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.nojekyll

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CHANGELOG.html

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<h2 id="toc-title">On this page</h2>
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<ul>
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<li><a href="#changelog" id="toc-changelog" class="nav-link active" data-scroll-target="#changelog">Changelog</a></li>
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<li><a href="#changelog" id="toc-changelog" class="nav-link active" data-scroll-target="#changelog">Changelog</a>
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<ul class="collapse">
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<li><a href="#v0.2.0" id="toc-v0.2.0" class="nav-link" data-scroll-target="#v0.2.0">v0.2.0</a>
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<li><a href="#added" id="toc-added" class="nav-link" data-scroll-target="#added">Added</a></li>
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</ul></li>
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<li><a href="#v0.1.0" id="toc-v0.1.0" class="nav-link" data-scroll-target="#v0.1.0">v0.1.0</a>
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<div class="toc-actions"><ul><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/edit/main/CHANGELOG.md" class="toc-action"><i class="bi bi-github"></i>Edit this page</a></li><li><a href="https://github.com/pythonhealthdatascience/stars-reproduce-allen-2020/issues/new" class="toc-action"><i class="bi empty"></i>Report an issue</a></li></ul></div></nav>
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<h1>Changelog</h1>
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<p>All notable changes to this project will be documented in this file.</p>
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<p>The format is based on <a href="https://keepachangelog.com/en/1.1.0/">Keep a Changelog</a>, and this project adheres to <a href="https://semver.org/spec/v2.0.0.html">Semantic Versioning</a>. Dates formatted as YYYY-MM-DD as per <a href="https://www.iso.org/iso-8601-date-and-time-format.html">ISO standard</a>.</p>
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<h2 class="anchored" data-anchor-id="v0.2.0">v0.2.0</h2>
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<p><strong>Release date:</strong> 3rd June 2024</p>
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<p><strong>Contributors:</strong> Amy Heather</p>
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<p>Completed work on reproducing items from the agreed scope.</p>
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<section id="added" class="level3">
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<h3 class="anchored" data-anchor-id="added">Added</h3>
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<ul>
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<li>Attempted reproduction of items from the original study.</li>
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</ul>
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</section>
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<section id="v0.1.0" class="level2">
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<h2 class="anchored" data-anchor-id="v0.1.0">v0.1.0</h2>
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<p><strong>Release date:</strong> 22nd May 2024</p>
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<p><strong>Contributors:</strong> Amy Heather</p>
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<p>Defined scope for the reproducibility assessment.</p>
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<h3 class="anchored" data-anchor-id="added-1">Added</h3>
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<ul>
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<li>Basic repository which includes a page defining the agreed scope for the reproducibility assessment.</li>
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</ul>
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</main> <!-- /main -->

evaluation/badges.html

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<p>This page evaluates the extent to which the author-published research artefacts meet the criteria of badges related to reproducibility from various organisations and journals.</p>
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<summary>Code</summary>
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<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>
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<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

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<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

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<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>
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evaluation/posts/2024_05_23/index.html

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evaluation/posts/2024_05_24/index.html

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<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>
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<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>
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<p>If timed, 13.33-13.57.</p>
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<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>
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<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>
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<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>
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evaluation/posts/2024_06_03/index.html

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evaluation/posts/2024_06_04/index.html

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<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>
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<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>
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evaluation/reporting.html

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search.json

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"text": "All notable changes to this project will be documented in this file.\nThe format is based on Keep a Changelog, and this project adheres to Semantic Versioning. Dates formatted as YYYY-MM-DD as per ISO standard.\n\n\nRelease date: 3rd June 2024\nContributors: Amy Heather\nCompleted work on reproducing items from the agreed scope.\n\n\n\nAttempted reproduction of items from the original study.\n\n\n\n\n\nRelease date: 22nd May 2024\nContributors: Amy Heather\nDefined scope for the reproducibility assessment.\n\n\n\nBasic repository which includes a page defining the agreed scope for the reproducibility assessment."
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"text": "Release date: 22nd May 2024\nContributors: Amy Heather\nDefined scope for the reproducibility assessment.\n\n\n\nBasic repository which includes a page defining the agreed scope for the reproducibility assessment."
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