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Quarto GHA Workflow Runner committed May 13, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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51caae59
db1e9dd5
10 changes: 8 additions & 2 deletions content/AFSC-BSAI-AtkaMackerel.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.553">
<meta name="generator" content="quarto-1.4.554">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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<a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">SWFSC sardine case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../content/PIFS-opakapaka.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">PIFSC Opakapaka case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
Expand Down Expand Up @@ -291,7 +297,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
</li>
<li>TMB version: 1.9.11<br>
</li>
<li>FIMS commit: 97281c2<br>
<li>FIMS commit: fe5836b<br>
</li>
<li>Stock name: BSAI Atka mackerel<br>
</li>
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127 changes: 68 additions & 59 deletions content/AFSC-GOA-pollock.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.553">
<meta name="generator" content="quarto-1.4.554">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

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<a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">SWFSC sardine case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../content/PIFS-opakapaka.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">PIFSC Opakapaka case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
Expand Down Expand Up @@ -270,40 +276,41 @@ <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/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmpz7KfHb/downloaded_packages</code></pre>
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmp4GCWNR/downloaded_packages</code></pre>
</div>
<details class="code-fold">
<summary>Code</summary>
<div class="sourceCode cell-code" id="cb3"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"kaskr/TMB_contrib_R/TMBhelper"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>RcppParallel (NA -&gt; 5.1.7 ) [CRAN]
numDeriv (NA -&gt; 2016.8-1.1) [CRAN]
ps (NA -&gt; 1.7.6 ) [CRAN]
distribut... (NA -&gt; 0.4.0 ) [CRAN]
tensorA (NA -&gt; 0.36.2.1 ) [CRAN]
abind (NA -&gt; 1.4-5 ) [CRAN]
backports (NA -&gt; 1.4.1 ) [CRAN]
processx (NA -&gt; 3.8.4 ) [CRAN]
desc (NA -&gt; 1.4.3 ) [CRAN]
callr (NA -&gt; 3.7.6 ) [CRAN]
posterior (NA -&gt; 1.5.0 ) [CRAN]
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; 1.1.3 ) [CRAN]
pkgbuild (NA -&gt; 1.4.4 ) [CRAN]
loo (NA -&gt; 2.7.0 ) [CRAN]
gridExtra (NA -&gt; 2.3 ) [CRAN]
inline (NA -&gt; 0.3.19 ) [CRAN]
StanHeaders (NA -&gt; 2.32.7 ) [CRAN]
rstan (NA -&gt; 2.32.6 ) [CRAN]
tmbstan (NA -&gt; 1.0.91 ) [CRAN]
<pre><code>RcppParallel (NA -&gt; 5.1.7 ) [CRAN]
numDeriv (NA -&gt; 2016.8-1.1) [CRAN]
farver (2.1.1 -&gt; 2.1.2 ) [CRAN]
ps (NA -&gt; 1.7.6 ) [CRAN]
distribut... (NA -&gt; 0.4.0 ) [CRAN]
tensorA (NA -&gt; 0.36.2.1 ) [CRAN]
abind (NA -&gt; 1.4-5 ) [CRAN]
backports (NA -&gt; 1.4.1 ) [CRAN]
processx (NA -&gt; 3.8.4 ) [CRAN]
desc (NA -&gt; 1.4.3 ) [CRAN]
callr (NA -&gt; 3.7.6 ) [CRAN]
posterior (NA -&gt; 1.5.0 ) [CRAN]
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; 1.1.3 ) [CRAN]
pkgbuild (NA -&gt; 1.4.4 ) [CRAN]
loo (NA -&gt; 2.7.0 ) [CRAN]
gridExtra (NA -&gt; 2.3 ) [CRAN]
inline (NA -&gt; 0.3.19 ) [CRAN]
StanHeaders (NA -&gt; 2.32.7 ) [CRAN]
rstan (NA -&gt; 2.32.6 ) [CRAN]
tmbstan (NA -&gt; 1.0.91 ) [CRAN]

The downloaded binary packages are in
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmpz7KfHb/downloaded_packages
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmp4GCWNR/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmpz7KfHb/remotes1c73d437de/kaskr-TMB_contrib_R-d275e52/TMBhelper/DESCRIPTION’ ... OK
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmp4GCWNR/remotes16291d626851/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
Expand All @@ -315,27 +322,28 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"NOAA-FIMS/FIMS"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>sys (NA -&gt; 3.4.2 ) [CRAN]
askpass (NA -&gt; 1.2.0 ) [CRAN]
openssl (NA -&gt; 2.1.2 ) [CRAN]
curl (NA -&gt; 5.2.1 ) [CRAN]
ini (NA -&gt; 0.3.1 ) [CRAN]
httr2 (NA -&gt; 1.0.1 ) [CRAN]
gitcreds (NA -&gt; 0.1.2 ) [CRAN]
zip (NA -&gt; 2.3.1 ) [CRAN]
rstudioapi (NA -&gt; 0.16.0) [CRAN]
credentials (NA -&gt; 2.0.1 ) [CRAN]
whisker (NA -&gt; 0.4.1 ) [CRAN]
gh (NA -&gt; 1.4.1 ) [CRAN]
gert (NA -&gt; 2.0.1 ) [CRAN]
crayon (NA -&gt; 1.5.2 ) [CRAN]
clipr (NA -&gt; 0.8.0 ) [CRAN]
usethis (NA -&gt; 2.2.3 ) [CRAN]
<pre><code>sys (NA -&gt; 3.4.2 ) [CRAN]
askpass (NA -&gt; 1.2.0 ) [CRAN]
openssl (NA -&gt; 2.1.2 ) [CRAN]
curl (NA -&gt; 5.2.1 ) [CRAN]
ini (NA -&gt; 0.3.1 ) [CRAN]
httr2 (NA -&gt; 1.0.1 ) [CRAN]
gitcreds (NA -&gt; 0.1.2 ) [CRAN]
zip (NA -&gt; 2.3.1 ) [CRAN]
rstudioapi (NA -&gt; 0.16.0) [CRAN]
credentials (NA -&gt; 2.0.1 ) [CRAN]
farver (2.1.1 -&gt; 2.1.2 ) [CRAN]
whisker (NA -&gt; 0.4.1 ) [CRAN]
gh (NA -&gt; 1.4.1 ) [CRAN]
gert (NA -&gt; 2.0.1 ) [CRAN]
crayon (NA -&gt; 1.5.2 ) [CRAN]
clipr (NA -&gt; 0.8.0 ) [CRAN]
usethis (NA -&gt; 2.2.3 ) [CRAN]

The downloaded binary packages are in
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmpz7KfHb/downloaded_packages
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmp4GCWNR/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmpz7KfHb/remotes1c73ec95e71/NOAA-FIMS-FIMS-97281c2/DESCRIPTION’ ... OK
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmp4GCWNR/remotes162915268fc2/NOAA-FIMS-FIMS-fe5836b/DESCRIPTION’ ... OK
* preparing ‘FIMS’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
Expand All @@ -348,23 +356,24 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
<div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a>remotes<span class="sc">::</span><span class="fu">install_github</span>(<span class="st">"r4ss/r4ss"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
</details>
<div class="cell-output cell-output-stdout">
<pre><code>systemfonts (NA -&gt; 1.0.6 ) [CRAN]
parallelly (NA -&gt; 1.37.1 ) [CRAN]
listenv (NA -&gt; 0.9.1 ) [CRAN]
globals (NA -&gt; 0.16.3 ) [CRAN]
svglite (NA -&gt; 2.1.3 ) [CRAN]
xml2 (NA -&gt; 1.3.6 ) [CRAN]
future (NA -&gt; 1.33.2 ) [CRAN]
kableExtra (NA -&gt; 1.4.0 ) [CRAN]
furrr (NA -&gt; 0.3.1 ) [CRAN]
forcats (NA -&gt; 1.0.0 ) [CRAN]
corpcor (NA -&gt; 1.6.10 ) [CRAN]
coda (NA -&gt; 0.19-4.1) [CRAN]
<pre><code>systemfonts (NA -&gt; 1.0.6 ) [CRAN]
farver (2.1.1 -&gt; 2.1.2 ) [CRAN]
parallelly (NA -&gt; 1.37.1 ) [CRAN]
listenv (NA -&gt; 0.9.1 ) [CRAN]
globals (NA -&gt; 0.16.3 ) [CRAN]
svglite (NA -&gt; 2.1.3 ) [CRAN]
xml2 (NA -&gt; 1.3.6 ) [CRAN]
future (NA -&gt; 1.33.2 ) [CRAN]
kableExtra (NA -&gt; 1.4.0 ) [CRAN]
furrr (NA -&gt; 0.3.1 ) [CRAN]
forcats (NA -&gt; 1.0.0 ) [CRAN]
corpcor (NA -&gt; 1.6.10 ) [CRAN]
coda (NA -&gt; 0.19-4.1) [CRAN]

The downloaded binary packages are in
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmpz7KfHb/downloaded_packages
/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T//Rtmp4GCWNR/downloaded_packages
── R CMD build ─────────────────────────────────────────────────────────────────
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmpz7KfHb/remotes1c731d24aa05/r4ss-r4ss-44d3882/DESCRIPTION’ ... OK
* checking for file ‘/private/var/folders/3m/p59k4qdj0f17st0gn2cmj3640000gn/T/Rtmp4GCWNR/remotes162922920587/r4ss-r4ss-44d3882/DESCRIPTION’ ... OK
* preparing ‘r4ss’:
* checking DESCRIPTION meta-information ... OK
* checking for LF line-endings in source and make files and shell scripts
Expand Down Expand Up @@ -400,7 +409,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
</li>
<li>TMB version: 1.9.11<br>
</li>
<li>FIMS commit: 97281c2<br>
<li>FIMS commit: fe5836b<br>
</li>
<li>Stock name: Gulf of Alaska (GOA) Walleye Pollock<br>
</li>
Expand Down
10 changes: 8 additions & 2 deletions content/NEFSC-yellowtail.html
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<html xmlns="http://www.w3.org/1999/xhtml" lang="en" xml:lang="en"><head>

<meta charset="utf-8">
<meta name="generator" content="quarto-1.4.553">
<meta name="generator" content="quarto-1.4.554">

<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

Expand Down Expand Up @@ -194,6 +194,12 @@
<a href="../content/SWFSC-sardine.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">SWFSC sardine case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
<a href="../content/PIFS-opakapaka.html" class="sidebar-item-text sidebar-link">
<span class="menu-text">PIFSC Opakapaka case study</span></a>
</div>
</li>
<li class="sidebar-item">
<div class="sidebar-item-container">
Expand Down Expand Up @@ -292,7 +298,7 @@ <h2 class="anchored" data-anchor-id="the-setup">The setup</h2>
</li>
<li>TMB version: 1.9.11<br>
</li>
<li>FIMS commit: 97281c2<br>
<li>FIMS commit: fe5836b<br>
</li>
<li>Stock name: Southern New England-Mid Atlantic Yellowtail Flounder<br>
</li>
Expand Down
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