Built site for gh-pages

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-6952149d
+28590848

evaluation/badges.html

@@ -260,7 +260,7 @@ <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="491adcfb" class="cell" data-execution_count="1">
+<div id="2de915d8" 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>
@@ -393,7 +393,7 @@ <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="c4b28bbc" class="cell" data-execution_count="2">
+<div id="8ca3d216" 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/scope.html

@@ -891,7 +891,7 @@ <h2 class="anchored" data-anchor-id="outside-scope">Outside scope</h2>
     </div>
   </div>
 </footer>
-<script>var lightboxQuarto = GLightbox({"selector":".lightbox","loop":false,"descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom"});
+<script>var lightboxQuarto = GLightbox({"selector":".lightbox","openEffect":"zoom","loop":false,"descPosition":"bottom","closeEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

logbook/logbook.html

@@ -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="reproduce" data-listing-date-sort="1720738800000" data-listing-file-modified-sort="1720774057352" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="202">
+<div class="quarto-post image-right" data-index="0" data-categories="reproduce" data-listing-date-sort="1720738800000" data-listing-file-modified-sort="1720776880344" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="2" data-listing-word-count-sort="230">
 <div class="thumbnail">
 <p><a href="../logbook/posts/2024_07_12/index.html" class="no-external"></a></p><a href="../logbook/posts/2024_07_12/index.html" class="no-external">
 <p class="card-img-top"><img src="posts/2024_07_12/supplementary_figure.png"  class="thumbnail-image card-img"/></p>

logbook/posts/2024_07_03/index.html

@@ -302,7 +302,7 @@ <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="7305d77b" class="cell" data-execution_count="1">
+<div id="e78c3243" 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

@@ -545,7 +545,7 @@ <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="44453594" class="cell" data-execution_count="1">
+<div id="b9cbfa2e" 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

@@ -621,7 +621,7 @@ <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="beddc5e2" class="cell" data-execution_count="1">
+<div id="fde93d2c" 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

@@ -378,7 +378,7 @@ <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="e55e855e" class="cell" data-execution_count="1">
+<div id="2f107553" 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>
@@ -614,7 +614,7 @@ <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="5e1d31c8" class="cell" data-execution_count="2">
+<div id="f68eb1b9" 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

@@ -404,7 +404,7 @@ <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="053e87b1" class="cell" data-execution_count="1">
+<div id="81d5c1df" 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>
@@ -495,7 +495,7 @@ <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="2a8ed071" class="cell" data-execution_count="2">
+<div id="562c070f" 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>
@@ -551,7 +551,7 @@ <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="8feac8ec" class="cell" data-execution_count="3">
+<div id="c5dbe17e" 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

@@ -394,7 +394,7 @@ <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="42d85402" class="cell" data-execution_count="1">
+<div id="7e23cc24" 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

@@ -260,6 +260,7 @@ <h2 id="toc-title">On this page</h2>
 
   <ul>
   <li><a href="#working-on-the-supplementary-figure" id="toc-working-on-the-supplementary-figure" class="nav-link active" data-scroll-target="#working-on-the-supplementary-figure">09.00-09.07, 09.14-09.24, 09.36-09.40: Working on the supplementary figure</a></li>
+  <li><a href="#untimed-consensus-on-reproduction-success" id="toc-untimed-consensus-on-reproduction-success" class="nav-link" data-scroll-target="#untimed-consensus-on-reproduction-success">Untimed: Consensus on reproduction success</a></li>
   <li><a href="#timings" id="toc-timings" class="nav-link" data-scroll-target="#timings">Timings</a></li>
   </ul>
 <div class="toc-actions"><ul><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-huang-2019/edit/main/logbook/posts/2024_07_12/index.qmd" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-huang-2019/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
@@ -299,9 +300,13 @@ <h2 class="anchored" data-anchor-id="working-on-the-supplementary-figure">09.00-
 </div>
 <p>I then realised I was mistaken, and that perhaps I should have interpreted this as being double and triple the <code>ecr_pt</code> (which is used when model decides whether patient needs ECR: <code>PROB_ECR = ecr_pt / ais_pt</code>). This looked right, and very similar to the paper, with the exception that my angioINR wait times curves peak much lower.</p>
 </section>
+<section id="untimed-consensus-on-reproduction-success" class="level2">
+<h2 class="anchored" data-anchor-id="untimed-consensus-on-reproduction-success">Untimed: Consensus on reproduction success</h2>
+<p>Shared with Tom and Alison. Tom and Alison both agreed with decisions (reproduced Figure 5 and in-text 1 and 2, and not other items).</p>
+</section>
 <section id="timings" class="level2">
 <h2 class="anchored" data-anchor-id="timings">Timings</h2>
-<div id="cd0d5311" class="cell" data-execution_count="1">
+<div id="fdf2115a" 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>