Built site for gh-pages

.nojekyll

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-5f6b94ac
+c0d4a9d1

evaluation/badges.html

@@ -266,7 +266,7 @@ <h1 class="title">Journal badges</h1>
 <p><em>Caveat: Please note that these criteria are based on available information about each badge online, and that we have likely differences in our procedure (e.g.&nbsp;allowed troubleshooting for execution and reproduction, not under tight time pressure to complete). Moreover, we focus only on reproduction of the discrete-event simulation, and not on other aspects of the article. We cannot guarantee that the badges below would have been awarded in practice by these journals.</em></p>
 <section id="criteria" class="level2">
 <h2 class="anchored" data-anchor-id="criteria">Criteria</h2>
-<div id="2abc3ef2" class="cell" data-execution_count="1">
+<div id="972ad03f" class="cell" data-execution_count="1">
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> IPython.display <span class="im">import</span> display, Markdown</span>
@@ -399,7 +399,7 @@ <h2 class="anchored" data-anchor-id="criteria">Criteria</h2>
 </section>
 <section id="badges" class="level2">
 <h2 class="anchored" data-anchor-id="badges">Badges</h2>
-<div id="b205b80c" class="cell" data-execution_count="2">
+<div id="9b110d6f" class="cell" data-execution_count="2">
 <details class="code-fold">
 <summary>Code</summary>
 <div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Full badge names</span></span>

evaluation/reporting.html

@@ -1064,7 +1064,7 @@ <h2 class="anchored" data-anchor-id="des-checklist-derived-from-ispor-sdm">DES c
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","loop":false,"openEffect":"zoom","descPosition":"bottom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

evaluation/scope.html

@@ -899,7 +899,7 @@ <h2 class="anchored" data-anchor-id="outside-scope">Outside scope</h2>
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","closeEffect":"zoom","openEffect":"zoom","loop":false,"descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","loop":false});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

logbook/logbook.html

@@ -268,7 +268,7 @@ <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-list
 
 <div class="quarto-listing quarto-listing-container-default" id="listing-listing">
 <div class="list quarto-listing-default">
-<div class="quarto-post image-right" data-index="0" data-categories="compendium" data-listing-date-sort="1721257200000" data-listing-file-modified-sort="1721303001709" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="815">
+<div class="quarto-post image-right" data-index="0" data-categories="compendium" data-listing-date-sort="1721257200000" data-listing-file-modified-sort="1721304354345" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="931">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_07_18/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_07_18/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>

logbook/posts/2024_07_03/index.html

@@ -310,7 +310,7 @@ <h2 class="anchored" data-anchor-id="check-journal-article-license-and-upload">1
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="f026761a" class="cell" data-execution_count="1">
+<div id="7a941647" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_04/index.html

@@ -553,7 +553,7 @@ <h2 class="anchored" data-anchor-id="look-over-code-and-set-up-environment">16.0
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="8dabbfba" class="cell" data-execution_count="1">
+<div id="6a543ccd" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb8"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb8-1"><a href="#cb8-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb8-2"><a href="#cb8-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb8-3"><a href="#cb8-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_05/index.html

@@ -629,7 +629,7 @@ <h2 class="anchored" data-anchor-id="continuing-to-troubleshoot-in-text-results-
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="d8d7834d" class="cell" data-execution_count="1">
+<div id="e6f5582e" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb10"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb10-1"><a href="#cb10-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb10-2"><a href="#cb10-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb10-3"><a href="#cb10-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_08/index.html

@@ -386,7 +386,7 @@ <h2 class="anchored" data-anchor-id="adding-seeds">09.50-10.49, 11.02-11.05, 11.
 <li>Difference: 5.84 minutes</li>
 </ul>
 <p>Hence, I feel we can mark in-text result 1 as reproduced at this time (11.14), with starter seed of 200.</p>
-<div id="ad228eb5" class="cell" data-execution_count="1">
+<div id="873a8ed2" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb2"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb2-1"><a href="#cb2-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
@@ -622,7 +622,7 @@ <h2 class="anchored" data-anchor-id="returning-to-figure-2">15.31-16.55: Returni
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="d4eb74e5" class="cell" data-execution_count="2">
+<div id="365a5c87" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb12"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb12-1"><a href="#cb12-1" aria-hidden="true" tabindex="-1"></a><span class="co"># Minutes used prior to today</span></span>
 <span id="cb12-2"><a href="#cb12-2" aria-hidden="true" tabindex="-1"></a>used_to_date <span class="op">=</span> <span class="dv">443</span></span>
 <span id="cb12-3"><a href="#cb12-3" aria-hidden="true" tabindex="-1"></a></span>

logbook/posts/2024_07_09/index.html

@@ -412,7 +412,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 <p>For this scenario analysis, the “day time working hours of all human resources are extended by up to 2h, extending resource access to all patients” (<span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span>). Given how the model scheduling is set-up, it is assumed that this means we simply adjust the schedule to end at 5, 6 or 7pm (and that that would simply shortern the night staff time).</p>
 <p>I ran these scenarios, processing and saving the relevant model results.</p>
 <p>For in-text result 3, I can see that the results do not match up to the paper. I am not surprised by this though - as the model had no seed control, as it is not mentioned in the paper, we can assume that it might not have been used by the original study, and so variation between the scenarios could (in part) reflect model stochasticity.</p>
-<div id="a5019579" class="cell" data-execution_count="1">
+<div id="4893f856" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb4"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> pandas <span class="im">as</span> pd</span>
 <span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>pd.read_csv(<span class="st">"txt3.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
@@ -503,7 +503,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 </div>
 </div>
 <p>To test this assumption, I ran the model again for baseline with two further seeds. We can see the importance of seed control here. For example, with seed 700, we see a broader range of results, with the result for 6pm (13.32) is much higher than for the other two seeds and, compared with their 5pm results, we would’ve seen less of a reduction. Similarly, if we compared the 5pm seed 700 result with the 6pm seed 500 result, we would see a much greater reduction.</p>
-<div id="2040afe2" class="cell" data-execution_count="2">
+<div id="8fccd32f" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb5"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>pd.read_csv(<span class="st">"txt3_seeds.csv"</span>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-display" data-execution_count="2">
 <div>
@@ -559,7 +559,7 @@ <h2 class="anchored" data-anchor-id="starting-on-figure-3-and-in-text-result-3">
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="75a62d20" class="cell" data-execution_count="3">
+<div id="2953f33d" class="cell" data-execution_count="3">
 <div class="sourceCode cell-code" id="cb6"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb6-1"><a href="#cb6-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb6-2"><a href="#cb6-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb6-3"><a href="#cb6-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_11/index.html

@@ -411,7 +411,7 @@ <h2 class="anchored" data-anchor-id="figure-5">15.32-16.31, 16.35-17.00: Figure
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="152e2af8" class="cell" data-execution_count="1">
+<div id="a80da9b1" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_12/index.html

@@ -330,7 +330,7 @@ <h2 class="anchored" data-anchor-id="tidy-and-email-author">10.30-10.50: Tidy an
 </section>
 <section id="timings-for-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-reproduction">Timings for reproduction</h2>
-<div id="419a52f5" class="cell" data-execution_count="1">
+<div id="d0d71b46" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>
@@ -419,7 +419,7 @@ <h2 class="anchored" data-anchor-id="des-checklist-derived-from-ispor-sdm">13.19
 </section>
 <section id="timings-for-evaluation" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-evaluation">Timings for evaluation</h2>
-<div id="a8e2f026" class="cell" data-execution_count="2">
+<div id="f92f624e" class="cell" data-execution_count="2">
 <div class="sourceCode cell-code" id="cb3"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb3-1"><a href="#cb3-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb3-2"><a href="#cb3-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb3-3"><a href="#cb3-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_15/index.html

@@ -362,7 +362,7 @@ <h2 class="anchored" data-anchor-id="consensus-on-evaluation">08.22-08.30, 08.37
 </section>
 <section id="timings-for-evaluation" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-evaluation">Timings for evaluation</h2>
-<div id="2d73f4f7" class="cell" data-execution_count="1">
+<div id="61bff89a" class="cell" data-execution_count="1">
 <div class="sourceCode cell-code" id="cb1"><pre class="sourceCode python code-with-copy"><code class="sourceCode python"><span id="cb1-1"><a href="#cb1-1" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> sys</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

logbook/posts/2024_07_18/index.html

@@ -284,8 +284,13 @@ <h3 class="anchored" data-anchor-id="docker">Docker</h3>
   libicui18n.so.66: cannot open shared object file: No such file or directory</code></pre>
 <p>I briefly tried adding <code>containerit</code> to my <code>renv</code> to try that and see if it was simpler, although decided to pause on that and remove it and keep trying as before, as I kept getting errors and it wasn’t a quick-fix. I removed it from <code>DESCRIPTION</code> then ran <code>renv::clean()</code>, <code>renv::snapshot()</code>.</p>
 <p>I add <code>libicu-dev</code> and tried again. This failed with the same error as before.</p>
-<p>Looking at the <a href="https://hub.docker.com/layers/rocker/rstudio/4.4/images/sha256-853bc686c132b6f07ec024142612d7d01ea4d2a0716fe269d36adf4d4487c19c?context=explore">rocker rstudio image</a>, it runs on <code>ubunutu 22.04</code>. <a href="https://docs.posit.co/connect/admin/r/dependencies/">Posit</a> lists system dependencies for ubunutu 22.04 as <code>apt install -y libcairo2-dev libssl-dev make libcurl4-openssl-dev libmysqlclient-dev unixodbc-dev libnode-dev default-jdk libxml2-dev git libfontconfig1-dev libfreetype6-dev libssh2-1-dev zlib1g-dev libglpk-dev libjpeg-dev imagemagick libmagick++-dev gsfonts cmake libpng-dev libtiff-dev python3 libglu1-mesa-dev libgl1-mesa-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libsodium-dev libicu-dev tcl tk tk-dev tk-table libfribidi-dev libharfbuzz-dev libudunits2-dev</code>. I replaced the line in my Dockerfile and tried again. This failed with the same error as before.</p>
+<p>Looking at the <a href="https://hub.docker.com/layers/rocker/rstudio/4.4/images/sha256-853bc686c132b6f07ec024142612d7d01ea4d2a0716fe269d36adf4d4487c19c?context=explore">rocker rstudio image</a>, it runs on <code>ubunutu 22.04</code>. <a href="https://docs.posit.co/connect/admin/r/dependencies/">Posit</a> lists system dependencies for ubunutu 22.04 as <code>apt install -y libcairo2-dev libssl-dev make libcurl4-openssl-dev libmysqlclient-dev unixodbc-dev libnode-dev default-jdk libxml2-dev git libfontconfig1-dev libfreetype6-dev libssh2-1-dev zlib1g-dev libglpk-dev libjpeg-dev imagemagick libmagick++-dev gsfonts cmake libpng-dev libtiff-dev python3 libglu1-mesa-dev libgl1-mesa-dev libgdal-dev gdal-bin libgeos-dev libproj-dev libsqlite3-dev libsodium-dev libicu-dev tcl tk tk-dev tk-table libfribidi-dev libharfbuzz-dev libudunits2-dev</code>. I replaced the line in my Dockerfile and tried again. This failed with the same error as before (so returned it to the simpler list).</p>
 <p>I found <a href="https://github.com/Bioconductor/bioconductor_docker/issues/59">this issue</a> with the same error, where it appears there is an issue with the stringi binary being built for the wrong Ubunutu since <code>libicui18n.so.66</code> is for 20.04, although the fix appeared to be that they fixed the bioconductor container, and it wasn’t super clear to me what I should do.</p>
+<p>Based on <a href="https://gist.github.com/aforsythe/b588c950965d5a6b4810bed4cf85873b">this example</a> linked from <a href="https://forum.posit.co/t/restore-renv-lock-file-without-redownloading-packages/102690/9">this issue</a>, I tried switching <code>libicu-dev</code> to <code>libicu</code>. However, this returned error <code>Unable to locate package libicu</code>. I then instead tried adding <code>RUN R -e "install.packages('stringi')"</code> before <code>renv::restore()</code>. That ran successfully, but hit a new error:</p>
+<pre><code>Error in dyn.load(file, DLLpath = DLLpath, ...) : 
+  unable to load shared object '/home/code/renv/staging/2/openssl/libs/openssl.so':
+  libssl.so.1.1: cannot open shared object file: No such file or directory</code></pre>
+<p><code>libssl</code> is in the list of system dependencies that were being installed. A quick google shows there are issues related to <code>libssl.so.1.1</code> on <code>Ubuntu 22.04</code>. I tried doing the simplest solution first - installing it seperately (as that worked for <code>stringi</code> above).</p>
 </section>
 <section id="fix-quarto-github-action" class="level3">
 <h3 class="anchored" data-anchor-id="fix-quarto-github-action">Fix Quarto GitHub action</h3>