Built site for gh-pages

Author: Quarto GHA Workflow Runner

.nojekyll

@@ -1 +1 @@
-8b4e12e5
+863b43c4

evaluation/badges.html

@@ -246,7 +246,7 @@ <h1 class="title">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="014c22ab" class="cell" data-execution_count="1">
+<div id="f259227c" 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>
@@ -378,7 +378,7 @@ <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="340ffed1" class="cell" data-execution_count="2">
+<div id="15119721" 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/logbook.html

@@ -242,13 +242,14 @@ <h5 class="quarto-listing-category-title">Categories</h5><div class="quarto-list
 
 
 <p>These diary entries record daily progress in reproduction of the study, providing a transparent and detailed record of work.</p>
+<p><a href="https://github.com/amyheather/brokenlinktest">Broken link test</a></p>
 
 
 
 
 <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="guidelines" data-listing-date-sort="1717545600000" data-listing-file-modified-sort="1717753540399" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="8" data-listing-word-count-sort="1439">
+<div class="quarto-post image-right" data-index="0" data-categories="guidelines" data-listing-date-sort="1717545600000" data-listing-file-modified-sort="1717753776938" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="8" data-listing-word-count-sort="1439">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_06_05/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_06_05/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -281,7 +282,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="guidelines" data-listing-date-sort="1717459200000" data-listing-file-modified-sort="1717753540399" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="4" data-listing-word-count-sort="696">
+<div class="quarto-post image-right" data-index="1" data-categories="guidelines" data-listing-date-sort="1717459200000" data-listing-file-modified-sort="1717753776938" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="4" data-listing-word-count-sort="696">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_06_04/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_06_04/index.html" class="no-external">
 <div class="listing-item-img-placeholder card-img-top" >&nbsp;</div>
@@ -314,7 +315,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="2" data-categories="reproduce" data-listing-date-sort="1717372800000" data-listing-file-modified-sort="1717753540395" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="879">
+<div class="quarto-post image-right" data-index="2" data-categories="reproduce" data-listing-date-sort="1717372800000" data-listing-file-modified-sort="1717753776938" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="879">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_06_03/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_06_03/index.html" class="no-external">
 <p class="card-img-top"><img src="../original_study/article_fig2.png"  class="thumbnail-image card-img"/></p>
@@ -347,7 +348,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="3" data-categories="reproduce" data-listing-date-sort="1716508800000" data-listing-file-modified-sort="1717753540395" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="458">
+<div class="quarto-post image-right" data-index="3" data-categories="reproduce" data-listing-date-sort="1716508800000" data-listing-file-modified-sort="1717753776934" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="3" data-listing-word-count-sort="458">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_05_24/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_05_24/index.html" class="no-external">
 <p class="card-img-top"><img src="posts/2024_05_24/figure_1a.png"  class="thumbnail-image card-img"/></p>
@@ -380,7 +381,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="4" data-categories="read,reproduce" data-listing-date-sort="1716422400000" data-listing-file-modified-sort="1717753540391" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="13" data-listing-word-count-sort="2543">
+<div class="quarto-post image-right" data-index="4" data-categories="read,reproduce" data-listing-date-sort="1716422400000" data-listing-file-modified-sort="1717753776934" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="13" data-listing-word-count-sort="2543">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_05_23/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_05_23/index.html" class="no-external">
 <p class="card-img-top"><img src="../original_study/article_fig4.png"  class="thumbnail-image card-img"/></p>
@@ -416,7 +417,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="5" data-categories="setup,read,scope" data-listing-date-sort="1716336000000" data-listing-file-modified-sort="1717753540387" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="9" data-listing-word-count-sort="1786">
+<div class="quarto-post image-right" data-index="5" data-categories="setup,read,scope" data-listing-date-sort="1716336000000" data-listing-file-modified-sort="1717753776930" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="9" data-listing-word-count-sort="1786">
 <div class="thumbnail">
 <p><a href="../evaluation/posts/2024_05_22/index.html" class="no-external"></a></p><a href="../evaluation/posts/2024_05_22/index.html" class="no-external">
 <p class="card-img-top"><img src="../original_study/article_fig1.png"  class="thumbnail-image card-img"/></p>

evaluation/posts/2024_05_22/index.html

@@ -475,7 +475,7 @@ <h3 class="anchored" data-anchor-id="untimed-uploading-to-zenodo">Untimed: Uploa
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="c0b57e04" class="cell" data-execution_count="1">
+<div id="a14574d0" 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>

evaluation/posts/2024_05_23/index.html

@@ -547,7 +547,7 @@ <h3 class="anchored" data-anchor-id="reproduction-2">15.23-16.35 Reproduction</h
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="ae7b6236" class="cell" data-execution_count="1">
+<div id="c2fdcdcb" class="cell" data-execution_count="1">
 <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><span class="im">import</span> sys</span>
 <span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>sys.path.append(<span class="st">'../'</span>)</span>
 <span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a><span class="im">from</span> timings <span class="im">import</span> calculate_times</span>

evaluation/posts/2024_05_24/index.html

@@ -290,7 +290,7 @@ <h3 class="anchored" data-anchor-id="untimed-exploring-methods-for-overlaying-fi
 <p>Exploring methods for overlaying figures. Not timed as not about reproduction of this study, but about how we are going to do this each time when reproducing.</p>
 <p>Decided that it’s not helpful to do this - spend more time fiddling around with getting them to resize and overlay correctly - and that the simplest option here would be to compare by eye.</p>
 <p>If timed, 13.33-13.57.</p>
-<div id="c49fe371" class="cell" data-execution_count="1">
+<div id="1bac9507" 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> cv2</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a><span class="im">import</span> matplotlib.pyplot <span class="im">as</span> plt</span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a></span>
@@ -312,7 +312,7 @@ <h3 class="anchored" data-anchor-id="untimed-exploring-methods-for-overlaying-fi
 </div>
 </div>
 </div>
-<div id="14751c25" class="cell" data-execution_count="2">
+<div id="63a6ace4" class="cell" data-execution_count="2">
 <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"># Overlay transparently</span></span>
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>combined <span class="op">=</span> cv2.addWeighted(original,<span class="fl">0.4</span>,overlay_resize,<span class="fl">0.1</span>,<span class="dv">0</span>)</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a></span>
@@ -332,7 +332,7 @@ <h3 class="anchored" data-anchor-id="untimed-exploring-methods-for-overlaying-fi
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="e3e59fd0" class="cell" data-execution_count="3">
+<div id="045427fc" class="cell" data-execution_count="3">
 <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>

evaluation/posts/2024_06_03/index.html

@@ -386,7 +386,7 @@ <h3 class="anchored" data-anchor-id="tidying-the-notebook-and-creating-reproduct
 </section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="87f513d6" class="cell" data-execution_count="1">
+<div id="d874f284" 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>

evaluation/posts/2024_06_05/index.html

@@ -387,7 +387,7 @@ <h3 class="anchored" data-anchor-id="comparison-of-my-stress-des-against-the-ori
 <h3 class="anchored" data-anchor-id="comparing-best-practice-audit-results-with-monks-and-harper">Comparing best practice audit results with Monks and Harper</h3>
 <p>Compared my decisions for the best practice audit against those made in Monks and Harper.</p>
 <p>Their GitHub is <a href="https://github.com/TomMonks/des_sharing_lit_review">TomMonks/des_sharing_lit_review</a>, which provides the file <code>bp_audit.zip</code>. I used the provided code to clean this and saved it as <code>bp_audit_clean.csv</code>, which can then view here:</p>
-<div id="50a08803" class="cell" data-execution_count="1">
+<div id="d30bceb9" 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> pandas <span class="im">as</span> pd</span>
 <span id="cb1-2"><a href="#cb1-2" aria-hidden="true" tabindex="-1"></a></span>
 <span id="cb1-3"><a href="#cb1-3" aria-hidden="true" tabindex="-1"></a><span class="co"># Import review results</span></span>

evaluation/reporting.html

@@ -1191,7 +1191,7 @@ <h2 class="anchored" data-anchor-id="des-checklist-derived-from-ispor-sdm">DES c
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"closeEffect":"zoom","openEffect":"zoom","loop":false,"selector":".lightbox","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","closeEffect":"zoom","loop":false,"selector":".lightbox"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

search.json

@@ -25,7 +25,7 @@
     "href": "evaluation/logbook.html",
     "title": "Logbook",
     "section": "",
-    "text": "These diary entries record daily progress in reproduction of the study, providing a transparent and detailed record of work.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDay 6\n\n\n\n\n\n\nguidelines\n\n\n\n\n\n\n\n\n\nJun 5, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 5\n\n\n\n\n\n\nguidelines\n\n\n\n\n\n\n\n\n\nJun 4, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 4\n\n\n\n\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nJun 3, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 3\n\n\n\n\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nMay 24, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 2\n\n\n\n\n\n\nread\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nMay 23, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 1\n\n\n\n\n\n\nsetup\n\n\nread\n\n\nscope\n\n\n\n\n\n\n\n\n\nMay 22, 2024\n\n\nAmy Heather\n\n\n\n\n\n\nNo matching items"
+    "text": "These diary entries record daily progress in reproduction of the study, providing a transparent and detailed record of work.\nBroken link test\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nDay 6\n\n\n\n\n\n\nguidelines\n\n\n\n\n\n\n\n\n\nJun 5, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 5\n\n\n\n\n\n\nguidelines\n\n\n\n\n\n\n\n\n\nJun 4, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 4\n\n\n\n\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nJun 3, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 3\n\n\n\n\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nMay 24, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 2\n\n\n\n\n\n\nread\n\n\nreproduce\n\n\n\n\n\n\n\n\n\nMay 23, 2024\n\n\nAmy Heather\n\n\n\n\n\n\n\n\n\n\n\n\nDay 1\n\n\n\n\n\n\nsetup\n\n\nread\n\n\nscope\n\n\n\n\n\n\n\n\n\nMay 22, 2024\n\n\nAmy Heather\n\n\n\n\n\n\nNo matching items"
   },
   {
     "objectID": "evaluation/posts/2024_06_03/index.html",