Built site for gh-pages

.nojekyll

@@ -1 +1 @@
-44968607
+a85e44b2

CHANGELOG.html

@@ -174,9 +174,13 @@ <h2 id="toc-title">On this page</h2>
   <ul>
   <li><a href="#changelog" id="toc-changelog" class="nav-link active" data-scroll-target="#changelog">Changelog</a>
   <ul class="collapse">
-  <li><a href="#v0.1.0---2024-08-12" id="toc-v0.1.0---2024-08-12" class="nav-link" data-scroll-target="#v0.1.0---2024-08-12">v0.1.0 - 2024-08-12</a>
+  <li><a href="#v0.2.0---2024-10-02" id="toc-v0.2.0---2024-10-02" class="nav-link" data-scroll-target="#v0.2.0---2024-10-02">v0.2.0 - 2024-10-02</a>
   <ul class="collapse">
   <li><a href="#added" id="toc-added" class="nav-link" data-scroll-target="#added">Added</a></li>
+  </ul></li>
+  <li><a href="#v0.1.0---2024-08-12" id="toc-v0.1.0---2024-08-12" class="nav-link" data-scroll-target="#v0.1.0---2024-08-12">v0.1.0 - 2024-08-12</a>
+  <ul class="collapse">
+  <li><a href="#added-1" id="toc-added-1" class="nav-link" data-scroll-target="#added-1">Added</a></li>
   <li><a href="#changed" id="toc-changed" class="nav-link" data-scroll-target="#changed">Changed</a></li>
   </ul></li>
   </ul></li>
@@ -193,11 +197,25 @@ <h2 id="toc-title">On this page</h2>
 <h1>Changelog</h1>
 <p>All notable changes to this project will be documented in this file.</p>
 <p>The format is based on <a href="https://keepachangelog.com/en/1.1.0/">Keep a Changelog</a>, and this project adheres to <a href="https://semver.org/spec/v2.0.0.html">Semantic Versioning</a>. Dates formatted as YYYY-MM-DD as per <a href="https://www.iso.org/iso-8601-date-and-time-format.html">ISO standard</a>.</p>
+<section id="v0.2.0---2024-10-02" class="level2">
+<h2 class="anchored" data-anchor-id="v0.2.0---2024-10-02">v0.2.0 - 2024-10-02</h2>
+<p>Conducted reproduction, evaluated code and article, organised research compendium, and test run by second STARS team member.</p>
+<section id="added" class="level3">
+<h3 class="anchored" data-anchor-id="added">Added</h3>
+<ul>
+<li>Reproduction of the model in <code>reproduction/</code></li>
+<li>Evaluation of the code and article against guidelines (in <code>evaluation/</code>)</li>
+<li>Summary report and reflections from reproduction</li>
+<li>Organised and documented reproduction to form a <code>research compendium</code></li>
+<li>Test-run of model by Tom Monks, attempting to run code from <code>reproduction/</code></li>
+</ul>
+</section>
+</section>
 <section id="v0.1.0---2024-08-12" class="level2">
 <h2 class="anchored" data-anchor-id="v0.1.0---2024-08-12">v0.1.0 - 2024-08-12</h2>
 <p>Set up repository and defined scope of reproduction.</p>
-<section id="added" class="level3">
-<h3 class="anchored" data-anchor-id="added">Added</h3>
+<section id="added-1" class="level3">
+<h3 class="anchored" data-anchor-id="added-1">Added</h3>
 <ul>
 <li>Code from original study</li>
 <li>Article and supplementary materials</li>

evaluation/badges.html

@@ -258,7 +258,7 @@ <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="bd505068" class="cell" data-execution_count="1">
+<div id="7c9cd249" 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>
@@ -390,7 +390,7 @@ <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="3c5378fe" class="cell" data-execution_count="2">
+<div id="7b9eef8b" 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>

listings.json

@@ -2,6 +2,7 @@
   {
     "listing": "/logbook/logbook.html",
     "items": [
+      "/logbook/posts/2024_10_01/index.html",
       "/logbook/posts/2024_09_04/index.html",
       "/logbook/posts/2024_08_13/index.html",
       "/logbook/posts/2024_08_12/index.html",

logbook/logbook.html

@@ -245,7 +245,7 @@ <h1 class="title">Logbook</h1>
 <!-- margin-sidebar -->
     <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
 
-    <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-listing-category category-default"><div class="category" data-category="">All <span class="quarto-category-count">(4)</span></div><div class="category" data-category="compendium">compendium <span class="quarto-category-count">(1)</span></div><div class="category" data-category="evaluation">evaluation <span class="quarto-category-count">(1)</span></div><div class="category" data-category="read">read <span class="quarto-category-count">(1)</span></div><div class="category" data-category="report">report <span class="quarto-category-count">(1)</span></div><div class="category" data-category="reproduction">reproduction <span class="quarto-category-count">(3)</span></div><div class="category" data-category="scope">scope <span class="quarto-category-count">(1)</span></div><div class="category" data-category="setup">setup <span class="quarto-category-count">(1)</span></div></div></div>
+    <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-listing-category category-default"><div class="category" data-category="">All <span class="quarto-category-count">(5)</span></div><div class="category" data-category="compendium">compendium <span class="quarto-category-count">(1)</span></div><div class="category" data-category="evaluation">evaluation <span class="quarto-category-count">(1)</span></div><div class="category" data-category="read">read <span class="quarto-category-count">(1)</span></div><div class="category" data-category="report">report <span class="quarto-category-count">(1)</span></div><div class="category" data-category="reproduction">reproduction <span class="quarto-category-count">(4)</span></div><div class="category" data-category="scope">scope <span class="quarto-category-count">(1)</span></div><div class="category" data-category="setup">setup <span class="quarto-category-count">(1)</span></div></div></div>
 <!-- main -->
 <main class="content quarto-banner-title-block column-page-left" id="quarto-document-content">
 
@@ -260,7 +260,40 @@ <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="reproduction" data-listing-date-sort="1725408000000" data-listing-file-modified-sort="1725875554904" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="58">
+<div class="quarto-post image-right" data-index="0" data-categories="reproduction" data-listing-date-sort="1727827200000" data-listing-file-modified-sort="1727882093689" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="67">
+<div class="thumbnail">
+<p><a href="../logbook/posts/2024_10_01/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_10_01/index.html" class="no-external">
+<div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
+</a><p><a href="../logbook/posts/2024_10_01/index.html" class="no-external"></a></p>
+</div>
+<div class="body">
+<h3 class="no-anchor listing-title">
+<a href="../logbook/posts/2024_10_01/index.html" class="no-external">Day 5</a>
+</h3>
+<div class="listing-subtitle">
+<a href="../logbook/posts/2024_10_01/index.html" class="no-external"></a>
+</div>
+<div class="listing-categories">
+<div class="listing-category" onclick="window.quartoListingCategory('reproduction'); return false;">
+reproduction
+</div>
+</div>
+<div class="listing-description">
+<a href="../logbook/posts/2024_10_01/index.html" class="no-external">Test-run of reproduction package, informing author/s and archiving repository.</a>
+</div>
+</div>
+<div class="metadata">
+<a href="../logbook/posts/2024_10_01/index.html" class="no-external">
+<div class="listing-date">
+Oct 2, 2024
+</div>
+<div class="listing-author">
+Amy Heather
+</div>
+</a>
+</div>
+</div>
+<div class="quarto-post image-right" data-index="1" data-categories="reproduction" data-listing-date-sort="1725408000000" data-listing-file-modified-sort="1727882093689" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="1" data-listing-word-count-sort="58">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_09_04/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_09_04/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -293,7 +326,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="reproduction,report,evaluation,compendium" data-listing-date-sort="1723507200000" data-listing-file-modified-sort="1725875554900" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="537">
+<div class="quarto-post image-right" data-index="2" data-categories="reproduction,report,evaluation,compendium" data-listing-date-sort="1723507200000" data-listing-file-modified-sort="1727882093688" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="537">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_08_13/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_08_13/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -335,7 +368,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="reproduction" data-listing-date-sort="1723420800000" data-listing-file-modified-sort="1725875554900" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="437">
+<div class="quarto-post image-right" data-index="3" data-categories="reproduction" data-listing-date-sort="1723420800000" data-listing-file-modified-sort="1727882093688" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="437">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_08_12/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_08_12/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -368,7 +401,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="3" data-categories="setup,read,scope" data-listing-date-sort="1722470400000" data-listing-file-modified-sort="1725875554900" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="553">
+<div class="quarto-post image-right" data-index="4" data-categories="setup,read,scope" data-listing-date-sort="1722470400000" data-listing-file-modified-sort="1727882093688" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="553">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_08_01/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_08_01/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>

logbook/posts/2024_08_01/index.html

@@ -321,7 +321,7 @@ <h2 class="anchored" data-anchor-id="read-article-and-consensus-on-scope.">14.53
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="250c6f3a" class="cell" data-execution_count="1">
+<div id="1d4c7cfb" 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_08_12/index.html

@@ -317,7 +317,7 @@ <h2 class="anchored" data-anchor-id="write-plotting-function">16.29-17.00: Write
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="1007a23c" class="cell" data-execution_count="1">
+<div id="eecdbbfa" 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>

logbook/posts/2024_08_13/index.html

@@ -307,7 +307,7 @@ <h2 class="anchored" data-anchor-id="untimed-reproduction-success">Untimed: Repr
 </section>
 <section id="timings-for-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-reproduction">Timings for reproduction</h2>
-<div id="5b8aae4c" class="cell" data-execution_count="1">
+<div id="113f5134" 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>
@@ -354,7 +354,7 @@ <h2 class="anchored" data-anchor-id="ispor-sdm">10.59-11.23: ISPOR-SDM</h2>
 </section>
 <section id="timings-for-evaluation" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-evaluation">Timings for evaluation</h2>
-<div id="2b3f2171" class="cell" data-execution_count="2">
+<div id="d85fd33c" 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_09_04/index.html

@@ -270,7 +270,7 @@ <h2 class="anchored" data-anchor-id="consensus-on-reproduction">10.15-10.16: Con
 </section>
 <section id="timings-for-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="timings-for-reproduction">Timings for reproduction</h2>
-<div id="b7944264" class="cell" data-execution_count="1">
+<div id="b38a2338" 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>