Built site for gh-pages

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@@ -1 +1 @@
-aecc6fcf
+3753e498

content/AFSC-BSAI-AtkaMackerel.html

@@ -303,7 +303,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: BSAI Atka mackerel<br>
 </li>

content/AFSC-GOA-pollock.html

@@ -282,7 +282,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 <div class="cell-output cell-output-stdout">
 <pre><code>
 The downloaded binary packages are in
-    /var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T//Rtmpx51r4H/downloaded_packages</code></pre>
+    /var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T//RtmpH8rI7I/downloaded_packages</code></pre>
 </div>
 <details class="code-fold">
 <summary>Code</summary>
@@ -303,19 +303,19 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 matrixStats  (NA -&gt; 1.3.0     ) [CRAN]
 checkmate    (NA -&gt; 2.3.1     ) [CRAN]
 BH           (NA -&gt; 1.84.0-0  ) [CRAN]
-QuickJSR     (NA -&gt; 1.3.0     ) [CRAN]
+QuickJSR     (NA -&gt; 1.3.1     ) [CRAN]
 pkgbuild     (NA -&gt; 1.4.4     ) [CRAN]
 loo          (NA -&gt; 2.8.0     ) [CRAN]
 gridExtra    (NA -&gt; 2.3       ) [CRAN]
 inline       (NA -&gt; 0.3.19    ) [CRAN]
-StanHeaders  (NA -&gt; 2.32.9    ) [CRAN]
+StanHeaders  (NA -&gt; 2.32.10   ) [CRAN]
 rstan        (NA -&gt; 2.32.6    ) [CRAN]
 tmbstan      (NA -&gt; 1.0.91    ) [CRAN]
 
 The downloaded binary packages are in
-    /var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T//Rtmpx51r4H/downloaded_packages
+    /var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T//RtmpH8rI7I/downloaded_packages
 ── R CMD build ─────────────────────────────────────────────────────────────────
-* checking for file ‘/private/var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T/Rtmpx51r4H/remotes13ae73c62cf0/kaskr-TMB_contrib_R-d275e52/TMBhelper/DESCRIPTION’ ... OK
+* checking for file ‘/private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpH8rI7I/remotesd1a1d0ad1a9/kaskr-TMB_contrib_R-d275e52/TMBhelper/DESCRIPTION’ ... OK
 * preparing ‘TMBhelper’:
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files and shell scripts
@@ -329,7 +329,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 <div class="cell-output cell-output-stdout">
 <pre><code>
 ── R CMD build ─────────────────────────────────────────────────────────────────
-* checking for file ‘/private/var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T/Rtmpx51r4H/remotes13ae3224f8a3/NOAA-FIMS-FIMS-ecd2d80/DESCRIPTION’ ... OK
+* checking for file ‘/private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpH8rI7I/remotesd1ae6f52fe/NOAA-FIMS-FIMS-39d0743/DESCRIPTION’ ... OK
 * preparing ‘FIMS’:
 * checking DESCRIPTION meta-information ... OK
 * cleaning src
@@ -354,7 +354,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 rstudioapi  (NA -&gt; 0.16.0  ) [CRAN]
 xml2        (NA -&gt; 1.3.6   ) [CRAN]
 ini         (NA -&gt; 0.3.1   ) [CRAN]
-httr2       (NA -&gt; 1.0.1   ) [CRAN]
+httr2       (NA -&gt; 1.0.2   ) [CRAN]
 gitcreds    (NA -&gt; 0.1.2   ) [CRAN]
 future      (NA -&gt; 1.33.2  ) [CRAN]
 kableExtra  (NA -&gt; 1.4.0   ) [CRAN]
@@ -365,9 +365,9 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 coda        (NA -&gt; 0.19-4.1) [CRAN]
 
 The downloaded binary packages are in
-    /var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T//Rtmpx51r4H/downloaded_packages
+    /var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T//RtmpH8rI7I/downloaded_packages
 ── R CMD build ─────────────────────────────────────────────────────────────────
-* checking for file ‘/private/var/folders/h9/l1shxhdd69nct08ylzq0n6q00000gn/T/Rtmpx51r4H/remotes13ae4cc1dc4/r4ss-r4ss-b6976cd/DESCRIPTION’ ... OK
+* checking for file ‘/private/var/folders/xz/lz5thm6s3vb1vdkk77vmkgbr0000gn/T/RtmpH8rI7I/remotesd1a750caa4c/r4ss-r4ss-b6976cd/DESCRIPTION’ ... OK
 * preparing ‘r4ss’:
 * checking DESCRIPTION meta-information ... OK
 * checking for LF line-endings in source and make files and shell scripts
@@ -403,7 +403,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: Gulf of Alaska (GOA) Walleye Pollock<br>
 </li>
@@ -483,7 +483,7 @@ <h2 class="anchored" data-anchor-id="run-fims-model">Run FIMS model</h2>
 <span id="cb12-20"><a href="#cb12-20" aria-hidden="true" tabindex="-1"></a>opt <span class="ot">&lt;-</span> TMBhelper<span class="sc">::</span><span class="fu">fit_tmb</span>(obj, <span class="at">getsd=</span><span class="cn">FALSE</span>, <span class="at">newtonsteps=</span><span class="dv">0</span>, <span class="at">control=</span><span class="fu">list</span>(<span class="at">trace=</span><span class="dv">100</span>))</span>
 <span id="cb12-21"><a href="#cb12-21" aria-hidden="true" tabindex="-1"></a><span class="do">## opt &lt;- with(obj, nlminb(start=par, objective=fn, gradient=gr))</span></span>
 <span id="cb12-22"><a href="#cb12-22" aria-hidden="true" tabindex="-1"></a><span class="fu">max</span>(<span class="fu">abs</span>(obj<span class="sc">$</span><span class="fu">gr</span>())) <span class="co"># from Cole, can use TMBhelper::fit_tmb to get val to &lt;1e-10</span></span>
-<span id="cb12-23"><a href="#cb12-23" aria-hidden="true" tabindex="-1"></a>rep2 <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>() <span class="do">## FIMS after estimation</span></span>
+<span id="cb12-23"><a href="#cb12-23" aria-hidden="true" tabindex="-1"></a>rep2 <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best) <span class="do">## FIMS after estimation</span></span>
 <span id="cb12-24"><a href="#cb12-24" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb12-25"><a href="#cb12-25" aria-hidden="true" tabindex="-1"></a><span class="do">## Output plotting</span></span>
 <span id="cb12-26"><a href="#cb12-26" aria-hidden="true" tabindex="-1"></a>out1 <span class="ot">&lt;-</span> <span class="fu">get_long_outputs</span>(rep1, rep0) <span class="sc">%&gt;%</span></span>
@@ -577,7 +577,7 @@ <h2 class="anchored" data-anchor-id="extra-analyses">Extra analyses</h2>
 <span id="cb13-10"><a href="#cb13-10" aria-hidden="true" tabindex="-1"></a>  parameters<span class="sc">$</span>p[i] <span class="ot">&lt;-</span> xseq[j]</span>
 <span id="cb13-11"><a href="#cb13-11" aria-hidden="true" tabindex="-1"></a>  obj2 <span class="ot">&lt;-</span> <span class="fu">MakeADFun</span>(<span class="at">data =</span> <span class="fu">list</span>(), parameters, <span class="at">DLL =</span> <span class="st">"FIMS"</span>, <span class="at">silent =</span> <span class="cn">TRUE</span>, <span class="at">map=</span>map)</span>
 <span id="cb13-12"><a href="#cb13-12" aria-hidden="true" tabindex="-1"></a>  opt2 <span class="ot">&lt;-</span> TMBhelper<span class="sc">::</span><span class="fu">fit_tmb</span>(obj2, <span class="at">getsd=</span><span class="cn">FALSE</span>, <span class="at">newtonsteps=</span><span class="dv">0</span>, <span class="at">control=</span><span class="fu">list</span>(<span class="at">trace=</span><span class="dv">0</span>))</span>
-<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a>  out <span class="ot">&lt;-</span> obj2<span class="sc">$</span><span class="fu">report</span>()</span>
+<span id="cb13-13"><a href="#cb13-13" aria-hidden="true" tabindex="-1"></a>  out <span class="ot">&lt;-</span> obj2<span class="sc">$</span><span class="fu">report</span>(obj2<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span>
 <span id="cb13-14"><a href="#cb13-14" aria-hidden="true" tabindex="-1"></a>  res[[j]] <span class="ot">&lt;-</span> <span class="fu">data.frame</span>(<span class="at">j=</span>j, <span class="at">lnR0=</span>xseq[j], <span class="at">total=</span>out<span class="sc">$</span>jnll, <span class="at">index=</span>out<span class="sc">$</span>index_nll,</span>
 <span id="cb13-15"><a href="#cb13-15" aria-hidden="true" tabindex="-1"></a>                         <span class="at">age=</span>out<span class="sc">$</span>age_comp_nll,<span class="at">recruit=</span>out<span class="sc">$</span>rec_nll, <span class="at">maxgrad=</span><span class="fu">max</span>(<span class="fu">abs</span>(obj<span class="sc">$</span><span class="fu">gr</span>())))</span>
 <span id="cb13-16"><a href="#cb13-16" aria-hidden="true" tabindex="-1"></a>}</span>

content/NEFSC-yellowtail.html

@@ -304,7 +304,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: Southern New England-Mid Atlantic Yellowtail Flounder<br>
 </li>
@@ -588,7 +588,7 @@ <h2 class="anchored" data-anchor-id="script-that-sets-up-and-runs-the-model">Scr
 <span id="cb3-245"><a href="#cb3-245" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-246"><a href="#cb3-246" aria-hidden="true" tabindex="-1"></a>sdr <span class="ot">&lt;-</span> TMB<span class="sc">::</span><span class="fu">sdreport</span>(obj)</span>
 <span id="cb3-247"><a href="#cb3-247" aria-hidden="true" tabindex="-1"></a>sdr_fixed <span class="ot">&lt;-</span> <span class="fu">summary</span>(sdr, <span class="st">"fixed"</span>)</span>
-<span id="cb3-248"><a href="#cb3-248" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>()</span>
+<span id="cb3-248"><a href="#cb3-248" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span>
 <span id="cb3-249"><a href="#cb3-249" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-250"><a href="#cb3-250" aria-hidden="true" tabindex="-1"></a><span class="do">### Plotting</span></span>
 <span id="cb3-251"><a href="#cb3-251" aria-hidden="true" tabindex="-1"></a></span>

content/NWFSC-petrale.html

@@ -305,7 +305,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: West Coast Petrale Sole<br>
 </li>
@@ -600,7 +600,7 @@ <h2 class="anchored" data-anchor-id="get-fims-output-and-plot-results">Get FIMS
 <div class="cell">
 <details class="code-fold">
 <summary>Code</summary>
-<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>()</span>
+<div class="sourceCode cell-code" id="cb6"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span>
 <span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a><span class="co"># copy input data to use as basis for results</span></span>
 <span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a>results_frame <span class="ot">&lt;-</span> age_frame<span class="sc">@</span>data</span>
 <span id="cb6-4"><a href="#cb6-4" aria-hidden="true" tabindex="-1"></a>results_frame<span class="sc">$</span>expected <span class="ot">&lt;-</span> <span class="cn">NA</span></span>

content/PIFS-opakapaka.html

@@ -305,7 +305,7 @@ <h2 class="anchored" data-anchor-id="run-fims-model">Run FIMS Model</h2>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a>obj <span class="ot">&lt;-</span> <span class="fu">MakeADFun</span>(<span class="at">data =</span> <span class="fu">list</span>(), parameters, <span class="at">DLL =</span> <span class="st">"FIMS"</span>, <span class="at">silent =</span> <span class="cn">TRUE</span>)</span>
 <span id="cb1-4"><a href="#cb1-4" aria-hidden="true" tabindex="-1"></a>opt <span class="ot">&lt;-</span> <span class="fu">nlminb</span>(obj<span class="sc">$</span>par, obj<span class="sc">$</span>fn, obj<span class="sc">$</span>gr, <span class="at">control =</span> <span class="fu">list</span>(<span class="at">eval.max =</span> <span class="dv">10000</span>, <span class="at">iter.max =</span> <span class="dv">10000</span>))</span>
 <span id="cb1-5"><a href="#cb1-5" aria-hidden="true" tabindex="-1"></a><span class="co">#print(opt)</span></span>
-<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>()</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<span id="cb1-6"><a href="#cb1-6" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 </details>
 </div>
 </section>

content/SEFSC-scamp.html

@@ -302,7 +302,7 @@ <h2 class="anchored" data-anchor-id="setup-description">Setup description</h2>
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: South Atlantic scamp grouper<br>
 </li>
@@ -693,7 +693,7 @@ <h2 class="anchored" data-anchor-id="add-your-script-that-sets-up-and-runs-the-m
 <span id="cb3-335"><a href="#cb3-335" aria-hidden="true" tabindex="-1"></a><span class="co"># TMB reporting</span></span>
 <span id="cb3-336"><a href="#cb3-336" aria-hidden="true" tabindex="-1"></a>sdr <span class="ot">&lt;-</span> TMB<span class="sc">::</span><span class="fu">sdreport</span>(obj)</span>
 <span id="cb3-337"><a href="#cb3-337" aria-hidden="true" tabindex="-1"></a>sdr_fixed <span class="ot">&lt;-</span> <span class="fu">summary</span>(sdr, <span class="st">"fixed"</span>)</span>
-<span id="cb3-338"><a href="#cb3-338" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>()</span>
+<span id="cb3-338"><a href="#cb3-338" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span>
 <span id="cb3-339"><a href="#cb3-339" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-340"><a href="#cb3-340" aria-hidden="true" tabindex="-1"></a><span class="co"># print(sdr_fixed)</span></span>
 <span id="cb3-341"><a href="#cb3-341" aria-hidden="true" tabindex="-1"></a></span>

content/SWFSC-sardine.html

@@ -309,7 +309,7 @@ <h2 class="anchored" data-anchor-id="add-a-chunk-of-code-describing-your-setup">
 </li>
 <li>TMB version: 1.9.14<br>
 </li>
-<li>FIMS commit: ecd2d80<br>
+<li>FIMS commit: 39d0743<br>
 </li>
 <li>Stock name: Pacific sardine northern subpopulation<br>
 </li>
@@ -709,7 +709,7 @@ <h2 class="anchored" data-anchor-id="add-your-script-that-sets-up-and-runs-the-m
 <span id="cb3-379"><a href="#cb3-379" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-380"><a href="#cb3-380" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-381"><a href="#cb3-381" aria-hidden="true" tabindex="-1"></a>obj <span class="ot">&lt;-</span> <span class="fu">MakeADFun</span>(<span class="at">data =</span> <span class="fu">list</span>(), parameters, <span class="at">DLL =</span> <span class="st">"FIMS"</span>, <span class="at">silent =</span> <span class="cn">TRUE</span>)</span>
-<span id="cb3-382"><a href="#cb3-382" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>()</span>
+<span id="cb3-382"><a href="#cb3-382" aria-hidden="true" tabindex="-1"></a>report <span class="ot">&lt;-</span> obj<span class="sc">$</span><span class="fu">report</span>(obj<span class="sc">$</span>env<span class="sc">$</span>last.par.best)</span>
 <span id="cb3-383"><a href="#cb3-383" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb3-384"><a href="#cb3-384" aria-hidden="true" tabindex="-1"></a><span class="co">#Are there flags for when something is going wrong with the model where initial values</span></span>
 <span id="cb3-385"><a href="#cb3-385" aria-hidden="true" tabindex="-1"></a><span class="co">#are all 0?</span></span>