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pythonhealthdatascience · Aug 13, 2024 · b8b58b3 · b8b58b3
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diff --git a/.nojekyll b/.nojekyll
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+46d3f757
diff --git a/CHANGELOG.html b/CHANGELOG.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="./reproduction/reproduction.html">
+    <a class="dropdown-item" href="./reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/CONTRIBUTING.html b/CONTRIBUTING.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="./reproduction/reproduction.html">
+    <a class="dropdown-item" href="./reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/evaluation/artefacts.html b/evaluation/artefacts.html
@@ -125,7 +125,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/evaluation/badges.html b/evaluation/badges.html
@@ -159,7 +159,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -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="16f6ade1" class="cell" data-execution_count="1">
+<div id="faf36a0a" 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="22203700" class="cell" data-execution_count="2">
+<div id="1e1a0a4d" 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>

diff --git a/evaluation/reflections.html b/evaluation/reflections.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -204,6 +204,7 @@ <h1 class="title">Reflections</h1>
 <section id="what-would-have-helped-facilitate-this-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="what-would-have-helped-facilitate-this-reproduction">What would have helped facilitate this reproduction?</h2>
 <p><strong>Figure</strong> - provide code to produce the figure</p>
+<p><strong>Note:</strong> Although not needed for the reproduction itself, when I tried to amend the <strong>name and location of the csv file</strong> output the model for use in tests, this was very tricky to do as it was hard coded into the scripts and I found difficult to amend due to how the model is run and set up.</p>
 </section>
 <section id="what-did-help-facilitate-this-reproduction" class="level2">
 <h2 class="anchored" data-anchor-id="what-did-help-facilitate-this-reproduction">What did help facilitate this reproduction?</h2>
@@ -212,6 +213,7 @@ <h2 class="anchored" data-anchor-id="what-did-help-facilitate-this-reproduction"
 <p><strong>Environment</strong> - stated version of Python and provided requirements file (simpy, with version given in the app repository).</p>
 <p><strong>Simple results spreadsheet</strong> - the layout of the results spreadsheet was simple, understandable and easy to read, making it easy to adapt into figures</p>
 <p><strong>Simple figures</strong> - the figures were simply (just means and CI which are already calculated).</p>
+<p><strong>Speed of model</strong> - the model was super quick (seconds!) which made it really easy to run and re-run each time.</p>
 </section>
 <section id="full-list-of-troubleshooting-steps" class="level2">
 <h2 class="anchored" data-anchor-id="full-list-of-troubleshooting-steps">Full list of troubleshooting steps</h2>

diff --git a/evaluation/reporting.html b/evaluation/reporting.html
@@ -125,7 +125,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/evaluation/reproduction_report.html b/evaluation/reproduction_report.html
diff --git a/evaluation/reproduction_success.html b/evaluation/reproduction_success.html
diff --git a/evaluation/scope.html b/evaluation/scope.html
@@ -125,7 +125,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/index.html b/index.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
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         <li>
-    <a class="dropdown-item" href="./reproduction/reproduction.html">
+    <a class="dropdown-item" href="./reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -233,7 +233,6 @@ <h2 class="anchored" data-anchor-id="about">About</h2>
 <section id="project-team" class="level2">
 <h2 class="anchored" data-anchor-id="project-team">Project team</h2>
 <!-- ORCID icon CC 1.0 from https://figshare.com/articles/figure/ORCID_iD_icon_graphics/5008697/4 -->
-<!-- TODO: Moved authors conducting and supporting reproduction out of the list and into the appropriate section -->
 <p>Conducting this reproduction:</p>
 <ul>
 <li><a href="https://github.com/amyheather">Amy Heather</a> <a href="https://orcid.org/0000-0002-6596-3479"><img src="quarto_site/ORCIDiD_icon16x16.png" class="img-fluid" alt="ORCID icon"></a></li>

diff --git a/logbook/logbook.html b/logbook/logbook.html
@@ -165,7 +165,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -260,7 +260,7 @@ <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="reproduction" data-listing-date-sort="1723507200000" data-listing-file-modified-sort="1723546468730" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="363">
+<div class="quarto-post image-right" data-index="0" data-categories="reproduction" data-listing-date-sort="1723507200000" data-listing-file-modified-sort="1723555880390" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="363">
 <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>
@@ -293,7 +293,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="reproduction" data-listing-date-sort="1723420800000" data-listing-file-modified-sort="1723546468730" 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="1" data-categories="reproduction" data-listing-date-sort="1723420800000" data-listing-file-modified-sort="1723555880390" 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>
@@ -326,7 +326,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="setup,read,scope" data-listing-date-sort="1722470400000" data-listing-file-modified-sort="1723546468730" 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="2" data-categories="setup,read,scope" data-listing-date-sort="1722470400000" data-listing-file-modified-sort="1723555880390" 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>

diff --git a/logbook/posts/2024_08_01/index.html b/logbook/posts/2024_08_01/index.html
@@ -141,7 +141,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../../../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../../../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -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="dbc93c3c" class="cell" data-execution_count="1">
+<div id="5fbac7c8" 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>

diff --git a/logbook/posts/2024_08_12/index.html b/logbook/posts/2024_08_12/index.html
@@ -141,7 +141,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../../../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../../../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -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="184b493a" class="cell" data-execution_count="1">
+<div id="bc9d54c7" 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>

diff --git a/logbook/posts/2024_08_13/index.html b/logbook/posts/2024_08_13/index.html
@@ -161,7 +161,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../../../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../../../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -303,7 +303,7 @@ <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="45d9a8af" class="cell" data-execution_count="1">
+<div id="4fdc9680" 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>
@@ -350,7 +350,7 @@ <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="b2253469" class="cell" data-execution_count="2">
+<div id="ebcea995" 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>

diff --git a/original_study/charm/CHARM_INFO.html b/original_study/charm/CHARM_INFO.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/original_study/charm/CONTRIBUTING.html b/original_study/charm/CONTRIBUTING.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/quarto_site/license.html b/quarto_site/license.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>

diff --git a/quarto_site/reproduction_readme.html b/quarto_site/reproduction_readme.html
@@ -105,7 +105,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>
@@ -243,6 +243,7 @@ <h3 class="anchored" data-anchor-id="step-2.-running-the-model">Step 2. Running
 <section id="reproduction-specs-and-runtime" class="level2">
 <h2 class="anchored" data-anchor-id="reproduction-specs-and-runtime">Reproduction specs and runtime</h2>
 <p>TBC</p>
+<p>The run time for <code>reproduction.ipynb</code> or the tests is only a couple of seconds.</p>
 <!-- Hint: On Linux, you can find specs by running the following commands in the terminal:
 cat /etc/os-release  # Shows operating system and version
 lscpu  # Shows computer model

diff --git a/quarto_site/study_publication.html b/quarto_site/study_publication.html
@@ -125,7 +125,7 @@
  <span class="dropdown-text">README</span></a>
   </li>  
         <li>
-    <a class="dropdown-item" href="../reproduction/reproduction.html">
+    <a class="dropdown-item" href="../reproduction/scripts/reproduction.html">
  <span class="dropdown-text">Reproduction</span></a>
   </li>  
     </ul>