Built site for gh-pages

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@@ -1 +1 @@
-4cf01359
+afbefdf0

evaluation/reporting.html

@@ -240,8 +240,8 @@ <h2 class="anchored" data-anchor-id="stress-des">STRESS-DES</h2>
 <p>Of the <strong>24</strong> items in the checklist:</p>
 <ul>
 <li><strong>14</strong> were met fully (✅)</li>
-<li><strong>6</strong> were partially met (🟡)</li>
-<li><strong>3</strong> were not met (❌)</li>
+<li><strong>5</strong> were partially met (🟡)</li>
+<li><strong>4</strong> were not met (❌)</li>
 <li><strong>1</strong> was not applicable (N/A)</li>
 </ul>
 <table class="table">
@@ -413,8 +413,8 @@ <h2 class="anchored" data-anchor-id="stress-des">STRESS-DES</h2>
 <tr class="even">
 <td>5.2 Random sampling</td>
 <td>State the algorithm used to generate random samples in the software/programming language used e.g.&nbsp;Mersenne Twister.<br>If common random numbers are used, state how seeds (or random number streams) are distributed among sampling processes.</td>
-<td>🟡 Partially</td>
-<td>Sampling described for arrivals but not for length of time with resources. Doesn’t mention whether seeds are used.<br><br><code>Methods: Model Properties: Patients</code>: “Patients are generated by a Poissone process with an inter-arrival time as specified in Table 1.”<br><img src="../original_study/tab1.jpg" class="img-fluid" alt="Table 1. DES model inputs"><br><span class="citation" data-cites="huang_optimizing_2019">Huang et al. (<a href="#ref-huang_optimizing_2019" role="doc-biblioref">2019</a>)</span></td>
+<td>❌ Not met</td>
+<td>Doesn’t mention algorithm or whether seeds or streams are used (know from code that it does not though).</td>
 </tr>
 <tr class="odd">
 <td>5.3 Model execution</td>
@@ -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({"loop":false,"closeEffect":"zoom","openEffect":"zoom","selector":".lightbox","descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"descPosition":"bottom","openEffect":"zoom","selector":".lightbox","closeEffect":"zoom","loop":false});
 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({"openEffect":"zoom","selector":".lightbox","closeEffect":"zoom","loop":false,"descPosition":"bottom"});
+<script>var lightboxQuarto = GLightbox({"loop":false,"selector":".lightbox","descPosition":"bottom","closeEffect":"zoom","openEffect":"zoom"});
 window.onload = () => {
   lightboxQuarto.on('slide_before_load', (data) => {
     const { slideIndex, slideNode, slideConfig, player, trigger } = data;

listings.json

@@ -2,6 +2,8 @@
   {
     "listing": "/logbook/logbook.html",
     "items": [
+      "/logbook/posts/2024_11_04/index.html",
+      "/logbook/posts/2024_11_21/index.html",
       "/logbook/posts/2024_10_02/index.html",
       "/logbook/posts/2024_09_03/index.html",
       "/logbook/posts/2024_08_15/index.html",

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="30a68679" class="cell" data-execution_count="1">
+<div id="e8c5be50" 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="57f8c8a8" class="cell" data-execution_count="1">
+<div id="6da6d2dd" 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="31606a8a" class="cell" data-execution_count="1">
+<div id="a4468a81" 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="fd14d6ff" class="cell" data-execution_count="1">
+<div id="98e94722" 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="6e038fe0" class="cell" data-execution_count="2">
+<div id="3c009544" 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="80dead31" class="cell" data-execution_count="1">
+<div id="3ac18b18" 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="c047285c" class="cell" data-execution_count="2">
+<div id="7a2a201d" 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="d51d1846" class="cell" data-execution_count="3">
+<div id="2e7a29c8" 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="df55e5b9" class="cell" data-execution_count="1">
+<div id="13ede0b7" 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

@@ -234,7 +234,7 @@
       <h1 class="title">Day 8</h1>
                                 <div class="quarto-categories">
                 <div class="quarto-category">reproduce</div>
-                <div class="quarto-category">guidelines</div>
+                <div class="quarto-category">evaluation</div>
                 <div class="quarto-category">compendium</div>
               </div>
                   </div>
@@ -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="57cd25f3" class="cell" data-execution_count="1">
+<div id="15c0be67" 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="1e580268" class="cell" data-execution_count="2">
+<div id="be35c8f4" 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

@@ -233,7 +233,7 @@
     <div class="quarto-title column-body">
       <h1 class="title">Day 9</h1>
                                 <div class="quarto-categories">
-                <div class="quarto-category">guidelines</div>
+                <div class="quarto-category">evaluation</div>
                 <div class="quarto-category">compendium</div>
               </div>
                   </div>
@@ -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="1dbd3595" class="cell" data-execution_count="1">
+<div id="412ec882" 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>