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@@ -1 +1 @@
-ab301283
+76a8bf31

evaluation/badges.html

@@ -233,7 +233,7 @@ <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">(5)</span></div><div class="category" data-category="guidelines">guidelines <span class="quarto-category-count">(1)</span></div><div class="category" data-category="read">read <span class="quarto-category-count">(2)</span></div><div class="category" data-category="reproduce">reproduce <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">(6)</span></div><div class="category" data-category="guidelines">guidelines <span class="quarto-category-count">(2)</span></div><div class="category" data-category="read">read <span class="quarto-category-count">(2)</span></div><div class="category" data-category="reproduce">reproduce <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>
 <!-- main -->
 <main class="content quarto-banner-title-block column-page-left" id="quarto-document-content">
 
@@ -248,7 +248,40 @@ <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="guidelines" data-listing-date-sort="1717459200000" data-listing-file-modified-sort="1717517080833" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="7" data-listing-word-count-sort="1367">
+<div class="quarto-post image-right" data-index="0" data-categories="guidelines" data-listing-date-sort="1717545600000" data-listing-file-modified-sort="1717583956371" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="6" data-listing-word-count-sort="1147">
+<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>
+</a><p><a href="../evaluation/posts/2024_06_05/index.html" class="no-external"></a></p>
+</div>
+<div class="body">
+<h3 class="no-anchor listing-title">
+<a href="../evaluation/posts/2024_06_05/index.html" class="no-external">Day 6</a>
+</h3>
+<div class="listing-subtitle">
+<a href="../evaluation/posts/2024_06_05/index.html" class="no-external"></a>
+</div>
+<div class="listing-categories">
+<div class="listing-category" onclick="window.quartoListingCategory('guidelines'); return false;">
+guidelines
+</div>
+</div>
+<div class="listing-description">
+<a href="../evaluation/posts/2024_06_05/index.html" class="no-external">Evaluation against reporting guidelines - finished STRESS-DES, and did for ISPOR-SDM.</a>
+</div>
+</div>
+<div class="metadata">
+<a href="../evaluation/posts/2024_06_05/index.html" class="no-external">
+<div class="listing-date">
+Jun 5, 2024
+</div>
+<div class="listing-author">
+Amy Heather
+</div>
+</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="1717583956371" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="7" data-listing-word-count-sort="1378">
 <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>
@@ -281,7 +314,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="1" data-categories="reproduce" data-listing-date-sort="1717372800000" data-listing-file-modified-sort="1717517080829" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="961">
+<div class="quarto-post image-right" data-index="2" data-categories="reproduce" data-listing-date-sort="1717372800000" data-listing-file-modified-sort="1717583956367" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="5" data-listing-word-count-sort="961">
 <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>
@@ -314,7 +347,7 @@ <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="1716508800000" data-listing-file-modified-sort="1717517080829" 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="1717583956367" 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>
@@ -347,7 +380,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="3" data-categories="read,reproduce" data-listing-date-sort="1716422400000" data-listing-file-modified-sort="1717517080825" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="14" data-listing-word-count-sort="2636">
+<div class="quarto-post image-right" data-index="4" data-categories="read,reproduce" data-listing-date-sort="1716422400000" data-listing-file-modified-sort="1717583956363" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="14" data-listing-word-count-sort="2636">
 <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>
@@ -383,7 +416,7 @@ <h3 class="no-anchor listing-title">
 </a>
 </div>
 </div>
-<div class="quarto-post image-right" data-index="4" data-categories="setup,read,scope" data-listing-date-sort="1716336000000" data-listing-file-modified-sort="1717517080821" 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="1717583956359" data-listing-date-modified-sort="NaN" data-listing-reading-time-sort="9" data-listing-word-count-sort="1786">
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 <p class="card-img-top"><img src="../original_study/article_fig1.png"  class="thumbnail-image card-img"/></p>

evaluation/logbook.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="38bcab96" class="cell" data-execution_count="1">
+<div id="975bf738" 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_22/index.html

@@ -560,7 +560,7 @@ <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="b466043d" class="cell" data-execution_count="1">
+<div id="51836e92" 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_23/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="6ce0f861" class="cell" data-execution_count="1">
+<div id="90722956" 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="336cf355" class="cell" data-execution_count="2">
+<div id="59f32e52" 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="eafbe4f3" class="cell" data-execution_count="3">
+<div id="533a1e8e" 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_05_24/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="c16c5f3c" class="cell" data-execution_count="1">
+<div id="04221382" 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_03/index.html

@@ -298,7 +298,7 @@ <h3 class="anchored" data-anchor-id="sharing-research-artefacts">Sharing researc
 <li>Remote execution/Online coding environment - Zenodo doesn’t but GitLab does. I was largely working with Zenodo as that was the archived version, but in this case, did say met criteria via GitLab. Importance of which code is chosen when there are two versions. I didn’t initially think it met criteria until checked the GitLab too. Have recommended both are referred to. But do they meet criteria if changes are made to repository after publication? After submission? For example, if we asked them to add a license.</li>
 </ul>
 <p>Compared my decisions for the best practice audit against those made in Monks and Harper. Don’t think I would normally plan to do this. Their GitHub is <a href="https://github.com/TomMonks/des_sharing_lit_review">TomMonks/des_sharing_lit_review</a>, which provides the file <code>share_sim_data_extract.zip</code>. I used the provided code to clean this and saved it as <code>share_sim_data_extract_clean.csv</code>, which can then view here:</p>
-<div id="ea7d1975" class="cell" data-execution_count="1">
+<div id="8ac3438b" 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>
@@ -456,7 +456,7 @@ <h2 class="anchored" data-anchor-id="reporting-guidelines">Reporting guidelines<
 <li>Experiementation aims - is it applicable? The DES model, as I understand, just tests one scenario - a worst case scenario - so it’s not really “scenario based analysis” comparing scenarios - but it does have A scenario and justification for it?</li>
 <li>Algorithms - is this applicable in this example? Parameters are just from sampling from distributions, or proportions. Assuming its applicable, and that distribing those distributions answers this question?</li>
 <li>Queues - wasn’t certain about this, as I don’t really know what order they get allocated to units. but that’s not a queue? but it kind of is - in that, at the start of the day, they are waiting to be assigned?</li>
-<li>Entry/exit points - they are in model on days they need dialysis, and then leave again? unless get unallocated? and then they never return if their state turns to dead? this isn’t really spelled out though.</li>
+<li>Entry/exit points - have said not met as can’t find this stated, but also, not sure what the answer is. They are in model on days they need dialysis, and then leave again? unless get unallocated? and then they never return if their state turns to dead?</li>
 </ul>
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