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2 changes: 1 addition & 1 deletion .nojekyll
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/imputation /posts/2023-09-26_date_functions_and_imputation
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4 changes: 2 additions & 2 deletions posts/2023-06-27__hackathon_app/index.html
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<li><p>Run participants R-scripts on the cloud and compare the produced file to a solution file. Let participants autonomously get feedback on their work.</p></li>
</ol>
<p>In this blog post I want to highlight some of the thoughts that went into this application. Please keep in mind that this work was done under tight time restraints.</p>
<p>The <a href="https://zxqguo-stefan0pascal-thoma.shinyapps.io/data_upload/?_ga=2.75919894.2036952320.1679990144-1584712930.1674550185">hackathon application</a> is still online (although data-upload is switched off) and the <a href="https://github.com/StefanThoma/hackathon_app">GitHub repository</a> is publicly available. The application is embedded into this post right after this paragraph. I have also uploaded to GitHub a <code>.zip</code> file of the workspace to which hackathon participants had access via <a href="https://posit.cloud">posit cloud</a>. For more context you can watch <a href="https://www.cdisc.org/events/webinar/admiral-hackathon-kickoff">recordings of the hackathon-meetings</a>.</p>
<p>The <a href="https://zxqguo-stefan0pascal-thoma.shinyapps.io/data_upload/?_ga=2.75919894.2036952320.1679990144-1584712930.1674550185">hackathon application</a> is still online (although data-upload is switched off) and the <a href="https://github.com/StefanThoma/hackathon_app">GitHub repository</a> is publicly available. The application is embedded into this post right after this paragraph. I have also uploaded to GitHub a <code>.zip</code> file of the workspace to which hackathon participants had access via <a href="https://posit.cloud">posit cloud</a>. For more context you can watch <a href="https://www.cdisc.org/cosa">recordings of the hackathon-meetings</a>.</p>
<div class="cell">
<iframe src="https://zxqguo-stefan0pascal-thoma.shinyapps.io/data_upload/?_ga=2.75919894.2036952320.1679990144-1584712930.1674550185" width="672" height="400px" data-external="1">
</iframe>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:42.927745</p>
<p>2023-11-27 19:13:48.333469</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-06-19_shiny_run_script/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-06-19_shiny_run_script/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:33.340574</p>
<p>2023-11-27 19:13:38.746856</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/admiral/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/admiral/renv.lock">R environment</a></p>
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6 changes: 3 additions & 3 deletions posts/2023-06-27_hackathon_writeup/index.html
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<!--------------- my typical setup ----------------->
<!--------------- post begins here ----------------->
<p>This January and February (2023), the <code>admiral</code> development team and the CDISC Open Source Alliance jointly hosted the admiral hackathon. The idea was to build a community of <code>admiral</code> users, and help participants familiarize themselves with R and <code>admiral</code>. This whole effort was led by <a href="https://www.linkedin.com/in/thomasneitmann/">Thomas Neitmann</a> and was supported by <a href="https://www.linkedin.com/in/zelos-zhu-7969a1103/">Zelos Zhu</a>, <a href="https://www.linkedin.com/in/sadchla-mascary/">Sadchla Mascary</a>, and me – <a href="https://www.linkedin.com/in/stefan-thoma-77537bb5/">Stefan Thoma</a>.</p>
<p>The hackathon event was structured in two parts. First, we offered an <em>Introduction to R</em> for SAS programmers, a three hour workshop for R beginners to get them up to speed. Here we covered practical R basics, talking about how the R-workflow differs from a SAS workflow, and discussed common R functions - mostly from the tidyverse. This ensured that hackathon participants were familiar with core R concepts. The <a href="https://www.cdisc.org/events/webinar/pre-admiral-hackathon-workshop-introduction-r-sas-programmers">workshop recording</a> and the <a href="https://pharmaverse.github.io/intro-to-r-for-sas-programmers-workshop/">course materials</a> are available online.</p>
<p>The hackathon event was structured in two parts. First, we offered an <em>Introduction to R</em> for SAS programmers, a three hour workshop for R beginners to get them up to speed. Here we covered practical R basics, talking about how the R-workflow differs from a SAS workflow, and discussed common R functions - mostly from the tidyverse. This ensured that hackathon participants were familiar with core R concepts. The <a href="https://www.cdisc.org/cosa">workshop recording</a> and the <a href="https://pharmaverse.github.io/intro-to-r-for-sas-programmers-workshop/">course materials</a> are available online.</p>
<p>The main hackathon consisted of several ADAM data generating tasks based on a specs file and synthetic data. Participants were able to solve these tasks in groups at their own pace thanks to a online tool where participants could upload their task specific R scripts and they would get automatic feedback for the data-set produced by their script. Script upload through <a href="https://zxqguo-stefan0pascal-thoma.shinyapps.io/data_upload/">the feedback application</a> was available all through February, and we offered three additional online meetings throughout the month to discuss challenges and give some tips. If you are interested in learning more about the thoughts that went into the feedback application, you can read about it in <a href="https://pharmaverse.github.io/blog/posts/2023-06-27_hackathon_app/">this blogpost</a> or check out my <a href="https://github.com/StefanThoma/hackathon_app">public GitHub repository for such an application</a>.</p>
<section id="introduction-to-r-workshop" class="level2">
<h2 class="anchored" data-anchor-id="introduction-to-r-workshop"><em>Introduction to R</em> workshop</h2>
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<li><code>AZ_WAWA</code></li>
</ul>
<p>Although this was uncertain during the hackathon we were excited to provide a Certificate of Completion to all participants who uploaded a script to the Web Application.</p>
<p>A recording of the hackathon readout can be found in the <a href="https://www.cdisc.org/events/webinar/cosa-quarterly-spotlight-q1-2023">CDISC Open Source Alliance Quarterly Spotlight</a>.</p>
<p>A recording of the hackathon readout can be found in the <a href="https://www.cdisc.org/cosa">CDISC Open Source Alliance Quarterly Spotlight</a>.</p>
</section>
<section id="conclusion" class="level2">
<h2 class="anchored" data-anchor-id="conclusion">Conclusion</h2>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:51.728905</p>
<p>2023-11-27 19:13:36.963431</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-06-19_shiny_run_script/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-06-19_shiny_run_script/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:37.128939</p>
<p>2023-11-27 19:13:52.942147</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-01-09_welcome/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-01-09_welcome/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:38.469514</p>
<p>2023-11-27 19:13:40.019302</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-09_falcon/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-09_falcon/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:27.839956</p>
<p>2023-11-27 19:13:51.677601</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-10_blanks_and_nas/blanks_and_na.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-10_blanks_and_nas/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:53.276819</p>
<p>2023-11-27 19:13:41.390513</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-14_code_sections/code_sections.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-14_code_sections/renv.lock">R environment</a></p>
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</section>
<section id="development-workflow" class="level2">
<h2 class="anchored" data-anchor-id="development-workflow">Development workflow</h2>
<p>Every improvement, task, or feature we want to implement on <a href="https://github.com/pharmaverse/admiral">{admiral}</a> starts as an issue on our <a href="https://github.com/pharmaverse/admiral">GitHub repository</a>. It is the centerpiece of our development workflow, along with our <a href="https://pharmaverse.github.io/admiraldev/devel/articles/development_process.html">developer guides</a> which describe in detail the strategies, conventions, and workflows used in development. The guides help us keep the <a href="https://github.com/pharmaverse/admiral">{admiral}</a> package internally consistent (e.g.&nbsp;naming conventions, function logic) but also ensure that <a href="https://github.com/pharmaverse/admiral">{admiral}</a> adjacent packages follow the same conventions and share the user interface. This is further helped by the implemented CICD pipeline which ensures styling convention and spelling (and much more).</p>
<p>Every improvement, task, or feature we want to implement on <a href="https://github.com/pharmaverse/admiral">{admiral}</a> starts as an issue on our <a href="https://github.com/pharmaverse/admiral">GitHub repository</a>. It is the centerpiece of our development workflow, along with our <a href="https://pharmaverse.github.io/admiraldev/articles/programming_strategy.html">developer guides</a> which describe in detail the strategies, conventions, and workflows used in development. The guides help us keep the <a href="https://github.com/pharmaverse/admiral">{admiral}</a> package internally consistent (e.g.&nbsp;naming conventions, function logic) but also ensure that <a href="https://github.com/pharmaverse/admiral">{admiral}</a> adjacent packages follow the same conventions and share the user interface. This is further helped by the implemented CICD pipeline which ensures styling convention and spelling (and much more).</p>
<p>The core package developers team meets once a week (twice a week before a release) to discuss progress and priorities. Here, the role of product lead (currently <a href="https://www.linkedin.com/in/edoardo-mancini-7a4a40148/">Edoardo Mancini</a> at Roche) and technical lead (currently <a href="https://www.linkedin.com/in/ben-straub/">Ben Straub</a> at GSK) is to set priorities and track the release schedule. These stand-up meetings are centered around the <a href="https://github.com/orgs/pharmaverse/projects/12">project-board</a> which gives a complete overview of activities and progress. Issues are mostly self-assigned so developers can really chose what they want to work on.</p>
<div class="quarto-figure quarto-figure-center">
<figure class="figure">
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:29.564969</p>
<p>2023-11-27 19:13:33.556149</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-24_rounding/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-07-24_rounding/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:45.242711</p>
<p>2023-11-27 19:13:57.651626</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-08_study_day/code_sections.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-08_study_day/renv.lock">R environment</a></p>
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<p>2023-11-01 15:47:31.231853</p>
<p>2023-11-27 19:13:54.254558</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-14_rhino_submission_2/blanks_and_na.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-14_rhino_submission_2/renv.lock">R environment</a></p>
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<div id="quarto-appendix" class="default"><section id="last-updated" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Last updated</h2><div class="quarto-appendix-contents">

<p>2023-11-01 15:47:48.201548</p>
<p>2023-11-27 19:13:49.940918</p>
</div></section><section id="details" class="level2 appendix"><h2 class="anchored quarto-appendix-heading">Details</h2><div class="quarto-appendix-contents">

<p><a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-30_pharmaverse_story/index.qmd">source code</a>, <a href="https://github.com/pharmaverse/blog/tree/main/posts/2023-08-30_pharmaverse_story/renv.lock">R environment</a></p>
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