\", add = TRUE) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 FISHERY        9      12 #> 2 SURVEY1        8.1     4 #> 3 Combined       8.8    16 SSplotJABBAres(report, subplots = \"len\", add = TRUE, ylim = c(-0.2, 0.2)) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 FISHERY        2.1    12 #> 2 SURVEY1        3.4     4 #> 3 Combined       2.5    16 rmse <- SSrmse(report, quants = \"cpue\")$RMSE residuals <- SSrmse(report, quants = \"cpue\")$residuals  rmse #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 SURVEY1       21.6     4 #> 2 SURVEY2       27.7    12 #> 3 Combined      26.3    16  head(residuals) #>     Fleet Fleet_name Area   Yr Seas Subseas Month   Time Vuln_bio         Obs #> 925     2    SURVEY1    1 2013    1       2     7 2013.5 62947.50 144745.0000 #> 926     2    SURVEY1    1 2016    1       2     7 2016.5 49335.70  63760.3000 #> 927     2    SURVEY1    1 2019    1       2     7 2019.5 38132.00  59242.9000 #> 928     2    SURVEY1    1 2022    1       2     7 2022.5 34045.80  49649.7000 #> 929     3    SURVEY2    1 2011    1       2     7 2011.5  6306.83     11.5668 #> 930     3    SURVEY2    1 2012    1       2     7 2012.5  6544.96     13.9955 #>             Exp     Calc_Q      Eff_Q  SE SE_input         Dev        Like #> 925 101399.0000 1.61084000 1.61084000 0.3      0.3  0.35591400 7.03749e-01 #> 926  79472.2000 1.61084000 1.61084000 0.3      0.3 -0.22027600 2.69564e-01 #> 927  61424.7000 1.61084000 1.61084000 0.3      0.3 -0.03616590 7.26653e-03 #> 928  54842.4000 1.61084000 1.61084000 0.3      0.3 -0.09947210 5.49706e-02 #> 929     11.5342 0.00182885 0.00182885 0.7      0.7  0.00281831 8.10497e-06 #> 930     11.9698 0.00182885 0.00182885 0.7      0.7  0.15635300 2.49451e-02 #>     Like+log(s) SuprPer Use    residuals #> 925   -0.500223      NA   1  0.355910344 #> 926   -0.934409      NA   1 -0.220276535 #> 927   -1.196710      NA   1 -0.036166093 #> 928   -1.149000      NA   1 -0.099471269 #> 929   -0.356667      NA   1  0.002822391 #> 930   -0.331730      NA   1  0.156349038"},{"path":"https://pifscstockassessments.github.io/ss3diags/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Henning Winker. Author. Felipe Carvalho. Author. Massimiliano Cardinale. Author. Laurence Kell. Author. Megumi Oshima. Author, maintainer. Eric Fletcher. Author.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E (2024). ss3diags: Stock Synthesis Model Diagnostics Intergated Stock Assessments. R package version 2.1.1, https://github.com/PIFSCstockassessments/ss3diags.","code":"@Manual{,   title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments},   author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher},   year = {2024},   note = {R package version 2.1.1},   url = {https://github.com/PIFSCstockassessments/ss3diags}, }"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"ss3diags-","dir":"","previous_headings":"","what":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"R package ss3diags enables users apply advanced diagnostics evaluate Stock Synthesis model. Diagnostics include residual analyses, hindcast cross-validation techniques, retrospective analyses. Functions also allow users reproduce key model diagnostics plots presented paper ‘Cookbook Using Model Diagnostics Integrated Stock Assessments’ (Carvalho et al. 2021). ss3diags Github repository provides step--step R recipes : Run jitter analysis Conduct retrospective analysis Use hindcast cross-validation log-likelood profiling R0 Run ASPM diagnostic Evaluate model fit Stock Synthesis making use comprehensive collection R functions available R packages r4ss ss3diags.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"ss3diags currently supported CRAN. can install development version ss3diags GitHub : package installed can loaded : examples run common diagnostic tests SS models visualize results diagnostic tests using r4ss ss3diags packages, please refer articles package website.","code":"# install.packages(\"remotes\") remotes::install_github(\"PIFSCstockassessments/ss3diags\") library(ss3diags)"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"contributing-to-ss3diags","dir":"","previous_headings":"","what":"Contributing to ss3diags","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"like contribute ss3diags suggestions diagnostic tests include package, can submit new issue email Meg megumi.oshima@noaa.gov.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"reference","dir":"","previous_headings":"","what":"Reference","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"cite ss3diags publication can use","code":"citation(\"ss3diags\") #> To cite package 'ss3diags' in publications use: #>  #>   Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E #>   (2023). _ss3diags: Stock Synthesis Model Diagnostics for Intergated #>   Stock Assessments_. R package version 2.1.1, #>   <https://github.com/PIFSCstockassessments/ss3diags>. #>  #> A BibTeX entry for LaTeX users is #>  #>   @Manual{, #>     title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments}, #>     author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher}, #>     year = {2023}, #>     note = {R package version 2.1.1}, #>     url = {https://github.com/PIFSCstockassessments/ss3diags}, #>   }"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"disclaimer","dir":"","previous_headings":"","what":"Disclaimer","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"United States Department Commerce (DOC) GitHub project code provided ‘’ basis user assumes responsibility use. DOC relinquished control information longer responsibility protect integrity, confidentiality, availability information. claims Department Commerce stemming use GitHub project governed applicable Federal law. reference specific commercial products, processes, services service mark, trademark, manufacturer, otherwise, constitute imply endorsement, recommendation favoring Department Commerce. Department Commerce seal logo, seal logo DOC bureau, shall used manner imply endorsement commercial product activity DOC United States Government.”","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":null,"dir":"Reference","previous_headings":"","what":"Francis Weighting for compositional data — SScompsTA1.8","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"TA1.8 Francis function modified r4ss::SSMethod.TA1.8 r4ss::SSMethod.Cond.TA1.8 apply Francis weighting method TA1.8 length-, age-, generalized size-composition data, conditional age--length data Stock Synthesis model. conditional age--length data, mean age year calculated based recommendations Punt (2015). main purpose create dataframe annual observed expected mean length age fleet used calculate residuals testing model fit. function used SSplotRunstest SSplotJABBAres.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"","code":"SScompsTA1.8(   ss3rep,   type = c(\"len\", \"age\", \"size\", \"con\"),   fleet = NULL,   seas = NULL,   plotit = FALSE,   maxpanel = 1000 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"ss3rep Stock Synthesis output read r4SS function SS_output type string either 'len' (length composition data), 'size' (generalized size composition data), 'age' (age composition data), 'con' (conditional age length data) fleet vector one fleet numbers whose data analysed simultaneously, NULL, fleets analysed seas string indicating treat data multiple seasons 'comb' - combine seasonal data year plot Yr 'sep' - treat season separately, plotting Yr.S. .null(seas), assumed one season option 'comb' used. plotit TRUE, make illustrative plot like one panels Fig. 4 Francis (2011). maxpanel maximum number panels within plot, default 1000","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"ss_out data.frame observed, predicted mean length/age 95% confidence intervals based stage 1 stage 2 weighting runs_dat data.frame observed predicted mean length age year/fleet.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"Francis, R..C.C. (2011). Data weighting statistical fisheries stock assessment models. Canadian Journal Fisheries Aquatic Sciences 68: 1124-1138. #' Punt, .E. (2015). insights data weighting integrated stock assessments. Fish. Res. <http://dx.doi.org/10.1016/j.fishres.2015.12.006","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"Chris Francis, Andre Punt, Ian Taylor (modified Henning Winker Meg Oshima)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":null,"dir":"Reference","previous_headings":"","what":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using Multivariate Log-Normal Distribution. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"","code":"SSdeltaMVLN(   ss3rep,   Fref = NULL,   years = NULL,   mc = 5000,   weight = 1,   run = \"MVLN\",   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE,   variance_method = \"ww2019\",   bias_correct_mean = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt\"), correponding F_MSY F_Btgt years single year vector years mvln mc number monte-carlo simulations weight weighting option model ensembles weight*mc run qualifier model run plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI? variance_method Specify method approximating variance covariance multivariate lognormal distribution ww2019 Use approximation Walter Winker 2019 (Default backwards compatibility). 2T Use delta-method 2nd order Taylor series approximation. bias_correct_mean Specify Stock Synthesis MLE estimates bias corrected used specify mean multivariate lognormal distribution FALSE apply bias correction (Default backwards compatibility). TRUE Apply bias correction.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"output list maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values, kobe plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"Henning Winker (JRC-EC) Nicholas Ducharme-Barth (PIFSC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":null,"dir":"Reference","previous_headings":"","what":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"function generate kobe pdfs Multivariate Log-Normal Distribution including plotting option. version used older versions Stock Synthesis. newer versions (v3.24 newer), use SSdeltaMVLN().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"","code":"SSdeltaMVLN_old(   ss3rep,   status = c(\"Bratio\", \"F\"),   quants = c(\"SSB\", \"Recr\"),   Fref = c(\"MSY\", \"Ftrg\"),   years = NULL,   mc = 5000,   weight = 1,   run = \"MVLN\",   plot = TRUE,   addtrj = TRUE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"ss3rep r4ss::SSgetoutput()$replist1 status covarying stock status quantaties extract Hessian quants additional stock quantaties extract Hessian Fref Choice reference point stock SSB/XFref=c(\"MSY\",\"Ftrg\"),F_report_basis: 0 3 years single year vector years mvln mc number monte-carlo simulations weight weighting option model ensembles weight*mc run qualifier model run plot option show plot addtrj TRUE/FALSE add trajectory years. Default TRUE ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"output list kobe objects mle's","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":null,"dir":"Reference","previous_headings":"","what":"MCMC Joint Distributions — SSdiagsMCMC","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using MCMC. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"","code":"SSdiagsMCMC(   mcmc,   ss3rep,   Fref = NULL,   years = NULL,   run = \"MCMC\",   thin = 1,   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"mcmc file path folder derived_posteriors.sso file ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt), correponding F_MSY F_Btgt years single year vector years mvln run qualifier model run thin option use additional thinning plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"output list maximum likelihood estimates MCMC posterier distributions Kobe values Kobe plot","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"Henning Winker (JRC-EC), Massimiliano Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":null,"dir":"Reference","previous_headings":"","what":"MCMC Joint Distributions — SSdiagsMCMC_ancient","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using MCMC. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble(). Use Stock Synthesis models older 3.24, later versions use SSdiagsMCMC().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"","code":"SSdiagsMCMC_ancient(   mcmc,   ss3rep,   Fref = NULL,   years = NULL,   run = \"MCMC\",   thin = 1,   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"mcmc file path folder derived_posteriors.sso file ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt), correponding F_MSY F_Btgt years single year vector years mvln run qualifier model run thin option use additional thinning plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"output list maximum likelihood estimates MCMC posterier distributions Kobe values Kobe plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"Henning Winker (JRC-EC), Massimiliano Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":null,"dir":"Reference","previous_headings":"","what":"Mohn's Rho and Forecast Bias — SShcbias","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"function produces statistics retrospective analysis (Mohn's rho forecast bias). visualize retrospective forecasts Stock Synthesis model, use SSplotRetro().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"","code":"SShcbias(   summaryoutput,   quants = c(\"SSB\", \"F\"),   models = \"all\",   endyrvec = \"default\",   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"summaryoutput List created r4ss::SSsummarize() quants SSB F quantity models Optional subset models described r4ss function summaryoutput().  Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. verbose Report progress R GUI?","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean Absolute Scaled Error — SSmase","title":"Mean Absolute Scaled Error — SSmase","text":"MASE one-step ahead hindcasting cross-validations computes MASE prediction residuals indices. MASE calculated average ratio mean absolute error (MAE) prediction residuals (MAE.PR) Naive Predictions (MAE.base) MASE.adj sets MAE.base minimum MAE.base.adj (default=0.1) MASE.adj allow passing (MASE<1) MAE.PE < 0.1 thus accurate, obs show extremely little variation","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean Absolute Scaled Error — SSmase","text":"","code":"SSmase(   retroSummary,   quants = c(\"cpue\", \"len\", \"age\", \"con\"),   Season = \"default\",   models = \"all\",   endyrvec = \"default\",   indexselect = NULL,   MAE.base.adj = 0.1,   residuals = FALSE,   verbose = FALSE,   indexfleets = 1 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean Absolute Scaled Error — SSmase","text":"retroSummary raw list retrospective runs created r4ss::SSgetoutput(). Depending type data, function call r4ss::SSsummarize ss3diags:SSretroComps summarize list. quants data type, either \"cpue\" index data, \"len\" length composition data, \"age\" age composition data. Note, using \"age\" \"len\", SSretroComps() used extract summarize composition data first. Season option specify Season integer value 1-4 - Default uses first available, .e. usual Seas = 1 models Optional subset models described r4ss function summaryoutput().  Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. indexselect Vector fleet numbers model compare MAE.base.adj minimum MASE demoninator (naive predictions) MASE.adj (default = 0.1) residuals true, includes dataframe output prediction residuals naive prediction residuals. Default FALSE. verbose Report progress R GUI? indexfleets Single value vector length n = number models summary object fleet number(s) index compare.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean Absolute Scaled Error — SSmase","text":"MASE hcxval statistic","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mean Absolute Scaled Error — SSmase","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean Absolute Scaled Error — SSmase","text":"","code":"if (FALSE) { # calculate MASE for CPUE indices only for fleets 1 and 2 SSmase(retro.sma, quant = \"cpue\", indexselect = c(1:2)) }"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Model ensemble plots — SSplotEnsemble","title":"Model ensemble plots — SSplotEnsemble","text":"Plots model ensembles forecasts uncertainty represented MVLN MCMC posteriors","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model ensemble plots — SSplotEnsemble","text":"","code":"SSplotEnsemble(   kb,   subplots = c(\"stock\", \"harvest\", \"SSB\", \"F\", \"Recr\", \"Catch\"),   models = \"all\",   quantiles = list(c(0.025, 0.975)),   ylabs = NULL,   endyrvec = \"default\",   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = FALSE,   use_pdf = FALSE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = NULL,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   legendindex = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model ensemble plots — SSplotEnsemble","text":"kb kb type output created SSdeltaMVLN() subplots vector create subplots options: \"stock\" Fish Population \"harvest\" Harvest Rate \"SSB\" Spawning Stock Biomass \"F\" Fishing Mortality \"Recr\" Recruitment \"Catch\" Total Catch models option manually subset models kb[[\"run\"]] quantiles quantiles uncertainty plots. Input list, default 95TH percentile: list(c(0.025, 0.975)) ylabs y-axis labels quants endyrvec Optional single year vector years representing final year values show model. \"default\" set ending year specified model. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadealpha Transparency adjustment used make uncertainty regions, default 0.3 new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel TRUE/FALSE include labels indices. Default TRUE (currently used) indexQdigits Number significant digits catchability legend. Default 4 legendindex Allows add legend selected indices (plots)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Model ensemble plots — SSplotEnsemble","text":"Mostly adopted r4ss::SSplotComparisons Taylor et al","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Model ensemble plots — SSplotEnsemble","text":"","code":"if (FALSE) {  mvln <- SSdeltaMVLN(simple, run = \"Simple\") sspar(mfrow = c(3, 2), plot.cex = 0.7) SSplotEnsemble(mvln[[\"kb\"]], ylabs = mvln[[\"labels\"]], add = T, verbose = F) }"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic SSplot function — SSplotGeneric","title":"Generic SSplot function — SSplotGeneric","text":"Generalized version ss3diags SSplots functions. intended production","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic SSplot function — SSplotGeneric","text":"","code":"SSplotGeneric(   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic SSplot function — SSplotGeneric","text":"pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":null,"dir":"Reference","previous_headings":"","what":"Legend parameters for Generic SSplot — SSplotGenericLegend","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"Generalized version ss3diags SSplots functions specfic plot legend parameters. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"","code":"SSplotGenericLegend(   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":null,"dir":"Reference","previous_headings":"","what":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"Generalized version ss3diags SSplots functions specify par() pass plot attributes. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"","code":"SSplotGenericPar(   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = NULL,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\" )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":null,"dir":"Reference","previous_headings":"","what":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"Generalized version ss3diags SSplots functions specify uncertainty. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"","code":"SSplotGenericUncertainty(uncertainty = TRUE, mcmcVec = FALSE, models = \"all\")"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":null,"dir":"Reference","previous_headings":"","what":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"Plots one-step ahead hindcasting cross-validations computes MASE prediction residuals.MASE calculated average ratio mean absolute error (MAE) prediction residuals (MAE.PR) naive predictions (MAE.base). MASE.adj sets MAE.base minimum MAE.base.adj (default=0.1). MASE.adj allow passing (MASE<1) MAE.PE < 0.1 thus accurate obs show little annual variation","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"","code":"SSplotHCxval(   retroSummary,   subplots = c(\"cpue\", \"len\", \"age\"),   Season = \"default\",   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   endyrvec = \"default\",   xmin = NULL,   indexselect = NULL,   MAE.base.adj = 0.1,   show.mase.adj = TRUE,   indexUncertainty = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   xlim = \"default\",   ylimAdj = 1.15,   ylim = NULL,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = grey(0.5, 0.4),   shadecol2 = grey(0.5, 0.4),   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   indexfleets = 1,   plot = TRUE,   shadecol1 = grey(0.5, 0.4) )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"retroSummary List created r4ss::SSsummarize() SSretroComps() subplots optional use following: \"cpue\" Index abundance data \"len\" Length-composition data \"age\" Age-composition data Season option specify Season integer value 1-4. Default uses first available, .e. usual Seas = 1 print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. xmin optional number first year shown plot (available) indexselect Vector fleet numbers model compare MAE.base.adj minimum MASE denominator (naive predictions) MASE.adj (default = 0.1) show.mase.adj TRUE, show mase.adj plot indexUncertainty Show fixed uncertainty intervals index (estimated) col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. ylim -write ylimAdj specified xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon shadecol2 color uncertainty early years affected hindcast shadealpha Transparency adjustment used make default shadecol. (currently used) new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel Logical flag add catchability legend plot index fits. indexQdigits Number significant digits catchability legend indexfleets Fleet numbers model compare indices abundance. Can take different forms: integer: (default) create single comparison plot chosen index NULL: create separate plot index long fleet numbering across models. vector length equal number models: single fleet number model compared single plot list: list fleet numbers associated indices within model compared, list elements vector length names list elements matter can absent. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version shadecol1 uncertainty shading early years affected hindcast (currently used)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual plot — SSplotJABBAres","title":"Residual plot — SSplotJABBAres","text":"Plots residuals indices boxplot (color coded fleet) loess showing systematic trends time. function package JABBA (Just Another Bayesian Biomass Assessment).","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual plot — SSplotJABBAres","text":"","code":"SSplotJABBAres(   ss3rep,   subplots = c(\"cpue\", \"len\", \"age\", \"size\", \"con\")[1],   seas = NULL,   plot = TRUE,   print = lifecycle::deprecated(),   print_plot = FALSE,   png = lifecycle::deprecated(),   use_png = print_plot,   pdf = lifecycle::deprecated(),   use_pdf = FALSE,   indexselect = NULL,   miny = 3,   col = NULL,   pch = 21,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   xlim = \"default\",   ylim = \"default\",   ylimAdj = 1.1,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   legend = TRUE,   legendlabels = \"default\",   legendloc = \"bottomleft\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   boxcol = grey(0.8, 0.5),   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual plot — SSplotJABBAres","text":"ss3rep Stock Synthesis output read r4ss::SS_output() subplots string type data plot: \"cpue\" Index abundance data \"len\" Length-composition data \"age\" Age-composition data \"size\" Generalized size composition data \"con\" Conditional age--length data. seas string indicating treat data multiple seasons: \"comb\" Combine seasonal data year plot Yr \"sep\" Treat season separately, plotting Yr.S. NULL NULL, assumed one season option \"comb\" used. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. indexselect Vector fleet numbers model compare miny minimum abs values ylim col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylim Optional, min max values ylim override \"default\" value (-0.7, 0.5) ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag. Enables x- y-axis labels. type type plot drawn. details, see plot. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console boxcol color boxes new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual plot — SSplotJABBAres","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":null,"dir":"Reference","previous_headings":"","what":"KOBE phase plot — SSplotKobe","title":"KOBE phase plot — SSplotKobe","text":"Generates Kobe plot phase plot illustrating stock status uncertainty SSB/SSBmsy F/Fmsy","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"KOBE phase plot — SSplotKobe","text":"","code":"SSplotKobe(   kb,   joint = TRUE,   year = NULL,   posterior = c(\"points\", \"kernel\"),   xlab = expression(SSB/SSB[MSY]),   ylab = expression(F/F[MSY]),   ylim = NULL,   xlim = NULL,   fill = TRUE,   showMedian = TRUE,   legend = TRUE,   legendpos = \"right\",   legendcex = 0.7,   legendruns = TRUE,   yr.label = TRUE,   yr.int = 5,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"KOBE phase plot — SSplotKobe","text":"kb output SSdeltaMVLN()$kb joint option FALSE shows individual runs year option choose year kobe, last year default posterior visualization posterior c(\"points\",\"kernel\") xlab graphic parameter ylab graphic parameter ylim graphic parameter xlim graphic parameter fill shows color-coded quadrants showMedian option median trajectory. TRUE default legend option legend. TRUE default. legendpos legend position legendcex legend size legendruns show legend run labels yr.label show year along trajectory yr.int year intervals along trajectory verbose Output R console. Default TRUE","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"KOBE phase plot — SSplotKobe","text":"Kobe Quadrant percentages","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare Multiple SS Model Estimates — SSplotModelcomp","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"function plot SSB, B-ratio, F, Recruits, /Index Abundance fits multiple SS models. function uses object multiple SS models summarized r4ss::SSsummarize().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"","code":"SSplotModelcomp(   summaryoutput,   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   subplots = c(\"SSB\", \"Bratio\", \"Fvalue\", \"Recruits\", \"Index\", \"RecDevs\"),   brp = c(\"msy\", \"btargs\"),   fmsy = TRUE,   ylabs = c(\"SSB (t)\", expression(SSB/SSB[MSY]), \"Fishing mortality F\",     \"Recruits ('000s)\", \"Index\", \"Recruitment Deviations\"),   endyrvec = \"default\",   xmin = NULL,   indexselect = NULL,   indexUncertainty = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = \"default\",   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = NULL,   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   indexfleets = 1 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"summaryoutput List created r4ss::SSsummarize() plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. subplots option \"SSB\",\"Bratio\",\"Fvalue\",\"Recruits\",\"Index\" \"SSB\" Spawning Stock Biomass \"Bratio\" Stock Biomass relative biomass reference point \"Fvalue\" Fishing Mortality \"Recruits\" Age-0 Recruits \"Index\" Index abundance \"RecDev\" Recruitment Deviations brp option set reference point c(\"msy\",\"btargs\") fmsy specify Fvalue F/Fmsy starter file setting ylabs yaxis labels quants final year values show model. default set endyrvec Optional single year vector years representing final year values show model. \"default\" set ending year specified model. xmin NULL optional number first year shown plot (available) indexselect Vector fleet numbers model compare indexUncertainty Show fixed uncertainty intervals index (estimated) col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon shadealpha Transparency adjustment used make default shadecol new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel Logical. TRUE add catchability legend plot index fits (currently used) indexQdigits Number significant digits catchability legend indexfleets Fleet numbers model compare indices abundance. Can take different forms: integer (default): create single comparison plot chosen index NULL: create separate plot index long fleet numbering across models. vector length equal number models: single fleet number model compared single plot list: list fleet numbers associated indices within model compared, list elements vector length names list elements matter can absent.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"Mostly adopted r4ss::SSplotComparisons Taylor et al","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"Plots retrospective pattern, including (optional) one-step ahead forecast computes Mohn's Rho","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"","code":"SSplotRetro(   summaryoutput,   subplots = c(\"SSB\", \"F\"),   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   endyrvec = \"default\",   xlim = NULL,   xmin = NULL,   labels = NULL,   ylim = NULL,   forecast = TRUE,   forecastrho = TRUE,   showrho = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.7,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = grey(0.4, 0.6),   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   shadecol1 = grey(0.5, 0.4),   indexQlabel = TRUE,   indexQdigits = 4,   shadealpha = 0.3 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"summaryoutput List created r4ss::SSsummarize() subplots Optional vector subplots created: \"SSB\" Spawning Stock Biomass \"F\" Fishing Mortality plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. xmin optional minimum year shown plot (default first yr) labels yaxis label biomass (bony fish sharks) ylim option specify ylim range forecast Logical. TRUE, one-step ahead forecasts shown plot forecastrho Logical. TRUE, one-step ahead forecast rho value denoted plot showrho Logical flag include Mohn's rho value. Defaults TRUE col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. shadecol1 uncertainty shading early years affected hindcast indexQlabel Logical. TRUE, add catchability legend plot index fits (currently used) indexQdigits Number significant digits catchability legend shadealpha set transparency level (alpha) area uncertainty. Defaults 0.3 (currently used)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual Diagnostics — SSplotRunstest","title":"Residual Diagnostics — SSplotRunstest","text":"Function residual diagnostics. Plots residuals 3x sigma limits indices mean age length outputs runs test table. Note, want plot residuals, use SSrunstest().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual Diagnostics — SSplotRunstest","text":"","code":"SSplotRunstest(   ss3rep,   mixing = \"less\",   subplots = c(\"cpue\", \"len\", \"age\", \"size\", \"con\")[1],   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   indexselect = NULL,   miny = 1,   col = NULL,   pch = 21,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = \"default\",   ylim = \"default\",   ylimAdj = 1.4,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   legend = TRUE,   legendloc = \"top\",   legendcex = 1,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual Diagnostics — SSplotRunstest","text":"ss3rep Stock Synthesis output read r4ss::SS_output() mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation subplots optional flag : \"cpue\" Index abundance data \"len\" Length composition data \"size\" Generalized size composition data \"age\" Age composition data \"con\" Conditional age--length data plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. indexselect Vector fleet numbers model compare miny absolute value min max value ylim. Default 1 col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylim Optional, values y-axis range display plot. default: \"default\", range -1 1. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. legend Flag enable legend plot. TRUE default. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendcex Allows adjust legend cex pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Residual Diagnostics — SSplotRunstest","text":"dataframe runs test p-value, test passed failed, 3x sigma high low limits, type data used. Rows fleet. Note, runs test passed p-value > 0.05 (residuals random) failed p-value < 0.5 (residuals random)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual Diagnostics — SSplotRunstest","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":null,"dir":"Reference","previous_headings":"","what":"Read SS MCMC — SSreadMCMC","title":"Read SS MCMC — SSreadMCMC","text":"function read mcmc file outputs Stock Synthesis model","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read SS MCMC — SSreadMCMC","text":"","code":"SSreadMCMC(mcmcdir)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read SS MCMC — SSreadMCMC","text":"mcmcdir file path folder derived_posteriors.sso file","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read SS MCMC — SSreadMCMC","text":"Stock Synthesis mcmc output file","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read SS MCMC — SSreadMCMC","text":"Henning Winker (JRC-EC) & Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Composition Data from Multiple SS Models — SSretroComps","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"Wrapper get observed expected mean length/age multiple Stock Synthesis models.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"","code":"SSretroComps(retroModels)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"retroModels object list replists r4ss::SSgetoutput()","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"list observed expected mean Length/age comps (c.f. ss3rep[[\"cpue\"]])","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"Henning Winker","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":null,"dir":"Reference","previous_headings":"","what":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"Function calculating RMSE used SSplotJABBAres()","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"","code":"SSrmse(   ss3rep,   quants = c(\"cpue\", \"len\", \"age\", \"con\"),   seas = NULL,   indexselect = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"ss3rep output SS_output() quants dataset calculate RMSE . \"cpue\" index abundance, \"len\" length comp, \"age\" age composition, \"con\" conditional age--length. seas string indicating treat data multiple seasons 'comb' - combine seasonal data year plot Yr 'sep' - treat season separately, plotting Yr.S. .null(seas), assumed one season option 'comb' used. indexselect Vector fleet numbers model compare","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"returns list includes RMSE table output (fleet combined) dataframe residuals can used creating SSplotJABBAres() plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual Diagnostics Plot — SSrunstest","title":"Residual Diagnostics Plot — SSrunstest","text":"Function residual diagnostics. Outputs runs test table gives runs test p-values, runs test passed (p-value > 0.05, residuals random) failed (p-value < 0.05, residuals random), 3x sigma limits indices mean age length type input data (cpue, length comp, age comp, size comp, conditional age--length).","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual Diagnostics Plot — SSrunstest","text":"","code":"SSrunstest(   ss3rep,   mixing = \"less\",   quants = c(\"cpue\", \"len\", \"age\", \"con\")[1],   indexselect = NULL,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual Diagnostics Plot — SSrunstest","text":"ss3rep Stock Synthesis output read r4ss::SS_output() mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation quants optional use c(\"cpue\",\"len\",\"age\",\"con\"), default uses \"cpue\". \"cpue\" Index abundance data \"len\" Length composition data \"age\" Age composition data \"con\" Conditional age--length data indexselect Vector fleet numbers model compare verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Residual Diagnostics Plot — SSrunstest","text":"dataframe runs test p-value, test passed failed, 3x sigma high low limits, type data used. Rows fleet. Note, runs test passed p-value > 0.05 (residuals random) failed p-value < 0.5 (residuals random)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual Diagnostics Plot — SSrunstest","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Stock Status Settings — SSsettingsBratioF","title":"Get Stock Status Settings — SSsettingsBratioF","text":"function get Bratio F settings","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Stock Status Settings — SSsettingsBratioF","text":"","code":"SSsettingsBratioF(ss3rep, status = c(\"Bratio\", \"F\"), verbose = TRUE)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Stock Status Settings — SSsettingsBratioF","text":"ss3rep r4ss::SSgetoutput() status covarying stock status quantaties extract Hessian verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Stock Status Settings — SSsettingsBratioF","text":"output list Bratio F settings","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get Stock Status Settings — SSsettingsBratioF","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Indices — ensemble_plot_index","title":"Plot Indices — ensemble_plot_index","text":"function plot different fits single index abundance","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Indices — ensemble_plot_index","text":"","code":"ensemble_plot_index(   summaryoutput,   varlist,   indexfleets = 1,   verbose = TRUE,   legendloc = \"topright\",   legendcex = 1,   legendsp = 0.9,   legendncol = 1,   type = \"l\" )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Indices — ensemble_plot_index","text":"summaryoutput summaryoutput varlist variable list indexfleets Fleet vector index verbose Option output messages Rconsole legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See ?legend info string options. legendcex Allows adjust legend cex legendsp Space legend labels legendncol Number columns legend. type Type parameter passed points (default 'o' overplots points top lines)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":null,"dir":"Reference","previous_headings":"","what":"Runs Test for Residuals — ssruns_sig3","title":"Runs Test for Residuals — ssruns_sig3","text":"function uses randtests::runs.test perform runs test residuals determine randomly distributed. also calculates 3 x sigma limits","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runs Test for Residuals — ssruns_sig3","text":"","code":"ssruns_sig3(x, type = NULL, mixing = \"less\")"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Runs Test for Residuals — ssruns_sig3","text":"x residuals CPUE fits type c(\"resid\",\"observations\") mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation ","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Runs Test for Residuals — ssruns_sig3","text":"runs p value 3 x sigma limits","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Runs Test for Residuals — ssruns_sig3","text":"runs test conducted library(randtests)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Runs Test for Residuals — ssruns_sig3","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-210","dir":"Changelog","previous_headings":"","what":"ss3diags 2.1.0","title":"ss3diags 2.1.0","text":"RMSE calculations modularized standalone function can called independently SSplotJABBAres() SSrmse(). (#50) Bugfixes adjusting y-axis limits SSplotRunstest SSplotJABBAres: Use ylim parameter adjust y-axis limits. (#46) Added option remove median trajectory SSplotKobe() (#3) Added rlang, dplyr, magrittr dependencies. SSmase SSplotHcxval: Corrected validation messsage clarify validation issue fix issue code styler. (#33, #35) Added Date field DESCRIPTION. DESCRIPTION metadata now used generate package citations. (#25) Package vingettes formatted html_vignette reduce file size. Removed redundant PDF word document versions ss3diags_Handbook vignette. Enabled markdown support roxygen. Enabled Cross-reference links.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-203","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.3","title":"ss3diags 2.0.3","text":"Changed r4ss dependency 1.44.0 (CRAN version) . Replaced default R CMD CHECK workflow NOAA-fish-tools/ghactions4r’s version. Fixed Ensemble Quantile Shading Issues (#4) Replaced example datasets ss3diags cookbook, handbook current “simple” ensemble model. Fixup minor code documentation formatting issues. SSmase SSplotHcxval: Fixed code styler’s dollar subset conversion issues. example:`message(‘x$name 1,2,3,4’)`","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-202","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.2","title":"ss3diags 2.0.2","text":"Changed r4ss CRAN version (1.36.1) dependency development version legendfun -> r4ss::add_legend pngfun -> r4ss::save_png rc -> r4ss::rich_colors_short sspar -> r4ss::sspar Fix SSplotRetro.R indention causing issues code styler","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-201","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.1","title":"ss3diags 2.0.1","text":"Change SSplotJABBAres show combined seasonal data boxplots Fixup links Cookbook sripts. Formatted DESCRIPTION URL BugReports links PIFSCstockassessments repo add R package site.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-200","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.0","title":"ss3diags 2.0.0","text":"simple, cod-like, Stock Synthesis model, simulated via ss3sim, replaces Pacific North Hake (pac.hke) North Atlantic Shortfin Mako Shark (natl.sma) example datasets. SSplotRetro: fixed bug shading uncertainty area shows xlims specified. SSplotJABBAres: added ‘con’ option subplots argument conditional age--length data can plotted. Also added seas argument user can specify data combined across seasons within year kept separate. SScompsTA1.8: added seas argument users can specify data combined across seasons within year kept separate. SSplot functions (SSplotModelComp, SSplotEnsemble, SSplotHCxval, SSplotJABBAres, SSplotRetro): Marked plot, png, pdf, print, new deprecated. defunct future version. Added NEWS.md file track changes package.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-108","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.8","title":"ss3diags 1.0.8","text":"Fixed MASE","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-107","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.7","title":"ss3diags 1.0.7","text":"Bug fixes","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-106","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.6","title":"ss3diags 1.0.6","text":"Improved SSdiagsMCMC","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-105","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.5","title":"ss3diags 1.0.5","text":"Updated SSdeltaMVLN","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-104","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.4","title":"ss3diags 1.0.4","text":"Reference: authors changes","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-103","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.3","title":"ss3diags 1.0.3","text":"Added annF_ quantaties","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-102","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.2","title":"ss3diags 1.0.2","text":"Added aut","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-101","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.1","title":"ss3diags 1.0.1","text":"Added SSplotH","code":""}]
+[{"path":"https://pifscstockassessments.github.io/ss3diags/CODE_OF_CONDUCT.html","id":null,"dir":"","previous_headings":"","what":"Code of Conduct","title":"Code of Conduct","text":"follow NFMS Fisheries Toolbox Code Conduct. NFMS Fisheries Toolbox Code Conduct adapted Contributor Covenant, version 1.4, available https://www.contributor-covenant.org/version/1/4/code--conduct.html answers common questions code conduct, see https://www.contributor-covenant.org/faq","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/CONTRIBUTING.html","id":null,"dir":"","previous_headings":"","what":"Contributing to ss3diags","title":"Contributing to ss3diags","text":"Thank interest contributing! strive follow NMFS Fisheries Toolbox Contribution Guide. Note guidelines, rules, open collaborations ways may work better . Please feel free reach us opening issue repository emailing project maintatainer megumi.oshima@noaa.gov. project everyone participating governed NMFS Fisheries Toolbox Code Conduct. participating, expected uphold code. Please report unacceptable behavior fisheries.toolbox@noaa.gov. Note maintainers ss3diags access email account, unacceptable behavior maintainers can also reported .","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Jitter Analysis","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running retrospective (case dir_jitter). easy way get latest release stock synthesis use r4ss function get_ss3_exe(). run model dir_jitter first produce necessary output files. recommended jitter runs subdirectory model run. keep output files separate diagnostic tests may run.","code":"install_github(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_jitter <- file.path(tempdir(check = TRUE), \"jitter\") dir.create(dir_jitter, showWarnings = FALSE, recursive = TRUE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_jitter) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_jitter, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/Rtmp2ZDhQV/jitter/ss3 r4ss::run(dir = dir_jitter, exe = \"ss3\", verbose = FALSE) #> [1] \"ran model\""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"jitter","dir":"Articles","previous_headings":"","what":"Jitter","title":"Jitter Analysis","text":"example, run 50 jitters. jitter() function automates entire process need give arguments run produce total likelihoods run. Full documentation jitter() function can found r4ss website. analyze output 50 runs, use r4ss::SSgetoutput() r4ss::SSsummarize() shown . key sections may want check compare across models , likelihoods, derived quantities, estimated parameters. may also want check models converged. can check maximum gradients make sure small (< 0.0001). can also compare estimated spawning biomass, extreme values (+2x <0.5x base spawning biomass) suggests model didn’t converge.","code":"Njitter <- 50 jit.likes <- r4ss::jitter(   dir = dir_jitter,   Njitter = Njitter,   init_values_src = 1,   jitter_fraction = 0.1,   exe = \"ss3\",   printlikes = FALSE,   verbose = FALSE ) jit_mods <- SSgetoutput(   keyvec = 0:Njitter, # 0 to include reference run (Report0.sso)   getcomp = FALSE,   dirvec = dir_jitter,   getcovar = FALSE,   verbose = FALSE ) jit_summary <- SSsummarize(jit_mods, verbose = FALSE) head(jit_summary$likelihoods) #>       replist0     replist1     replist2     replist3     replist4     replist5 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>       replist6     replist7     replist8     replist9    replist10    replist11 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist12    replist13    replist14    replist15    replist16    replist17 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist18    replist19    replist20    replist21    replist22    replist23 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74853e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist24    replist25    replist26    replist27    replist28    replist29 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33480e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist30    replist31    replist32    replist33    replist34    replist35 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist36    replist37    replist38    replist39    replist40    replist41 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33480e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist42    replist43    replist44    replist45    replist46    replist47 #> 1  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02  7.54302e+02 #> 2  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10  1.33479e-10 #> 3  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01  1.74852e-01 #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 -7.11813e+00 #> 5  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02  3.66756e+02 #> 6  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02  2.31845e+02 #>      replist48    replist49    replist50       Label #> 1  7.54302e+02  7.54302e+02  7.54302e+02       TOTAL #> 2  1.33479e-10  1.33479e-10  1.33479e-10       Catch #> 3  1.74853e-01  1.74852e-01  1.74852e-01 Equil_catch #> 4 -7.11813e+00 -7.11813e+00 -7.11813e+00      Survey #> 5  3.66756e+02  3.66756e+02  3.66756e+02 Length_comp #> 6  2.31845e+02  2.31845e+02  2.31845e+02    Age_comp head(jit_summary$quants) #>   replist0 replist1 replist2 replist3 replist4 replist5 replist6 replist7 #> 1  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8  54773.8 #> 2  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4 #> 3  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4  26071.4 #> 4  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1  24096.1 #> 5  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1  22126.1 #> 6  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5  20143.5 #>   replist8 replist9 replist10 replist11 replist12 replist13 replist14 replist15 #> 1  54773.8  54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2  26071.4  26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3  26071.4  26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4  24096.1  24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5  22126.1  22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6  20143.5  20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist16 replist17 replist18 replist19 replist20 replist21 replist22 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist23 replist24 replist25 replist26 replist27 replist28 replist29 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist30 replist31 replist32 replist33 replist34 replist35 replist36 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist37 replist38 replist39 replist40 replist41 replist42 replist43 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>   replist44 replist45 replist46 replist47 replist48 replist49 replist50 #> 1   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8   54773.8 #> 2   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 3   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4   26071.4 #> 4   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1   24096.1 #> 5   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1   22126.1 #> 6   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5   20143.5 #>         Label   Yr #> 1  SSB_Virgin   NA #> 2 SSB_Initial   NA #> 3    SSB_2011 2011 #> 4    SSB_2012 2012 #> 5    SSB_2013 2013 #> 6    SSB_2014 2014 head(jit_summary$pars) #>    replist0  replist1  replist2  replist3  replist4  replist5  replist6 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>    replist7  replist8  replist9 replist10 replist11 replist12 replist13 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist14 replist15 replist16 replist17 replist18 replist19 replist20 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist21 replist22 replist23 replist24 replist25 replist26 replist27 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist28 replist29 replist30 replist31 replist32 replist33 replist34 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist35 replist36 replist37 replist38 replist39 replist40 replist41 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist42 replist43 replist44 replist45 replist46 replist47 replist48 #> 1  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 2 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 22.769000 #> 3 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 71.807200 #> 4  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165  0.142165 #> 5  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #> 6  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000  0.100000 #>   replist49 replist50                 Label Yr recdev #> 1  0.100000  0.100000 NatM_uniform_Fem_GP_1 NA  FALSE #> 2 22.769000 22.769000    L_at_Amin_Fem_GP_1 NA  FALSE #> 3 71.807200 71.807200    L_at_Amax_Fem_GP_1 NA  FALSE #> 4  0.142165  0.142165    VonBert_K_Fem_GP_1 NA  FALSE #> 5  0.100000  0.100000     CV_young_Fem_GP_1 NA  FALSE #> 6  0.100000  0.100000       CV_old_Fem_GP_1 NA  FALSE # Maximum gradient converged_grad <- which(jit_summary$maxgrad < 0.0001)  converged_ssb <- jit_summary$SpawnBio %>%   mutate(across(c(1:(Njitter + 1)),     .fns = ~ . / replist0   )) %>% # for each column, divide SSB by SSB from the reference run (replist)   select(-Label) %>%   pivot_longer(col = c(1:(Njitter + 1)), names_to = \"jitter\", values_to = \"SSB\") %>%   pivot_wider(names_from = Yr, values_from = SSB) %>%   mutate(rownumber = seq(1, nrow(.))) %>%   tibble::column_to_rownames(\"jitter\") %>%   filter_at(vars(1:(ncol(.) - 1)), all_vars((.) < 2 & (.) > 0.5)) %>% # keep only rows where SSB is a reasonable value   select(rownumber) %>%   pull(rownumber) converged_mods <- intersect(converged_grad, converged_ssb) # getting which models are in both groups converged_jitters <- jit_mods[converged_grad] converged_sum <- SSsummarize(converged_jitters, verbose = FALSE)"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Jitter.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Jitter Analysis","text":"compare likelihoods runs, plot shown . built functions (writing vignette) r4ss ss3diags generate likelihood plot, therefore provide code tidyverse syntax (using ggplot2) visualize results.  figure plots total likelihood jitter run red line indicates total likelihood value reference run. runs points red line, use converged parameter values run lowest likelihood value starting values base model. can also use r4ss::SSplotComparisons() compare spawning biomass trajectories jitter runs see impact different parameter values estimated quantities.","code":"converged_sum$likelihoods %>%   filter(str_detect(Label, \"TOTAL\")) %>%   select(-Label) %>%   pivot_longer(cols = everything(), names_to = \"jitter\", values_to = \"likelihood\") %>%   separate(jitter, into = c(\"replist\", \"jitter\"), sep = \"(?<=[A-Za-z])(?=[0-9])\") %>%   mutate(jitter = as.numeric(jitter)) %>%   ggplot(aes(x = jitter, y = likelihood)) +   geom_point(size = 3) +   geom_hline(aes(yintercept = likelihood[1]), color = \"red\") +   theme_classic() +   labs(     y = \"Total Likelihood\",     x = \"Jitter runs at a converged solution\"   ) SSplotComparisons(converged_sum,   subplots = 2,   ylimAdj = 1,   new = FALSE ) #> showing uncertainty for all models #> subplot 2: spawning biomass with uncertainty intervals"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Retrospective Analysis","text":"run stock synthesis model, 4 input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running retrospective (case dir_retro). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_retro <- file.path(tempdir(check = TRUE), \"retrospectives\") dir.create(dir_retro, showWarnings = FALSE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_retro) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_retro, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpWMaip6/retrospectives/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"retrospective-analysis","dir":"Articles","previous_headings":"","what":"Retrospective Analysis","title":"Retrospective Analysis","text":"4 input files SS executable file, can run retrospective analysis shown . running five one-year peels, run, one five years data removed reference model model re-run total five times (.e. peel 1 removes last year data, peel 2 removes last 2 years data, etc.) . number year peels can adjusted years argument. SS executable file using named something “ss3” (e.g. ss_opt_win.exe), need specify argument exe = \"ss_opt_win\". Full documentation retro() function can found r4ss website.","code":"r4ss::retro(dir = dir_retro, exe = \"ss3\", years = 0:-5, verbose = FALSE) #> Warning in base::sink(type = \"output\", split = FALSE): no sink to remove"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Retrospective Analysis","text":"visualize outputted results inspect retrospective patterns, need load report files R use SSplotRetro() function ss3diags. easiest way load multiple report files using r4ss::SSgetoutput() r4ss::SSsummarize() functions. default sub-directories peel, 0 5, labeled retro0 retro-5.  default settings plot spawning stock biomass time series peel, reference run (.e. original, full time series model) “Ref” line successive peel colored lines labeled terminal year value. solid line ends terminal year followed dashed line extending circle representing one year forecast estimate. Displaying projected SSB value helps assessing forecast bias. note, forecasts done automatically using r4ss::retro() based settings forecast.ss. grey shaded area represents 95% confidence intervals uncertainty around spawning biomass time series. Displayed center plot combined Mohn’s \\(\\rho\\) retrospective runs, parentheses forecast Mohn’s \\(\\rho\\).","code":"retro_mods <- r4ss::SSgetoutput(dirvec = file.path(dir_retro, \"retrospectives\", paste0(\"retro\", seq(0, -5, by = -1))), verbose = F) retroSummary <- r4ss::SSsummarize(retro_mods, verbose = F) SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE) #> Mohn's Rho stats, including one step ahead forecasts: #>   type     peel         Rho  ForecastRho #> 1  SSB     2021 -0.20753686 -0.221050163 #> 2  SSB     2020 -0.19601072 -0.227304734 #> 3  SSB     2019 -0.29238505 -0.338600758 #> 4  SSB     2018 -0.00474920 -0.007462034 #> 5  SSB     2017  0.08716428  0.098849082 #> 6  SSB Combined -0.12270351 -0.139113722"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Visualizing Output","what":"Customizing the Plot","title":"Retrospective Analysis","text":"Retro plots can customized many ways, common features may want specify : removing uncertainty intervals adjusting years shown x-axis turning 1-year ahead forecasting displaying combined \\(\\rho\\) value plot Examples changes shown , incrementally making adjustment.  Additionally, fishing mortality can plotted instead spawning biomass replacing subplots = \"SSB\" subplots = \"F\"","code":"r4ss::sspar(mfrow = c(2, 2), plot.cex = 0.8) retro1 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE) #> Mohn's Rho stats, including one step ahead forecasts: retro2 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022)) #> Mohn's Rho stats, including one step ahead forecasts: retro3 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022), forecast = FALSE) #> Mohn's Rho stats, including one step ahead forecasts: retro4 <- SSplotRetro(retroSummary, subplots = \"SSB\", add = TRUE, uncertainty = FALSE, xlim = c(2015, 2022), forecast = FALSE, showrho = FALSE, forecastrho = FALSE) #> Mohn's Rho stats, including one step ahead forecasts:"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/Retrospective-Analysis.html","id":"summary-table","dir":"Articles","previous_headings":"Visualizing Output","what":"Summary Table","title":"Retrospective Analysis","text":"addition retrospective plots, summary statistics table can produced using SShcbias(). table includes type estimate (SSB F) year removed “peel” Mohn’s \\(\\rho\\) forecast bias year overall (“Combined”). Mohn’s \\(\\rho\\) measure severity bias retrospective patterns forecast bias estimate bias forecasted quantities years data removed. rule thumb proposed Hurtado-Ferror et al. (2014) Mohn’s \\(\\rho\\) values long-lived species, \\(\\rho\\) value fall -0.15 0.20.","code":"SShcbias(retroSummary) #> Mohn's Rho stats, including one step ahead forecasts: #>    type     peel         Rho   ForcastRho #> 1   SSB     2021 -0.20753686 -0.221050163 #> 2   SSB     2020 -0.19601072 -0.227304734 #> 3   SSB     2019 -0.29238505 -0.338600758 #> 4   SSB     2018 -0.00474920 -0.007462034 #> 5   SSB     2017  0.08716428  0.098849082 #> 6   SSB Combined -0.12270351 -0.139113722 #> 7     F     2021  0.28425747  0.285936183 #> 8     F     2020  0.30941305  0.349748774 #> 9     F     2019  0.52629045  0.632574831 #> 10    F     2018  0.01822898  0.022822958 #> 11    F     2017 -0.04896989 -0.053882358 #> 12    F Combined  0.21784401  0.247440078"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"ASPM","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running ASPM (case dir_aspm). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_tmp <- tempdir(check = TRUE) dir_aspm <- file.path(dir_tmp, \"aspm\") dir.create(dir_aspm, showWarnings = FALSE, recursive = TRUE) list.files(files_path) ## [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_tmp) ## [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_tmp, version = \"v3.30.21\") ## The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpOZxxeY/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"aspm","dir":"Articles","previous_headings":"","what":"ASPM","title":"ASPM","text":"4 input files, need determine components need turned run ASPM. ASPM depend index abundance catch data, composition data, recruitment deviations, etc. need turned . provide example includes multiple types data recruitment deviations, however, exact steps necessary individual model may vary depending complexity components included. Therefore steps may fully comprehensive model sure check components may need change. , show use r4ss functions make necessary changes control.ss ss.par files.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"generate-files","dir":"Articles","previous_headings":"ASPM","what":"Generate files","title":"ASPM","text":"order get ss.par file, need run model . also produce new data control file use input files. run model dir_tmp copy new files dir_aspm.","code":"r4ss::run(dir = dir_tmp, verbose = FALSE, exe = \"ss3\") ## [1] \"ran model\" files <- c(\"data_echo.ss_new\", \"control.ss_new\", \"starter.ss\", \"forecast.ss\", \"ss.par\", \"ss3\") file.copy(from = file.path(dir_tmp, files), to = dir_aspm) ## [1] TRUE TRUE TRUE TRUE TRUE TRUE"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"recruitment-deviations","dir":"Articles","previous_headings":"ASPM","what":"Recruitment Deviations","title":"ASPM","text":"Set recruitment devations ss.par 0.","code":"par <- SS_readpar_3.30(   parfile = file.path(dir_aspm, \"ss.par\"),   datsource = file.path(dir_aspm, \"data_echo.ss_new\"),   ctlsource = file.path(dir_aspm, \"control.ss_new\"),   verbose = FALSE ) par$recdev1 ##       year      recdev ##  [1,] 2011 -0.06005247 ##  [2,] 2012 -0.01284866 ##  [3,] 2013  0.13478706 ##  [4,] 2014  0.11410144 ##  [5,] 2015 -0.08325396 ##  [6,] 2016  0.14556845 ##  [7,] 2017 -0.12973978 ##  [8,] 2018 -0.18308123 ##  [9,] 2019  0.02442762 ## [10,] 2020 -0.08979813 ## [11,] 2021 -0.07812317 ## [12,] 2022  0.21801284 par$recdev_forecast ##       year recdev ##  [1,] 2023      0 ##  [2,] 2024      0 ##  [3,] 2025      0 ##  [4,] 2026      0 ##  [5,] 2027      0 ##  [6,] 2028      0 ##  [7,] 2029      0 ##  [8,] 2030      0 ##  [9,] 2031      0 ## [10,] 2032      0 par$recdev1[, \"recdev\"] <- 0  # Would run if forecasts recdevs were not already 0 # par$recdev_forecast[,\"recdev\"] <- 0 SS_writepar_3.30(   parlist = par,   outfile = file.path(dir_aspm, \"ss.par\"),   overwrite = T, verbose = FALSE ) ## $headerlines ## [1] \"# Number of parameters = 32 Objective function value = 754.301687441726  Maximum gradient component = 8.77017492766611e-07\" ## [2] \"# dummy_parm:\"                                                                                                              ## [3] \"1.00000000000\"                                                                                                              ##  ## $MG_parms ##                            INIT       ESTIM ## NatM_p_1_Fem_GP_1    0.10000000  0.10000000 ## L_at_Amin_Fem_GP_1  22.76900000 22.76899194 ## L_at_Amax_Fem_GP_1  71.80720000 71.80721125 ## VonBert_K_Fem_GP_1   0.14216500  0.14216482 ## CV_young_Fem_GP_1    0.10000000  0.10000000 ## CV_old_Fem_GP_1      0.10000000  0.10000000 ## Wtlen_1_Fem_GP_1     0.00000244  0.00000244 ## Wtlen_2_Fem_GP_1     3.34694000  3.34694000 ## Mat50%_Fem_GP_1     55.00000000 55.00000000 ## Mat_slope_Fem_GP_1  -0.25000000 -0.25000000 ## Eggs_alpha_Fem_GP_1  1.00000000  1.00000000 ## Eggs_beta_Fem_GP_1   0.00000000  0.00000000 ## NatM_p_1_Mal_GP_1    0.00000000  0.00000000 ## L_at_Amin_Mal_GP_1   0.00000000  0.00000000 ## L_at_Amax_Mal_GP_1   0.00000000  0.00000000 ## VonBert_K_Mal_GP_1   0.00000000  0.00000000 ## CV_young_Mal_GP_1    0.00000000  0.00000000 ## CV_old_Mal_GP_1      0.00000000  0.00000000 ## Wtlen_1_Mal_GP_1     0.00000244  0.00000244 ## Wtlen_2_Mal_GP_1     3.34694000  3.34694000 ## CohortGrowDev        1.00000000  1.00000000 ## FracFemale_GP_1      0.50000000  0.50000000 ##  ## $SR_parms ##               INIT    ESTIM ## SR_LN(R0)   8.9274 8.927395 ## SR_BH_steep 0.8000 0.800000 ## SR_sigmaR   0.6000 0.600000 ## SR_regime   0.0000 0.000000 ## SR_autocorr 0.0000 0.000000 ##  ## $recdev1 ##       year recdev ##  [1,] 2011      0 ##  [2,] 2012      0 ##  [3,] 2013      0 ##  [4,] 2014      0 ##  [5,] 2015      0 ##  [6,] 2016      0 ##  [7,] 2017      0 ##  [8,] 2018      0 ##  [9,] 2019      0 ## [10,] 2020      0 ## [11,] 2021      0 ## [12,] 2022      0 ##  ## $recdev_forecast ##       year recdev ##  [1,] 2023      0 ##  [2,] 2024      0 ##  [3,] 2025      0 ##  [4,] 2026      0 ##  [5,] 2027      0 ##  [6,] 2028      0 ##  [7,] 2029      0 ##  [8,] 2030      0 ##  [9,] 2031      0 ## [10,] 2032      0 ##  ## $init_F ## [1] 0.1 ##  ## $Q_parms ##                           INIT      ESTIM ## LnQ_base_SURVEY1(2)   0.476759  0.4767585 ## Q_extraSD_SURVEY1(2)  0.000000  0.0000000 ## LnQ_base_SURVEY2(3)  -6.304070 -6.3040672 ##  ## $S_parms ##                            INIT     ESTIM ## SizeSel_P_1_FISHERY(1) 56.51380 56.513807 ## SizeSel_P_2_FISHERY(1) 20.17930 20.179340 ## SizeSel_P_1_SURVEY1(2) 36.02330 36.023325 ## SizeSel_P_2_SURVEY1(2)  5.33502  5.335021 ## AgeSel_P_1_SURVEY2(3)   0.00000  0.000000 ## AgeSel_P_2_SURVEY2(3)   0.00000  0.000000"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"starter-file","dir":"Articles","previous_headings":"ASPM","what":"Starter File","title":"ASPM","text":"Change starter file read ss.par (init_values_src = 1) use new data control files.","code":"starter <- SS_readstarter(file = file.path(dir_aspm, \"starter.ss\"), verbose = FALSE) starter$datfile <- \"data_echo.ss_new\" starter$ctlfile <- \"control.ss_new\" starter$init_values_src <- 1 SS_writestarter(starter,   dir = dir_aspm,   overwrite = TRUE,   verbose = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"control-file","dir":"Articles","previous_headings":"ASPM","what":"Control File","title":"ASPM","text":"estimation phases following parameters may need changed: length selectivity age selectivity size selectivity steepness sigmaR recruitment deviations Additionally, likelihood components may need turned well. can using lambda options control file. examples include: length-composition data age-composition data size-composition data initial F","code":"control <- SS_readctl_3.30(   file = file.path(dir_aspm, \"control.ss_new\"),   datlist = file.path(dir_aspm, \"data_echo.ss_new\"),   verbose = FALSE )  control$SR_parms ##               LO HI   INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link ## SR_LN(R0)    6.0 12 8.9274  10.3  10.0       0     1            0        0 ## SR_BH_steep  0.2  1 0.8000   0.8   1.0       0    -4            0        0 ## SR_sigmaR    0.0  2 0.6000   0.8   0.8       0    -4            0        0 ## SR_regime   -5.0  5 0.0000   0.0   1.0       0    -4            0        0 ## SR_autocorr  0.0  0 0.0000   0.0   0.0       0   -99            0        0 ##             dev_minyr dev_maxyr dev_PH Block Block_Fxn ## SR_LN(R0)           0         0      0     0         0 ## SR_BH_steep         0         0      0     0         0 ## SR_sigmaR           0         0      0     0         0 ## SR_regime           0         0      0     0         0 ## SR_autocorr         0         0      0     0         0 # Would need to run if PHASES were positive for \"steep\" and \"sigmaR\" # control$SR_parms[c(2,3),\"PHASE\"] <- c(-4,-4) control$age_selex_parms ##                       LO HI INIT PRIOR PR_SD PR_type PHASE env_var&link ## AgeSel_P_1_SURVEY2(3)  0 20    0     5    99       0   -99            0 ## AgeSel_P_2_SURVEY2(3)  0 20    0     6    99       0   -99            0 ##                       dev_link dev_minyr dev_maxyr dev_PH Block Block_Fxn ## AgeSel_P_1_SURVEY2(3)        0         0         0      0     0         0 ## AgeSel_P_2_SURVEY2(3)        0         0         0      0     0         0 # would need to run if PHASES were positive for age selectivity # control$age_selex_parms[,\"PHASE\"] <- control$age_selex_parms[,\"PHASE\"] * -1 control$size_selex_parms[, \"PHASE\"] <- control$size_selex_parms[, \"PHASE\"] * -1 control$recdev_early_phase <- -4 control$recdev_phase <- -2  new_lambdas <- data.frame(   like_comp = c(4, 4, 5, 5, 7, 7, 9, 9, 9, 10),   fleet = c(1, 2, 1, 2, 1, 2, 1, 2, 3, 1),   phase = rep(1, 10),   value = rep(0, 10),   sizefreq_method = rep(1, 10) ) new_lambdas ##    like_comp fleet phase value sizefreq_method ## 1          4     1     1     0               1 ## 2          4     2     1     0               1 ## 3          5     1     1     0               1 ## 4          5     2     1     0               1 ## 5          7     1     1     0               1 ## 6          7     2     1     0               1 ## 7          9     1     1     0               1 ## 8          9     2     1     0               1 ## 9          9     3     1     0               1 ## 10        10     1     1     0               1 control$lambdas <- new_lambdas control$N_lambdas <- nrow(new_lambdas) SS_writectl_3.30(control,   outfile = file.path(dir_aspm, \"control.ss_new\"),   overwrite = TRUE, verbose = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"run-aspm","dir":"Articles","previous_headings":"ASPM","what":"Run ASPM","title":"ASPM","text":"","code":"r4ss::run(dir = dir_aspm, exe = \"ss3\", skipfinished = FALSE, verbose = FALSE) ## [1] \"ran model\""},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/aspm.html","id":"visualize-results","dir":"Articles","previous_headings":"ASPM","what":"Visualize Results","title":"ASPM","text":"compare ASPM model age-structured model, can use SSplotComparisons(). Comparing spawning biomass F estimates two models fits indices abundance can help understand enough information indices inform production function.","code":"mods <- SSgetoutput(dirvec = c(   dir_tmp,   dir_aspm ), verbose = FALSE)  mods_sum <- SSsummarize(mods, verbose = FALSE)  SSplotComparisons(mods_sum,   legendlabels = c(\"Ref\", \"ASPM\"),   subplots = c(2, 8, 14), new = F ) ## showing uncertainty for all models ## subplot 2: spawning biomass with uncertainty intervals ## subplot 8: F value with uncertainty ## subplot 14: index fits on a log scale"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Hindcast Cross-Validation","text":"HCxval implemented using ss3diags::SSplotHCxval(), produces novel HCxval diagnostic plot computes MASE scores indices abundance, mean lengths, mean ages observations falling within hindcast evaluation period.  plots , see , fleets, model fairly good prediction skills index abundance data (compared random walk). plots, white points white dashed line observed data included model truncated time series. larger colored points observed data retrospective peel (.e. data removed peel). smaller colored points dashed lines show model predicted values. “Ref” line model run complete time series data. grey shaded areas represent uncertainty data, darker portion indicating portion included model lighter portion indicating ones removed projected. MASE scores displayed MASE adjusted MASE parentheses.","code":"r4ss::sspar(mfrow = c(1, 2)) SSplotHCxval(retroSummary, subplots = \"cpue\", add = TRUE) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with only 1 of 5  prediction residuals for Index SURVEY1  #>  #>  Warning:  Unequal spacing of naive predictions residuals may influence the interpretation of MASE #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index SURVEY2 #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR  MAE.base  MASE.adj n.eval #> 1 SURVEY1      1 0.5026435 0.08879379 0.1766536 0.5026435      1 #> 2 SURVEY2      1 0.6149530 0.37737925 0.6136717 0.6149530      5"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"composition-data","dir":"Articles","previous_headings":"Visualizing Output","what":"Composition Data","title":"Hindcast Cross-Validation","text":"visualize mean length mean age, need add additional step. forecast length- age-composition information stored “ghost files” SS report.sso file, need use ss3diags::SSretroComps() extract summarize information creating plots.","code":"retroSummary_comps <- SSretroComps(retro_mods)  r4ss::sspar(mfrow = c(1, 2)) hcl <- SSplotHCxval(retroSummary_comps, subplots = \"len\", add = TRUE, ylim = c(40, 75)) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #>  Computing MASE with only 1 of 5  prediction residuals for Index SURVEY1  #>  #>  Warning:  Unequal spacing of naive predictions residuals may influence the interpretation of MASE #>  #> MASE stats by Index:"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Visualizing Output","what":"Customizing the Plot","title":"Hindcast Cross-Validation","text":"HCxval plots can customized many ways, common features may want specify : displaying specific fleet removing uncertainty intervals adjusting x- y-axis displaying adjusted MASE value plot Examples changes shown , incrementally making adjustment.","code":"r4ss::sspar(mfrow = c(2, 2)) SSplotHCxval(retroSummary_comps, subplots = \"len\", add = TRUE, indexselect = 1) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE, ylim = c(45, 70) ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 SSplotHCxval(retroSummary_comps,   subplots = \"len\", add = TRUE,   indexselect = 1, indexUncertainty = FALSE, ylim = c(45, 70), show.mase.adj = F ) #> Plotting Hindcast Cross-Validation (one-step-ahead)  #>  #>  Computing MASE with all 5 of 5  prediction residuals for Index FISHERY #>  #> MASE stats by Index: #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/hcxval.html","id":"summary-table","dir":"Articles","previous_headings":"","what":"Summary Table","title":"Hindcast Cross-Validation","text":"addition HCxval plots, summary statistics table can produced using ss3diags::SSmase(). table includes: Index - fleet Season MASE - MASE score MAE.PR - mean absolute error prediction residuals MASE.base - naive prediction MASE.adj - adjusted MASE score n.eval - number points prediction skill calculated Adjusted MASE gets invoked cases inter-annual variation observed values small (default MAE < 0.1 naive predictions log(y[t+1])-log(y[t])). reasoning prediction residuals must already accurate fall threshold. adjusted MASE essential keep naive prediction MAE denominator MASE maximum. show effect changing adjustment threshold default MAE.base.adj = 0.1 larger value MAE.base.adj = 0.15 MASE ratio mean absolute error prediction residuals MAE.PR residuals naive predictions MAE.base MASE.adj","code":"mase1 <- SSmase(retroSummary_comps, quant = \"len\", MAE.base.adj = 0.1) mase1 #>     Index Season      MASE     MAE.PR   MAE.base  MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.1034467      5 #> 2 SURVEY1      1 0.6526074 0.05142002 0.07879167 0.5142002      1 #> 3   joint        0.4628955 0.01719056 0.03713702 0.1719056      6 SSmase(retroSummary_comps, quant = \"len\", MAE.base.adj = 0.15) #>     Index Season      MASE     MAE.PR   MAE.base   MASE.adj n.eval #> 1 FISHERY      1 0.3591138 0.01034467 0.02880609 0.06896444      5 #> 2 SURVEY1      1 0.6526074 0.05142002 0.07879167 0.34280015      1 #> 3   joint        0.4628955 0.01719056 0.03713702 0.11460372      6 mase1$MAE.PR / mase1$MAE.base #> [1] 0.3591138 0.6526074 0.4628955 mase1$MASE #> [1] 0.3591138 0.6526074 0.4628955 mase1$MAE.PR / pmax(mase1$MAE.base, 0.1) #> [1] 0.1034467 0.5142002 0.1719056 mase1$MASE.adj #> [1] 0.1034467 0.5142002 0.1719056"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"model-inputs","dir":"Articles","previous_headings":"","what":"Model inputs","title":"Likelihood Profile","text":"run Stock Synthesis model, four input files required: starter.ss, forecast.ss, control.ss, data.ss. input files example model can found within ss3diags package accessed shown . Also, r4ss package installed, need install tutorial. need make sure SS executable file either path directory running profile (case dir_profile). easy way get latest release stock synthesis use r4ss function get_ss3_exe().","code":"install.packages(\"pak\") pak::pkg_install(\"r4ss/r4ss\") library(r4ss)  files_path <- system.file(\"extdata\", package = \"ss3diags\") dir_tmp <- tempdir(check = TRUE) dir_profile <- file.path(dir_tmp, \"profile\") dir.create(dir_profile, showWarnings = FALSE, recursive = TRUE) list.files(files_path) #> [1] \"control.ss\"  \"data.ss\"     \"forecast.ss\" \"starter.ss\" file.copy(from = list.files(files_path, full.names = TRUE), to = dir_tmp) #> [1] TRUE TRUE TRUE TRUE r4ss::get_ss3_exe(dir = dir_tmp, version = \"v3.30.21\") #> The stock synthesis executable for Linux v3.30.21 was downloaded to: /tmp/RtmpnhVp2Y/ss3"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"running-a-profile-on-r0","dir":"Articles","previous_headings":"","what":"Running a Profile on R0","title":"Likelihood Profile","text":"four input files SS executable file, can run likelihood profile shown . first step run model like profile . dir_tmp copy necessary files dir_profile. ’s best run profile subdirectory main model run keep output files separate diagnostic tests may run. input files dir_profile directory, need create vector values profile across. range increments choose depend model resolution want analyze likelihood profile. example use fairly coarse resolution speed total run time. also need modify starter file changing name control file read making sure likelihood calculated non-estimated quantities. run profile, use r4ss::profile() need specify partial string name parameter profiling (case “SR_LN” match “SR_LN(R0)”), vector values profile across. newctlfile control file adjusted values profilevec can named anything prefer, just needs match put starter file “ctlfile”. Full documentation profile() function can found r4ss website.","code":"r4ss::run(dir = dir_tmp, exe = \"ss3\", verbose = FALSE) #> [1] \"ran model\" files <- c(\"data.ss\", \"control.ss_new\", \"starter.ss\", \"forecast.ss\", \"ss.par\", \"ss3\") file.copy(from = file.path(dir_tmp, files), to = dir_profile) #> [1] TRUE TRUE TRUE TRUE TRUE TRUE CTL <- SS_readctl_3.30(file = file.path(dir_profile, \"control.ss_new\"), datlist = file.path(dir_profile, \"data.ss\"))  CTL$SR_parms #>               LO HI   INIT PRIOR PR_SD PR_type PHASE env_var&link dev_link #> SR_LN(R0)    6.0 12 8.9274  10.3  10.0       0     1            0        0 #> SR_BH_steep  0.2  1 0.8000   0.8   1.0       0    -4            0        0 #> SR_sigmaR    0.0  2 0.6000   0.8   0.8       0    -4            0        0 #> SR_regime   -5.0  5 0.0000   0.0   1.0       0    -4            0        0 #> SR_autocorr  0.0  0 0.0000   0.0   0.0       0   -99            0        0 #>             dev_minyr dev_maxyr dev_PH Block Block_Fxn #> SR_LN(R0)           0         0      0     0         0 #> SR_BH_steep         0         0      0     0         0 #> SR_sigmaR           0         0      0     0         0 #> SR_regime           0         0      0     0         0 #> SR_autocorr         0         0      0     0         0 # getting the estimated r0 value r0 <- CTL$SR_parms$INIT[1] # creating a vector that is +/- 1 unit away from the estimated value in increments of 0.2 r0_vec <- seq(r0 - 1, r0 + 1, by = 0.2) r0_vec #>  [1] 7.9274 8.1274 8.3274 8.5274 8.7274 8.9274 9.1274 9.3274 9.5274 9.7274 #> [11] 9.9274 START <- SS_readstarter(file = file.path(dir_profile, \"starter.ss\"), verbose = FALSE) START$prior_like <- 1 START$ctlfile <- \"control_modified.ss\" SS_writestarter(START, dir = dir_profile, overwrite = TRUE, verbose = F) profile(   dir = dir_profile,   newctlfile = \"control_modified.ss\",   string = \"SR_LN\",   profilevec = r0_vec,   exe = \"ss3\",   verbose = FALSE ) #> running profile i=1/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.9274  7.9274        1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=2/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  7.9274  8.1274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=3/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.1274  8.3274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=4/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.3274  8.5274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=5/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.5274  8.7274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=6/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.7274  8.9274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=7/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  8.9274  9.1274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=8/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.1274  9.3274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=9/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.3274  9.5274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=10/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.5274  9.7274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #> running profile i=11/11 #> Parameter names in control file matching input vector  #> 'strings' (n=1): SR_LN(R0) #> line numbers in control file (n=1): 120 #> Wrote new file to control_modified.ss with the following changes: #>   oldvals newvals oldphase newphase oldlos newlos oldhis newhis oldprior #> 1  9.7274  9.9274       -1       -1      6      6     12     12     10.3 #>   newprior oldprsd newprsd oldprtype newprtype     comment #> 1     10.3      10      10         0         0 # SR_LN(R0) #>     Value converged[whichruns]    TOTAL       Catch Equil_catch    Survey #> 1  7.9274                 TRUE 1067.570 4.40715e-01   16.620400  6.065520 #> 2  8.1274                 TRUE  940.077 2.29735e-01   12.985200  1.965820 #> 3  8.3274                 TRUE  844.236 1.08857e-01    9.799480 -2.132340 #> 4  8.5274                 TRUE  790.513 9.17170e-06    3.930790 -5.726270 #> 5  8.7274                 TRUE  762.562 6.48948e-08    0.271032 -7.140910 #> 6  8.9274                 TRUE  754.302 1.33458e-10    0.174869 -7.118110 #> 7  9.1274                 TRUE  758.927 2.10816e-13    1.337060 -6.106700 #> 8  9.3274                 TRUE  767.708 1.90347e-13    3.424990 -4.917570 #> 9  9.5274                 TRUE  777.243 1.15331e-13    6.433440 -3.857200 #> 10 9.7274                 TRUE  787.189 6.73658e-14   10.382600 -2.563580 #> 11 9.9274                 TRUE  798.152 4.05051e-14   15.279300 -0.380771 #>    Length_comp Age_comp Size_at_age Recruitment InitEQ_Regime #> 1      453.198  341.340     230.715   19.181500   0.00000e+00 #> 2      418.750  291.595     201.557   12.989400   0.00000e+00 #> 3      393.384  257.968     179.068    6.036600   0.00000e+00 #> 4      379.721  243.456     167.416    1.713560   1.54502e-30 #> 5      370.420  234.970     163.525    0.515980   1.54502e-30 #> 6      366.756  231.845     162.399    0.244060   1.54502e-30 #> 7      367.497  233.210     162.675    0.312441   0.00000e+00 #> 8      369.543  235.957     163.170    0.529082   0.00000e+00 #> 9      371.605  238.622     163.598    0.839498   1.54502e-30 #> 10     373.376  240.872     163.942    1.178030   0.00000e+00 #> 11     374.815  242.718     164.208    1.510550   0.00000e+00 #>    Forecast_Recruitment Parm_priors Parm_softbounds Parm_devs Crash_Pen #> 1                     0           0      0.00756177         0         0 #> 2                     0           0      0.00433602         0         0 #> 3                     0           0      0.00337783         0         0 #> 4                     0           0      0.00197985         0         0 #> 5                     0           0      0.00143663         0         0 #> 6                     0           0      0.00141332         0         0 #> 7                     0           0      0.00150262         0         0 #> 8                     0           0      0.00159065         0         0 #> 9                     0           0      0.00166199         0         0 #> 10                    0           0      0.00171844         0         0 #> 11                    0           0      0.00176282         0         0"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/likelihood.html","id":"visualizing-output","dir":"Articles","previous_headings":"","what":"Visualizing Output","title":"Likelihood Profile","text":"profile finished running, can visualize results determine conflict data sources. data sources reach negative log-likelihood (NLL) minimum R0 value, indicates good agreement . However, likely, one reach NLL minimum different R0 values global R0 value. sign conflict data sources may require consider data weighting.  profile plot shows changes log-likelihood across selected range values contributing data components. adjustable minimum contribution threshold component must meet appear figure (data source model show plot, contribution total likelihood may large enough). steepness trajectory indicates informative () data source . example, age data plot much steeper left side minimum R0 value index data, suggests age composition data informative model. can also plot data-type fleet-specific profiles using r4ss::PinerPlot(). plotting profile length composition data fleet likelihood survey data fleet. allow us see conflicts sources main drivers.","code":"profile_mods <- SSgetoutput(dirvec = dir_profile, keyvec = 1:length(r0_vec), verbose = FALSE) profile_mods_sum <- SSsummarize(profile_mods, verbose = FALSE) SSplotProfile(profile_mods_sum,   profile.string = \"SR_LN\",   profile.label = \"SR_LN(R0)\" ) #> Parameter matching profile.string=SR_LN: SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274 #> Likelihood components showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>                      frac_change include                            label #> TOTAL                     1.0000    TRUE                            Total #> Catch                     0.0014   FALSE                            Catch #> Equil_catch               0.0525    TRUE                Equilibrium catch #> Survey                    0.0422    TRUE                       Index data #> Length_comp               0.2759    TRUE                      Length data #> Age_comp                  0.3495    TRUE                         Age data #> Size_at_age               0.2181    TRUE                 Size-at-age data #> Recruitment               0.0605    TRUE                      Recruitment #> InitEQ_Regime             0.0000   FALSE Initital equilibrium recruitment #> Forecast_Recruitment      0.0000   FALSE             Forecast recruitment #> Parm_priors               0.0000   FALSE                           Priors #> Parm_softbounds           0.0000   FALSE                      Soft bounds #> Parm_devs                 0.0000   FALSE             Parameter deviations #> Crash_Pen                 0.0000   FALSE                    Crash penalty sspar(mfrow = c(1, 2)) PinerPlot(profile_mods_sum,   component = \"Length_like\",   main = \"Length\" ) #> Parameter matching profile.string = 'R0': 'SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274, #> Fleet-specific likelihoods showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>         frac_change include #> FISHERY      0.6825    TRUE #> SURVEY1      0.3208    TRUE #> SURVEY2      0.0000   FALSE PinerPlot(profile_mods_sum,   component = \"Surv_like\",   main = \"Survey\" ) #> Parameter matching profile.string = 'R0': 'SR_LN(R0) #> Parameter values (after subsetting based on input 'models'): 7.9274, 8.1274, 8.3274, 8.5274, 8.7274, 8.9274, 9.1274, 9.3274, 9.5274, 9.7274, 9.9274, #> Fleet-specific likelihoods showing max change as fraction of total change. #> To change which components are included, change input 'minfraction'. #>         frac_change include #> FISHERY      0.0000   FALSE #> SURVEY1      0.3218    TRUE #> SURVEY2      0.9202    TRUE"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"runs-test","dir":"Articles","previous_headings":"","what":"Runs Test","title":"Residual Analyses","text":"runs test nonparametric hypothesis test randomness data sequence calculates 2-sided p-value estimate number runs (.e., sequences values sign) reference value. runs test can diagnose model misspecification using residuals fits index composition data (Carvalho et al. 2017) testing non-random patterns residuals. addition, three-sigma limits can considered useful identifying potential outliers data point three standard deviations away expected residual process average unlikely given random process error observed residual distribution. example using “simple_small” SS model included within r4ss package. can read report file model output using r4ss::SS_output() function shown .  output SSplotRunstest() includes plot residuals fleet table results runs test ‘three-sigma limit’ values. plots , shaded area represents ‘three-sigma limit’, three residual standard deviations zero. individual residual points fall outside three-sigma limit, colored red. Green shaded area indicates residuals randomly distributed (p-value >= 0.05) whereas red shaded area indicates residuals randomly distributed. Failing runs test (p-value < 0.05) can indicative misspecification conflict indices composition data.","code":"library(r4ss)  files_path <- system.file(\"extdata\", \"simple_small\", package = \"r4ss\") report <- SS_output(dir = files_path, verbose = FALSE, printstats = FALSE) sspar(mfrow = c(1, 2)) SSplotRunstest(report, add = TRUE) #> Running Runs Test Diagnostics w/ plots forIndex #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Index: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1  0.159 Passed -0.7301441 0.7301441 cpue #> 2 SURVEY2  0.887 Passed -1.1052361 1.1052361 cpue"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"customizing-the-plot","dir":"Articles","previous_headings":"Runs Test","what":"Customizing the Plot","title":"Residual Analyses","text":"Runs test plots can customized needed. common features may want specify : plotting data types (default Index Abundance) plotting specific fleet(s) adjusting y-axis range Examples changes shown , incrementally making adjustment. plot data types, can specified subplots argument, options include “cpue”, “len”, “age”, “size”, “con”. “con” conditional size--age data “size” generalized size composition data. Fleets can specified using indexselect() function, takes vector fleet numbers plot.  Note small adjustment automatically added ylim provide extra white space. third plot, even though set y-axis range -0.5 0.5, y-axis goes -0.6 0.6. want extra space, set ylimAdj = 1 done 4th plot.","code":"sspar(mfrow = c(2, 2)) SSplotRunstest(report, subplots = \"len\", indexselect = 1, add = TRUE) #> Running Runs Test Diagnostics w/ plots forMean length #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean length: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 FISHERY  0.126 Passed -0.0613176 0.0613176  len SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE, ylim = c(-0.5, 0.5)) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age SSplotRunstest(report, subplots = \"age\", indexselect = 2, add = TRUE, ylim = c(-0.5, 0.5), ylimAdj = 1) #> Running Runs Test Diagnostics w/ plots forMean age #> Plotting Residual Runs Tests #> Residual Runs Test (/w plot) stats by Mean age: #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1   0.11 Passed -0.2743816 0.2743816  age"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"summary-table","dir":"Articles","previous_headings":"Runs Test","what":"Summary Table","title":"Residual Analyses","text":"addition residual plots, SSplotRunstest() produces summary table runs test output values, including: p-value runs test test passed failed (indicated green red shading plot) upper lower limits 3-sigma interval type data tested (CPUE, length-composition, age-composition, conditional age--length) produce summary table skip plot, e.g. faciliate automated processing, use SSrunstest().","code":"rcpue <- SSrunstest(report, quants = \"cpue\") #> Running Runs Test Diagnosics for Index #> Computing Residual Runs Tests #> Residual Runs Test stats by Index: rlen <- SSrunstest(report, quants = \"len\") #> Running Runs Test Diagnosics for Mean length #> Computing Residual Runs Tests #> Residual Runs Test stats by Mean length: rbind(rcpue, rlen) #>     Index runs.p   test  sigma3.lo sigma3.hi type #> 1 SURVEY1  0.159 Passed -0.7301441 0.7301441 cpue #> 2 SURVEY2  0.887 Passed -1.1052361 1.1052361 cpue #> 3 FISHERY  0.126 Passed -0.0613176 0.0613176  len #> 4 SURVEY1  0.841 Passed -0.1725225 0.1725225  len"},{"path":"https://pifscstockassessments.github.io/ss3diags/articles/residuals.html","id":"rmse","dir":"Articles","previous_headings":"","what":"RMSE","title":"Residual Analyses","text":"RMSE root mean square error useful evaluating far predictions fall observed data. ss3diags::SSplotJABBAres() function allows visualize full time series residuals fleets indicated data (index abundance composition). example , plot residuals index abundance, mean age (age-composition), mean length (length composition) fleets.  plots , point represents difference observed expected value (residual) color-coded correspond specific fleet. solid, color-coded vertical lines horizontal dashed line (y = 0) show distance 0 residual value. Box plots summarize spread residual values across fleets within year thick solid black line loess smoother fit residual points. Total RMSE displayed top right corner. assessing plot, important see patterns trends residuals, large overall RMSE , whether data different fleets generally agrees conflicts . retrieve just RMSE residual values without generating plot, SSrmse() produces named list 2 objects, RMSE residuals. can accessed shown . function useful automating analyses.","code":"sspar(mfrow = c(2, 2)) SSplotJABBAres(report, subplots = \"cpue\", add = TRUE) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 SURVEY1       21.6     4 #> 2 SURVEY2       27.7    12 #> 3 Combined      26.3    16 SSplotJABBAres(report, subplots = \"age\", add = TRUE) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 FISHERY        9      12 #> 2 SURVEY1        8.1     4 #> 3 Combined       8.8    16 SSplotJABBAres(report, subplots = \"len\", add = TRUE, ylim = c(-0.2, 0.2)) #> Plotting JABBA residual plot. #> is plot TRUE? TRUE #> drawing plot at #> Plot exists: #> RMSE stats by Index: #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 FISHERY        2.1    12 #> 2 SURVEY1        3.4     4 #> 3 Combined       2.5    16 rmse <- SSrmse(report, quants = \"cpue\")$RMSE residuals <- SSrmse(report, quants = \"cpue\")$residuals  rmse #> # A tibble: 3 × 3 #>   Fleet    RMSE.perc  Nobs #>   <chr>        <dbl> <int> #> 1 SURVEY1       21.6     4 #> 2 SURVEY2       27.7    12 #> 3 Combined      26.3    16  head(residuals) #>     Fleet Fleet_name Area   Yr Seas Subseas Month   Time Vuln_bio         Obs #> 925     2    SURVEY1    1 2013    1       2     7 2013.5 62947.50 144745.0000 #> 926     2    SURVEY1    1 2016    1       2     7 2016.5 49335.70  63760.3000 #> 927     2    SURVEY1    1 2019    1       2     7 2019.5 38132.00  59242.9000 #> 928     2    SURVEY1    1 2022    1       2     7 2022.5 34045.80  49649.7000 #> 929     3    SURVEY2    1 2011    1       2     7 2011.5  6306.83     11.5668 #> 930     3    SURVEY2    1 2012    1       2     7 2012.5  6544.96     13.9955 #>             Exp     Calc_Q      Eff_Q  SE SE_input         Dev        Like #> 925 101399.0000 1.61084000 1.61084000 0.3      0.3  0.35591400 7.03749e-01 #> 926  79472.2000 1.61084000 1.61084000 0.3      0.3 -0.22027600 2.69564e-01 #> 927  61424.7000 1.61084000 1.61084000 0.3      0.3 -0.03616590 7.26653e-03 #> 928  54842.4000 1.61084000 1.61084000 0.3      0.3 -0.09947210 5.49706e-02 #> 929     11.5342 0.00182885 0.00182885 0.7      0.7  0.00281831 8.10497e-06 #> 930     11.9698 0.00182885 0.00182885 0.7      0.7  0.15635300 2.49451e-02 #>     Like+log(s) SuprPer Use    residuals #> 925   -0.500223      NA   1  0.355910344 #> 926   -0.934409      NA   1 -0.220276535 #> 927   -1.196710      NA   1 -0.036166093 #> 928   -1.149000      NA   1 -0.099471269 #> 929   -0.356667      NA   1  0.002822391 #> 930   -0.331730      NA   1  0.156349038"},{"path":"https://pifscstockassessments.github.io/ss3diags/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Henning Winker. Author. Felipe Carvalho. Author. Massimiliano Cardinale. Author. Laurence Kell. Author. Megumi Oshima. Author, maintainer. Eric Fletcher. Author.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E (2024). ss3diags: Stock Synthesis Model Diagnostics Intergated Stock Assessments. R package version 2.2.0, https://github.com/PIFSCstockassessments/ss3diags.","code":"@Manual{,   title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments},   author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher},   year = {2024},   note = {R package version 2.2.0},   url = {https://github.com/PIFSCstockassessments/ss3diags}, }"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"ss3diags-","dir":"","previous_headings":"","what":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"R package ss3diags enables users apply advanced diagnostics evaluate Stock Synthesis model. Diagnostics include residual analyses, hindcast cross-validation techniques, retrospective analyses. Functions also allow users reproduce key model diagnostics plots presented paper ‘Cookbook Using Model Diagnostics Integrated Stock Assessments’ (Carvalho et al. 2021). ss3diags Github repository provides step--step R recipes : Run jitter analysis Conduct retrospective analysis Use hindcast cross-validation log-likelood profiling R0 Run ASPM diagnostic Evaluate model fit Stock Synthesis making use comprehensive collection R functions available R packages r4ss ss3diags.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"ss3diags currently supported CRAN. can install development version ss3diags GitHub : package installed can loaded : examples run common diagnostic tests SS models visualize results diagnostic tests using r4ss ss3diags packages, please refer articles package website.","code":"# install.packages(\"remotes\") remotes::install_github(\"PIFSCstockassessments/ss3diags\") library(ss3diags)"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"contributing-to-ss3diags","dir":"","previous_headings":"","what":"Contributing to ss3diags","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"like contribute ss3diags suggestions diagnostic tests include package, can submit new issue email Meg megumi.oshima@noaa.gov.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"reference","dir":"","previous_headings":"","what":"Reference","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"cite ss3diags publication can use","code":"citation(\"ss3diags\") #> To cite package 'ss3diags' in publications use: #>  #>   Winker H, Carvalho F, Cardinale M, Kell L, Oshima M, Fletcher E #>   (2023). _ss3diags: Stock Synthesis Model Diagnostics for Intergated #>   Stock Assessments_. R package version 2.1.1, #>   <https://github.com/PIFSCstockassessments/ss3diags>. #>  #> A BibTeX entry for LaTeX users is #>  #>   @Manual{, #>     title = {ss3diags: Stock Synthesis Model Diagnostics for Intergated Stock Assessments}, #>     author = {Henning Winker and Felipe Carvalho and Massimiliano Cardinale and Laurence Kell and Megumi Oshima and Eric Fletcher}, #>     year = {2023}, #>     note = {R package version 2.1.1}, #>     url = {https://github.com/PIFSCstockassessments/ss3diags}, #>   }"},{"path":"https://pifscstockassessments.github.io/ss3diags/index.html","id":"disclaimer","dir":"","previous_headings":"","what":"Disclaimer","title":"Stock Synthesis Model Diagnostics for Intergated Stock Assessments","text":"United States Department Commerce (DOC) GitHub project code provided ‘’ basis user assumes responsibility use. DOC relinquished control information longer responsibility protect integrity, confidentiality, availability information. claims Department Commerce stemming use GitHub project governed applicable Federal law. reference specific commercial products, processes, services service mark, trademark, manufacturer, otherwise, constitute imply endorsement, recommendation favoring Department Commerce. Department Commerce seal logo, seal logo DOC bureau, shall used manner imply endorsement commercial product activity DOC United States Government.”","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":null,"dir":"Reference","previous_headings":"","what":"Francis Weighting for compositional data — SScompsTA1.8","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"TA1.8 Francis function modified r4ss::SSMethod.TA1.8 r4ss::SSMethod.Cond.TA1.8 apply Francis weighting method TA1.8 length-, age-, generalized size-composition data, conditional age--length data Stock Synthesis model. conditional age--length data, mean age year calculated based recommendations Punt (2015). main purpose create dataframe annual observed expected mean length age fleet used calculate residuals testing model fit. function used SSplotRunstest SSplotJABBAres.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"","code":"SScompsTA1.8(   ss3rep,   type = c(\"len\", \"age\", \"size\", \"con\"),   fleet = NULL,   seas = NULL,   plotit = FALSE,   maxpanel = 1000 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"ss3rep Stock Synthesis output read r4SS function SS_output type string either 'len' (length composition data), 'size' (generalized size composition data), 'age' (age composition data), 'con' (conditional age length data) fleet vector one fleet numbers whose data analysed simultaneously, NULL, fleets analysed seas string indicating treat data multiple seasons 'comb' - combine seasonal data year plot Yr 'sep' - treat season separately, plotting Yr.S. .null(seas), assumed one season option 'comb' used. plotit TRUE, make illustrative plot like one panels Fig. 4 Francis (2011). maxpanel maximum number panels within plot, default 1000","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"ss_out data.frame observed, predicted mean length/age 95% confidence intervals based stage 1 stage 2 weighting runs_dat data.frame observed predicted mean length age year/fleet.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"references","dir":"Reference","previous_headings":"","what":"References","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"Francis, R..C.C. (2011). Data weighting statistical fisheries stock assessment models. Canadian Journal Fisheries Aquatic Sciences 68: 1124-1138. #' Punt, .E. (2015). insights data weighting integrated stock assessments. Fish. Res. <http://dx.doi.org/10.1016/j.fishres.2015.12.006","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SScompsTA1.8.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Francis Weighting for compositional data — SScompsTA1.8","text":"Chris Francis, Andre Punt, Ian Taylor (modified Henning Winker Meg Oshima)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":null,"dir":"Reference","previous_headings":"","what":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using Multivariate Log-Normal Distribution. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"","code":"SSdeltaMVLN(   ss3rep,   Fref = NULL,   years = NULL,   mc = 5000,   weight = 1,   run = \"MVLN\",   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE,   variance_method = \"ww2019\",   bias_correct_mean = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt\"), correponding F_MSY F_Btgt years single year vector years mvln mc number monte-carlo simulations weight weighting option model ensembles weight*mc run qualifier model run plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI? variance_method Specify method approximating variance covariance multivariate lognormal distribution ww2019 Use approximation Walter Winker 2019 (Default backwards compatibility). 2T Use delta-method 2nd order Taylor series approximation. bias_correct_mean Specify Stock Synthesis MLE estimates bias corrected used specify mean multivariate lognormal distribution FALSE apply bias correction (Default backwards compatibility). TRUE Apply bias correction.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"output list maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values, kobe plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN","text":"Henning Winker (JRC-EC) Nicholas Ducharme-Barth (PIFSC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":null,"dir":"Reference","previous_headings":"","what":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"function generate kobe pdfs Multivariate Log-Normal Distribution including plotting option. version used older versions Stock Synthesis. newer versions (v3.24 newer), use SSdeltaMVLN().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"","code":"SSdeltaMVLN_old(   ss3rep,   status = c(\"Bratio\", \"F\"),   quants = c(\"SSB\", \"Recr\"),   Fref = c(\"MSY\", \"Ftrg\"),   years = NULL,   mc = 5000,   weight = 1,   run = \"MVLN\",   plot = TRUE,   addtrj = TRUE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"ss3rep r4ss::SSgetoutput()$replist1 status covarying stock status quantaties extract Hessian quants additional stock quantaties extract Hessian Fref Choice reference point stock SSB/XFref=c(\"MSY\",\"Ftrg\"),F_report_basis: 0 3 years single year vector years mvln mc number monte-carlo simulations weight weighting option model ensembles weight*mc run qualifier model run plot option show plot addtrj TRUE/FALSE add trajectory years. Default TRUE ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"output list kobe objects mle's","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdeltaMVLN_old.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Joint Distributions for Stock Status Ratios — SSdeltaMVLN_old","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":null,"dir":"Reference","previous_headings":"","what":"MCMC Joint Distributions — SSdiagsMCMC","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using MCMC. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"","code":"SSdiagsMCMC(   mcmc,   ss3rep,   Fref = NULL,   years = NULL,   run = \"MCMC\",   thin = 1,   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"mcmc file path folder derived_posteriors.sso file ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt), correponding F_MSY F_Btgt years single year vector years mvln run qualifier model run thin option use additional thinning plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"output list maximum likelihood estimates MCMC posterier distributions Kobe values Kobe plot","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MCMC Joint Distributions — SSdiagsMCMC","text":"Henning Winker (JRC-EC), Massimiliano Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":null,"dir":"Reference","previous_headings":"","what":"MCMC Joint Distributions — SSdiagsMCMC_ancient","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"function generate joint distributions stock status ratios (SSB/SSBref F/Fref ref can MSY, SSB40, F40, etc.) using MCMC. function produces Kobe plot, maximum likelihood estimates MVLN Monte-Carlo distributions Kobe values can input SSplotEnsemble(). Use Stock Synthesis models older 3.24, later versions use SSdiagsMCMC().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"","code":"SSdiagsMCMC_ancient(   mcmc,   ss3rep,   Fref = NULL,   years = NULL,   run = \"MCMC\",   thin = 1,   plot = TRUE,   addprj = FALSE,   ymax = NULL,   xmax = NULL,   legendcex = 1,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"mcmc file path folder derived_posteriors.sso file ss3rep r4ss::SS_output Fref Choice Fratio c(\"MSY\",\"Btgt), correponding F_MSY F_Btgt years single year vector years mvln run qualifier model run thin option use additional thinning plot option show plot addprj include forecast years ymax ylim maximum xmax xlim maximum legendcex Allows adjust legend cex verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"output list maximum likelihood estimates MCMC posterier distributions Kobe values Kobe plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSdiagsMCMC_ancient.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"MCMC Joint Distributions — SSdiagsMCMC_ancient","text":"Henning Winker (JRC-EC), Massimiliano Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":null,"dir":"Reference","previous_headings":"","what":"Mohn's Rho and Forecast Bias — SShcbias","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"function produces statistics retrospective analysis (Mohn's rho forecast bias). visualize retrospective forecasts Stock Synthesis model, use SSplotRetro().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"","code":"SShcbias(   summaryoutput,   quants = c(\"SSB\", \"F\"),   models = \"all\",   endyrvec = \"default\",   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"summaryoutput List created r4ss::SSsummarize() quants SSB F quantity models Optional subset models described r4ss function summaryoutput().  Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. verbose Report progress R GUI?","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SShcbias.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mohn's Rho and Forecast Bias — SShcbias","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":null,"dir":"Reference","previous_headings":"","what":"Mean Absolute Scaled Error — SSmase","title":"Mean Absolute Scaled Error — SSmase","text":"MASE one-step ahead hindcasting cross-validations computes MASE prediction residuals indices. MASE calculated average ratio mean absolute error (MAE) prediction residuals (MAE.PR) Naive Predictions (MAE.base) MASE.adj sets MAE.base minimum MAE.base.adj (default=0.1) MASE.adj allow passing (MASE<1) MAE.PE < 0.1 thus accurate, obs show extremely little variation","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Mean Absolute Scaled Error — SSmase","text":"","code":"SSmase(   retroSummary,   quants = c(\"cpue\", \"len\", \"age\", \"con\"),   Season = \"default\",   models = \"all\",   endyrvec = \"default\",   indexselect = NULL,   MAE.base.adj = 0.1,   residuals = FALSE,   verbose = FALSE,   indexfleets = 1 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Mean Absolute Scaled Error — SSmase","text":"retroSummary raw list retrospective runs created r4ss::SSgetoutput(). Depending type data, function call r4ss::SSsummarize ss3diags:SSretroComps summarize list. quants data type, either \"cpue\" index data, \"len\" length composition data, \"age\" age composition data. Note, using \"age\" \"len\", SSretroComps() used extract summarize composition data first. Season option specify Season integer value 1-4 - Default uses first available, .e. usual Seas = 1 models Optional subset models described r4ss function summaryoutput().  Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. indexselect Vector fleet numbers model compare MAE.base.adj minimum MASE demoninator (naive predictions) MASE.adj (default = 0.1) residuals true, includes dataframe output prediction residuals naive prediction residuals. Default FALSE. verbose Report progress R GUI? indexfleets Single value vector length n = number models summary object fleet number(s) index compare.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Mean Absolute Scaled Error — SSmase","text":"MASE hcxval statistic","code":""},{"path":[]},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Mean Absolute Scaled Error — SSmase","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSmase.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Mean Absolute Scaled Error — SSmase","text":"","code":"if (FALSE) { # calculate MASE for CPUE indices only for fleets 1 and 2 SSmase(retro.sma, quant = \"cpue\", indexselect = c(1:2)) }"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":null,"dir":"Reference","previous_headings":"","what":"Model ensemble plots — SSplotEnsemble","title":"Model ensemble plots — SSplotEnsemble","text":"Plots model ensembles forecasts uncertainty represented MVLN MCMC posteriors","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Model ensemble plots — SSplotEnsemble","text":"","code":"SSplotEnsemble(   kb,   subplots = c(\"stock\", \"harvest\", \"SSB\", \"F\", \"Recr\", \"Catch\"),   models = \"all\",   quantiles = list(c(0.025, 0.975)),   ylabs = NULL,   endyrvec = \"default\",   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = FALSE,   use_pdf = FALSE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = NULL,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   legendindex = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Model ensemble plots — SSplotEnsemble","text":"kb kb type output created SSdeltaMVLN() subplots vector create subplots options: \"stock\" Fish Population \"harvest\" Harvest Rate \"SSB\" Spawning Stock Biomass \"F\" Fishing Mortality \"Recr\" Recruitment \"Catch\" Total Catch models option manually subset models kb[[\"run\"]] quantiles quantiles uncertainty plots. Input list, default 95TH percentile: list(c(0.025, 0.975)) ylabs y-axis labels quants endyrvec Optional single year vector years representing final year values show model. \"default\" set ending year specified model. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadealpha Transparency adjustment used make uncertainty regions, default 0.3 new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel TRUE/FALSE include labels indices. Default TRUE (currently used) indexQdigits Number significant digits catchability legend. Default 4 legendindex Allows add legend selected indices (plots)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Model ensemble plots — SSplotEnsemble","text":"Mostly adopted r4ss::SSplotComparisons Taylor et al","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotEnsemble.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Model ensemble plots — SSplotEnsemble","text":"","code":"if (FALSE) {  mvln <- SSdeltaMVLN(simple, run = \"Simple\") sspar(mfrow = c(3, 2), plot.cex = 0.7) SSplotEnsemble(mvln[[\"kb\"]], ylabs = mvln[[\"labels\"]], add = T, verbose = F) }"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":null,"dir":"Reference","previous_headings":"","what":"Generic SSplot function — SSplotGeneric","title":"Generic SSplot function — SSplotGeneric","text":"Generalized version ss3diags SSplots functions. intended production","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Generic SSplot function — SSplotGeneric","text":"","code":"SSplotGeneric(   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGeneric.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Generic SSplot function — SSplotGeneric","text":"pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":null,"dir":"Reference","previous_headings":"","what":"Legend parameters for Generic SSplot — SSplotGenericLegend","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"Generalized version ss3diags SSplots functions specfic plot legend parameters. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"","code":"SSplotGenericLegend(   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericLegend.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Legend parameters for Generic SSplot — SSplotGenericLegend","text":"legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":null,"dir":"Reference","previous_headings":"","what":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"Generalized version ss3diags SSplots functions specify par() pass plot attributes. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"","code":"SSplotGenericPar(   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = NULL,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\" )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericPar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Graphical Parameters for Stock Synthesis Generic plots. — SSplotGenericPar","text":"col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":null,"dir":"Reference","previous_headings":"","what":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"Generalized version ss3diags SSplots functions specify uncertainty. intended production.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"","code":"SSplotGenericUncertainty(uncertainty = TRUE, mcmcVec = FALSE, models = \"all\")"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotGenericUncertainty.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Uncertainty parameters for Stock Synthesis Generic plots. — SSplotGenericUncertainty","text":"uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":null,"dir":"Reference","previous_headings":"","what":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"Plots one-step ahead hindcasting cross-validations computes MASE prediction residuals.MASE calculated average ratio mean absolute error (MAE) prediction residuals (MAE.PR) naive predictions (MAE.base). MASE.adj sets MAE.base minimum MAE.base.adj (default=0.1). MASE.adj allow passing (MASE<1) MAE.PE < 0.1 thus accurate obs show little annual variation","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"","code":"SSplotHCxval(   retroSummary,   subplots = c(\"cpue\", \"len\", \"age\"),   Season = \"default\",   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   endyrvec = \"default\",   xmin = NULL,   indexselect = NULL,   MAE.base.adj = 0.1,   show.mase.adj = TRUE,   indexUncertainty = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   xlim = \"default\",   ylimAdj = 1.15,   ylim = NULL,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = grey(0.5, 0.4),   shadecol2 = grey(0.5, 0.4),   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   indexfleets = 1,   plot = TRUE,   shadecol1 = grey(0.5, 0.4) )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"retroSummary List created r4ss::SSsummarize() SSretroComps() subplots optional use following: \"cpue\" Index abundance data \"len\" Length-composition data \"age\" Age-composition data Season option specify Season integer value 1-4. Default uses first available, .e. usual Seas = 1 print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. xmin optional number first year shown plot (available) indexselect Vector fleet numbers model compare MAE.base.adj minimum MASE denominator (naive predictions) MASE.adj (default = 0.1) show.mase.adj TRUE, show mase.adj plot indexUncertainty Show fixed uncertainty intervals index (estimated) col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. ylim -write ylimAdj specified xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon shadecol2 color uncertainty early years affected hindcast shadealpha Transparency adjustment used make default shadecol. (currently used) new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel Logical flag add catchability legend plot index fits. indexQdigits Number significant digits catchability legend indexfleets Fleet numbers model compare indices abundance. Can take different forms: integer: (default) create single comparison plot chosen index NULL: create separate plot index long fleet numbering across models. vector length equal number models: single fleet number model compared single plot list: list fleet numbers associated indices within model compared, list elements vector length names list elements matter can absent. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version shadecol1 uncertainty shading early years affected hindcast (currently used)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotHCxval.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Hindcasting Cross-Validations of Multiple Models — SSplotHCxval","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual plot — SSplotJABBAres","title":"Residual plot — SSplotJABBAres","text":"Plots residuals indices boxplot (color coded fleet) loess showing systematic trends time. function package JABBA (Just Another Bayesian Biomass Assessment).","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual plot — SSplotJABBAres","text":"","code":"SSplotJABBAres(   ss3rep,   subplots = c(\"cpue\", \"len\", \"age\", \"size\", \"con\")[1],   seas = NULL,   plot = TRUE,   print = lifecycle::deprecated(),   print_plot = FALSE,   png = lifecycle::deprecated(),   use_png = print_plot,   pdf = lifecycle::deprecated(),   use_pdf = FALSE,   indexselect = NULL,   miny = 3,   col = NULL,   pch = 21,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   xlim = \"default\",   ylim = \"default\",   ylimAdj = 1.1,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   legend = TRUE,   legendlabels = \"default\",   legendloc = \"bottomleft\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   boxcol = grey(0.8, 0.5),   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual plot — SSplotJABBAres","text":"ss3rep Stock Synthesis output read r4ss::SS_output() subplots string type data plot: \"cpue\" Index abundance data \"len\" Length-composition data \"age\" Age-composition data \"size\" Generalized size composition data \"con\" Conditional age--length data. seas string indicating treat data multiple seasons: \"comb\" Combine seasonal data year plot Yr \"sep\" Treat season separately, plotting Yr.S. NULL NULL, assumed one season option \"comb\" used. plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. indexselect Vector fleet numbers model compare miny minimum abs values ylim col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylim Optional, min max values ylim override \"default\" value (-0.7, 0.5) ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag. Enables x- y-axis labels. type type plot drawn. details, see plot. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console boxcol color boxes new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotJABBAres.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual plot — SSplotJABBAres","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":null,"dir":"Reference","previous_headings":"","what":"KOBE phase plot — SSplotKobe","title":"KOBE phase plot — SSplotKobe","text":"Generates Kobe plot phase plot illustrating stock status uncertainty SSB/SSBmsy F/Fmsy","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"KOBE phase plot — SSplotKobe","text":"","code":"SSplotKobe(   kb,   joint = TRUE,   year = NULL,   posterior = c(\"points\", \"kernel\"),   xlab = expression(SSB/SSB[MSY]),   ylab = expression(F/F[MSY]),   ylim = NULL,   xlim = NULL,   fill = TRUE,   showMedian = TRUE,   legend = TRUE,   legendpos = \"right\",   legendcex = 0.7,   legendruns = TRUE,   yr.label = TRUE,   yr.int = 5,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"KOBE phase plot — SSplotKobe","text":"kb output SSdeltaMVLN()$kb joint option FALSE shows individual runs year option choose year kobe, last year default posterior visualization posterior c(\"points\",\"kernel\") xlab graphic parameter ylab graphic parameter ylim graphic parameter xlim graphic parameter fill shows color-coded quadrants showMedian option median trajectory. TRUE default legend option legend. TRUE default. legendpos legend position legendcex legend size legendruns show legend run labels yr.label show year along trajectory yr.int year intervals along trajectory verbose Output R console. Default TRUE","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotKobe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"KOBE phase plot — SSplotKobe","text":"Kobe Quadrant percentages","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":null,"dir":"Reference","previous_headings":"","what":"Compare Multiple SS Model Estimates — SSplotModelcomp","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"function plot SSB, B-ratio, F, Recruits, /Index Abundance fits multiple SS models. function uses object multiple SS models summarized r4ss::SSsummarize().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"","code":"SSplotModelcomp(   summaryoutput,   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   subplots = c(\"SSB\", \"Bratio\", \"Fvalue\", \"Recruits\", \"Index\", \"RecDevs\"),   brp = c(\"msy\", \"btargs\"),   fmsy = TRUE,   ylabs = c(\"SSB (t)\", expression(SSB/SSB[MSY]), \"Fishing mortality F\",     \"Recruits ('000s)\", \"Index\", \"Recruitment Deviations\"),   endyrvec = \"default\",   xmin = NULL,   indexselect = NULL,   indexUncertainty = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = \"default\",   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"l\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.9,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = NULL,   shadealpha = 0.3,   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   indexQlabel = TRUE,   indexQdigits = 4,   indexfleets = 1 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"summaryoutput List created r4ss::SSsummarize() plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. subplots option \"SSB\",\"Bratio\",\"Fvalue\",\"Recruits\",\"Index\" \"SSB\" Spawning Stock Biomass \"Bratio\" Stock Biomass relative biomass reference point \"Fvalue\" Fishing Mortality \"Recruits\" Age-0 Recruits \"Index\" Index abundance \"RecDev\" Recruitment Deviations brp option set reference point c(\"msy\",\"btargs\") fmsy specify Fvalue F/Fmsy starter file setting ylabs yaxis labels quants final year values show model. default set endyrvec Optional single year vector years representing final year values show model. \"default\" set ending year specified model. xmin NULL optional number first year shown plot (available) indexselect Vector fleet numbers model compare indexUncertainty Show fixed uncertainty intervals index (estimated) col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon shadealpha Transparency adjustment used make default shadecol new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. indexQlabel Logical. TRUE add catchability legend plot index fits (currently used) indexQdigits Number significant digits catchability legend indexfleets Fleet numbers model compare indices abundance. Can take different forms: integer (default): create single comparison plot chosen index NULL: create separate plot index long fleet numbering across models. vector length equal number models: single fleet number model compared single plot list: list fleet numbers associated indices within model compared, list elements vector length names list elements matter can absent.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotModelcomp.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Compare Multiple SS Model Estimates — SSplotModelcomp","text":"Mostly adopted r4ss::SSplotComparisons Taylor et al","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"Plots retrospective pattern, including (optional) one-step ahead forecast computes Mohn's Rho","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"","code":"SSplotRetro(   summaryoutput,   subplots = c(\"SSB\", \"F\"),   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   models = \"all\",   endyrvec = \"default\",   xlim = NULL,   xmin = NULL,   labels = NULL,   ylim = NULL,   forecast = TRUE,   forecastrho = TRUE,   showrho = TRUE,   col = NULL,   pch = NULL,   lty = 1,   lwd = 2,   tickEndYr = TRUE,   ylimAdj = 1.05,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   uncertainty = TRUE,   legend = TRUE,   legendlabels = \"default\",   legendloc = \"topright\",   legendorder = \"default\",   legendncol = 1,   legendcex = 1,   legendsp = 0.7,   legendindex = NULL,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   shadecol = grey(0.4, 0.6),   new = TRUE,   add = FALSE,   mcmcVec = FALSE,   shadecol1 = grey(0.5, 0.4),   indexQlabel = TRUE,   indexQdigits = 4,   shadealpha = 0.3 )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"summaryoutput List created r4ss::SSsummarize() subplots Optional vector subplots created: \"SSB\" Spawning Stock Biomass \"F\" Fishing Mortality plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. models Optional subset models summaryoutput (similar field different name): list created function r4ss::SSsummarize. Either \"\" vector numbers indicating columns summary tables. endyrvec Optional single year vector years representing final year values show model. default set ending year specified model. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. xmin optional minimum year shown plot (default first yr) labels yaxis label biomass (bony fish sharks) ylim option specify ylim range forecast Logical. TRUE, one-step ahead forecasts shown plot forecastrho Logical. TRUE, one-step ahead forecast rho value denoted plot showrho Logical flag include Mohn's rho value. Defaults TRUE col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. uncertainty Logical flag enable plots uncertainty intervals. Either single TRUE/FALSE value, vector TRUE/FALSE values around SSB F estimated timeseries, set integers corresponding choice models. legend Flag enable legend plot. TRUE default. legendlabels Optional vector labels include legend. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendorder Optional vector model numbers can used legend display model names order different represented summary input object. legendncol Number columns legend. legendcex Allows adjust legend cex legendsp Space legend labels legendindex Allows add legend selected indices (plots) pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console shadecol uncertainty shading hcxval horizon new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs mcmcVec Logical vector TRUE/FALSE values (single value) indicating whether input values MCMC use normal distribution around MLE. shadecol1 uncertainty shading early years affected hindcast indexQlabel Logical. TRUE, add catchability legend plot index fits (currently used) indexQdigits Number significant digits catchability legend shadealpha set transparency level (alpha) area uncertainty. Defaults 0.3 (currently used)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRetro.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrospective-Forecast with One-Step Ahead Hindcasting — SSplotRetro","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual Diagnostics — SSplotRunstest","title":"Residual Diagnostics — SSplotRunstest","text":"Function residual diagnostics. Plots residuals 3x sigma limits indices mean age length outputs runs test table. Note, want plot residuals, use SSrunstest().","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual Diagnostics — SSplotRunstest","text":"","code":"SSplotRunstest(   ss3rep,   mixing = \"less\",   subplots = c(\"cpue\", \"len\", \"age\", \"size\", \"con\")[1],   plot = TRUE,   print = deprecated(),   print_plot = FALSE,   png = deprecated(),   use_png = print_plot,   pdf = deprecated(),   use_pdf = FALSE,   indexselect = NULL,   miny = 1,   col = NULL,   pch = 21,   lty = 1,   lwd = 2,   tickEndYr = FALSE,   xlim = \"default\",   ylim = \"default\",   ylimAdj = 1.4,   xaxs = \"i\",   yaxs = \"i\",   xylabs = TRUE,   type = \"o\",   legend = TRUE,   legendloc = \"top\",   legendcex = 1,   pwidth = 6.5,   pheight = 5,   punits = \"in\",   res = 300,   ptsize = 10,   cex.main = 1,   plotdir = NULL,   filenameprefix = \"\",   par = list(mar = c(5, 4, 1, 1) + 0.1),   verbose = TRUE,   new = TRUE,   add = FALSE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual Diagnostics — SSplotRunstest","text":"ss3rep Stock Synthesis output read r4ss::SS_output() mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation subplots optional flag : \"cpue\" Index abundance data \"len\" Length composition data \"size\" Generalized size composition data \"age\" Age composition data \"con\" Conditional age--length data plot DEPRECATED. default, TRUE, Plots (subplots) drawn plot device. option explicitly disable option (FALSE), implemented. option flag defunct future version print DEPRECATED, please use print_plot. print_plot Flag enable plot graphic device print PNG PNG files. png DEPRECATED. Please use use_png. use_png Enables plots generated PNG files. Defaults print value pdf DEPRECATED. Please use use_pdf. use_pdf Enables plots generated pdf file. indexselect Vector fleet numbers model compare miny absolute value min max value ylim. Default 1 col Optional vector colors used lines. Input NULL pch Optional vector plot character values lty Optional vector line types lwd Optional vector line widths tickEndYr Logical flag: set TRUE FALSE switch turn /extra axis mark final year timeseries plots. xlim Optional, years use x-axis. Default value NULL (\"default\"), uses years available. ylim Optional, values y-axis range display plot. default: \"default\", range -1 1. ylimAdj Multiplier ylim parameter. Allows additional white space. xaxs Choice xaxs parameter See ?par info. yaxs Choice yaxs parameter. See ?par info. xylabs Logical flag: set TRUE FALSE include x- y-axis labels plot. Defaults TRUE type type plot drawn. details, see plot. legend Flag enable legend plot. TRUE default. legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See help(\"legend\") info string options. legendcex Allows adjust legend cex pwidth Default width plot printed plot units punits pheight Height plot printed plot units punits punits Measurement units pwidth pheight. Default \"\". \"px\" (pixels) \"\" (inches) \"cm\" (centimeters) \"mm\" (millimeters) res Resolution plots printed files. ptsize Point size plotted text plots printed files. See help(\"png\") details cex.main Character expansion plot titles. plotdir Directory output plot file written. default, directory model run. filenameprefix Additional text append output plot file name. separated default name underscore. par numerical vector form c(bottom, left, top, right) gives number lines margin specified four sides plot,passed par(). Entering NULL passes plot's default par() values (depends whether main title included ) verbose Flag print additional diagnostic messages R console new Deprecated. New plot windows created default (TRUE), option disable , via FALSE, unused. add suppresses par() create multiplot figs","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Residual Diagnostics — SSplotRunstest","text":"dataframe runs test p-value, test passed failed, 3x sigma high low limits, type data used. Rows fleet. Note, runs test passed p-value > 0.05 (residuals random) failed p-value < 0.5 (residuals random)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSplotRunstest.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual Diagnostics — SSplotRunstest","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":null,"dir":"Reference","previous_headings":"","what":"Read SS MCMC — SSreadMCMC","title":"Read SS MCMC — SSreadMCMC","text":"function read mcmc file outputs Stock Synthesis model","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Read SS MCMC — SSreadMCMC","text":"","code":"SSreadMCMC(mcmcdir)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Read SS MCMC — SSreadMCMC","text":"mcmcdir file path folder derived_posteriors.sso file","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Read SS MCMC — SSreadMCMC","text":"Stock Synthesis mcmc output file","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSreadMCMC.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Read SS MCMC — SSreadMCMC","text":"Henning Winker (JRC-EC) & Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":null,"dir":"Reference","previous_headings":"","what":"Retrieve Composition Data from Multiple SS Models — SSretroComps","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"Wrapper get observed expected mean length/age multiple Stock Synthesis models.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"","code":"SSretroComps(retroModels)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"retroModels object list replists r4ss::SSgetoutput()","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"list observed expected mean Length/age comps (c.f. ss3rep[[\"cpue\"]])","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSretroComps.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Retrieve Composition Data from Multiple SS Models — SSretroComps","text":"Henning Winker","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":null,"dir":"Reference","previous_headings":"","what":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"Function calculating RMSE used SSplotJABBAres()","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"","code":"SSrmse(   ss3rep,   quants = c(\"cpue\", \"len\", \"age\", \"con\"),   seas = NULL,   indexselect = NULL )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"ss3rep output SS_output() quants dataset calculate RMSE . \"cpue\" index abundance, \"len\" length comp, \"age\" age composition, \"con\" conditional age--length. seas string indicating treat data multiple seasons 'comb' - combine seasonal data year plot Yr 'sep' - treat season separately, plotting Yr.S. .null(seas), assumed one season option 'comb' used. indexselect Vector fleet numbers model compare","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrmse.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Function for calculating RMSE\nused for SSplotJABBAres() — SSrmse","text":"returns list includes RMSE table output (fleet combined) dataframe residuals can used creating SSplotJABBAres() plot","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":null,"dir":"Reference","previous_headings":"","what":"Residual Diagnostics Plot — SSrunstest","title":"Residual Diagnostics Plot — SSrunstest","text":"Function residual diagnostics. Outputs runs test table gives runs test p-values, runs test passed (p-value > 0.05, residuals random) failed (p-value < 0.05, residuals random), 3x sigma limits indices mean age length type input data (cpue, length comp, age comp, size comp, conditional age--length).","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Residual Diagnostics Plot — SSrunstest","text":"","code":"SSrunstest(   ss3rep,   mixing = \"less\",   quants = c(\"cpue\", \"len\", \"age\", \"con\")[1],   indexselect = NULL,   verbose = TRUE )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Residual Diagnostics Plot — SSrunstest","text":"ss3rep Stock Synthesis output read r4ss::SS_output() mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation quants optional use c(\"cpue\",\"len\",\"age\",\"con\"), default uses \"cpue\". \"cpue\" Index abundance data \"len\" Length composition data \"age\" Age composition data \"con\" Conditional age--length data indexselect Vector fleet numbers model compare verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Residual Diagnostics Plot — SSrunstest","text":"dataframe runs test p-value, test passed failed, 3x sigma high low limits, type data used. Rows fleet. Note, runs test passed p-value > 0.05 (residuals random) failed p-value < 0.5 (residuals random)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSrunstest.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Residual Diagnostics Plot — SSrunstest","text":"Henning Winker (JRC-EC) Laurance Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":null,"dir":"Reference","previous_headings":"","what":"Get Stock Status Settings — SSsettingsBratioF","title":"Get Stock Status Settings — SSsettingsBratioF","text":"function get Bratio F settings","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get Stock Status Settings — SSsettingsBratioF","text":"","code":"SSsettingsBratioF(ss3rep, status = c(\"Bratio\", \"F\"), verbose = TRUE)"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get Stock Status Settings — SSsettingsBratioF","text":"ss3rep r4ss::SSgetoutput() status covarying stock status quantaties extract Hessian verbose Report progress R GUI?","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Get Stock Status Settings — SSsettingsBratioF","text":"output list Bratio F settings","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/SSsettingsBratioF.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Get Stock Status Settings — SSsettingsBratioF","text":"Henning Winker (JRC-EC)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot Indices — ensemble_plot_index","title":"Plot Indices — ensemble_plot_index","text":"function plot different fits single index abundance","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot Indices — ensemble_plot_index","text":"","code":"ensemble_plot_index(   summaryoutput,   varlist,   indexfleets = 1,   verbose = TRUE,   legendloc = \"topright\",   legendcex = 1,   legendsp = 0.9,   legendncol = 1,   type = \"l\" )"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ensemble_plot_index.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot Indices — ensemble_plot_index","text":"summaryoutput summaryoutput varlist variable list indexfleets Fleet vector index verbose Option output messages Rconsole legendloc Location legend. Either string like \"topleft\" vector two numeric values representing fraction maximum x y dimensions, respectively. See ?legend info string options. legendcex Allows adjust legend cex legendsp Space legend labels legendncol Number columns legend. type Type parameter passed points (default 'o' overplots points top lines)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":null,"dir":"Reference","previous_headings":"","what":"Runs Test for Residuals — ssruns_sig3","title":"Runs Test for Residuals — ssruns_sig3","text":"function uses randtests::runs.test perform runs test residuals determine randomly distributed. also calculates 3 x sigma limits","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Runs Test for Residuals — ssruns_sig3","text":"","code":"ssruns_sig3(x, type = NULL, mixing = \"less\")"},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Runs Test for Residuals — ssruns_sig3","text":"x residuals CPUE fits type c(\"resid\",\"observations\") mixing c(\"less\",\"greater\",\"two.sided\"). Default less checking positive autocorrelation ","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Runs Test for Residuals — ssruns_sig3","text":"runs p value 3 x sigma limits","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"Runs Test for Residuals — ssruns_sig3","text":"runs test conducted library(randtests)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/reference/ssruns_sig3.html","id":"author","dir":"Reference","previous_headings":"","what":"Author","title":"Runs Test for Residuals — ssruns_sig3","text":"Henning Winker (JRC-EC) Laurence Kell (Sea++)","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-220","dir":"Changelog","previous_headings":"","what":"ss3diags 2.2.0","title":"ss3diags 2.2.0","text":"Add vignettes tutorials implementing interpreting diagnostic analyses (#78, #75, #73, #68). vignettes replaced “Cookbook recipe” R scripts updated code. Removed Rdata files (ss3diags::simple, ss3diags::retroSimple, ss3diags::mcmcSimple). objects now automatically produced vignettes. Removed deprecated data objects function arguments (#100). Created generic functions re-use common parameter documentation via roxygen tag @inheritParams (#66 #2). Update r4ss dependency. Replacing installation SS3 container R-CMD-Check GitHub Action workflow use r4ss::get_ss_exe() (#97).","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-211","dir":"Changelog","previous_headings":"","what":"ss3diags 2.1.1","title":"ss3diags 2.1.1","text":"Added new logo. Thanks @pdimens (#76, #77) Added options SSdeltaMVLN Variance-Coveriance approximation bias correction. Thanks @N-DucharmeBarth-NOAA (#64) Dependency resolves r4ss function name conflicts w/ dplyr kableExtra libraries (#83). Side effect nmfs-fish-tools/ghactions4r#69 Removed dplyr NAMESPACE. Removed roxygen import calls SSplotJABBAres() SSrmse(), appended dplyr function calls double colon operator (dplyr::) (#82) Updated default summaryoutput used SSplotModelComp() ss3diags::retroSimple default ss3rep used SSplotRunsTest() ss3diags::simple Updated ss3diags citation. Minor documentation link fixes.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-210","dir":"Changelog","previous_headings":"","what":"ss3diags 2.1.0","title":"ss3diags 2.1.0","text":"RMSE calculations modularized standalone function can called independently SSplotJABBAres() SSrmse(). (#50) Bugfixes adjusting y-axis limits SSplotRunstest SSplotJABBAres: Use ylim parameter adjust y-axis limits. (#46) Added option remove median trajectory SSplotKobe() (#3) Added rlang, dplyr, magrittr dependencies. SSmase SSplotHcxval: Corrected validation messsage clarify validation issue fix issue code styler. (#33, #35) Added Date field DESCRIPTION. DESCRIPTION metadata now used generate package citations. (#25) Package vingettes formatted html_vignette reduce file size. Removed redundant PDF word document versions ss3diags_Handbook vignette. Enabled markdown support roxygen. Enabled Cross-reference links.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-203","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.3","title":"ss3diags 2.0.3","text":"Changed r4ss dependency 1.44.0 (CRAN version) . Replaced default R CMD CHECK workflow NOAA-fish-tools/ghactions4r’s version. Fixed Ensemble Quantile Shading Issues (#4) Replaced example datasets ss3diags cookbook, handbook current “simple” ensemble model. Fixup minor code documentation formatting issues. SSmase SSplotHcxval: Fixed code styler’s dollar subset conversion issues. example:`message(‘x$name 1,2,3,4’)`","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-202","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.2","title":"ss3diags 2.0.2","text":"Changed r4ss CRAN version (1.36.1) dependency development version legendfun -> r4ss::add_legend pngfun -> r4ss::save_png rc -> r4ss::rich_colors_short sspar -> r4ss::sspar Fix SSplotRetro.R indention causing issues code styler","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-201","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.1","title":"ss3diags 2.0.1","text":"Change SSplotJABBAres show combined seasonal data boxplots Fixup links Cookbook sripts. Formatted DESCRIPTION URL BugReports links PIFSCstockassessments repo add R package site.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-200","dir":"Changelog","previous_headings":"","what":"ss3diags 2.0.0","title":"ss3diags 2.0.0","text":"simple, cod-like, Stock Synthesis model, simulated via ss3sim, replaces Pacific North Hake (pac.hke) North Atlantic Shortfin Mako Shark (natl.sma) example datasets. SSplotRetro: fixed bug shading uncertainty area shows xlims specified. SSplotJABBAres: added ‘con’ option subplots argument conditional age--length data can plotted. Also added seas argument user can specify data combined across seasons within year kept separate. SScompsTA1.8: added seas argument users can specify data combined across seasons within year kept separate. SSplot functions (SSplotModelComp, SSplotEnsemble, SSplotHCxval, SSplotJABBAres, SSplotRetro): Marked plot, png, pdf, print, new deprecated. defunct future version. Added NEWS.md file track changes package.","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-108","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.8","title":"ss3diags 1.0.8","text":"Fixed MASE","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-107","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.7","title":"ss3diags 1.0.7","text":"Bug fixes","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-106","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.6","title":"ss3diags 1.0.6","text":"Improved SSdiagsMCMC","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-105","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.5","title":"ss3diags 1.0.5","text":"Updated SSdeltaMVLN","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-104","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.4","title":"ss3diags 1.0.4","text":"Reference: authors changes","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-103","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.3","title":"ss3diags 1.0.3","text":"Added annF_ quantaties","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-102","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.2","title":"ss3diags 1.0.2","text":"Added aut","code":""},{"path":"https://pifscstockassessments.github.io/ss3diags/news/index.html","id":"ss3diags-101","dir":"Changelog","previous_headings":"","what":"ss3diags 1.0.1","title":"ss3diags 1.0.1","text":"Added SSplotH","code":""}]