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@@ -13,6 +13,7 @@
 /story /posts/2023-10-10_pharmaverse_story
 /point /posts/2023-10-30_floating_point
 /order /posts/2023-11-27_higher_order
+/up... /posts/2023-12-21_end_of__year__up...
 /category/r /#category=R
 /category/shiny /#category=shiny
 /category/community /#category=community

listings.json

@@ -2,6 +2,7 @@
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+      "/posts/2023-12-21_end_of__year__up.../end_of__year__update_from_the__pharmaverse__council.html",
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@@ -14,9 +15,9 @@
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       "/posts/2023-07-09_falcon/falcon.html",
       "/posts/2023-06-28_welcome/index.html",
+      "/posts/2023-06-27__hackathon_app/index.html",
       "/posts/2023-06-27_hackathon_writeup/index.html",
-      "/posts/2023-06-27_admiral/valuelevel/derive_param_computed.html",
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+      "/posts/2023-06-27_admiral/valuelevel/derive_param_computed.html"
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posts/2023-06-27__hackathon_app/index.html

@@ -215,12 +215,12 @@ <h2 id="toc-title">Table of contents</h2>
 
 <!--------------- my typical setup ----------------->
 <!--------------- post begins here ----------------->
-<p>We recently created a shiny application for the <a href="https://cosa.cdisc.org/events/Admiral"><code>admiral</code> hackathon</a> in February 2023. The <a href="https://cosa.cdisc.org/events/Admiral"><code>admiral</code> hackathon</a> was an event designed to make statistical programmers from the pharmaceutical industry more comfortable with the <a href="https://pharmaverse.github.io/admiral/cran-release/"><code>admiral</code></a> R package which allows users to efficiently transform data from one data standard (SDTM) to another (ADaM).</p>
+<p>We recently created a shiny application for the <a href="https://cosa.cdisc.org/events/Admiral"><code>admiral</code> hackathon</a> in February 2023. The <a href="https://cosa.cdisc.org/events/Admiral"><code>admiral</code> hackathon</a> was an event designed to make statistical programmers from the pharmaceutical industry more comfortable with the <a href="https://pharmaverse.github.io/admiral/"><code>admiral</code></a> R package which allows users to efficiently transform data from one data standard (SDTM) to another (ADaM).</p>
 <p>Hackathon participants formed groups of up to five people and were then tasked to create R-scripts that map the SDTM data to ADaM according to specifics defined in the metadata.</p>
 <p>The purpose of the shiny app was threefold:</p>
 <ol type="1">
 <li><p>Allow participants to easily register as a team.</p></li>
-<li><p>Let participants upload their R-scripts, so that the <a href="https://github.com/pharmaverse/admiral/graphs/contributors"><code>admiral</code> team</a> can see how the <a href="https://pharmaverse.github.io/admiral/cran-release/"><code>admiral</code></a> package is being used – and how the functions and the documentation could be improved.</p></li>
+<li><p>Let participants upload their R-scripts, so that the <a href="https://github.com/pharmaverse/admiral/graphs/contributors"><code>admiral</code> team</a> can see how the <a href="https://pharmaverse.github.io/admiral/"><code>admiral</code></a> package is being used – and how the functions and the documentation could be improved.</p></li>
 <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>
@@ -521,7 +521,7 @@ <h2 class="anchored" data-anchor-id="conclusion">Conclusion</h2>
 
 <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>2023-11-27 19:13:48.333469</p>
+<p>2024-01-04 14:09:38.214715</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>

posts/2023-06-27_admiral/valuelevel/derive_param_computed.html

@@ -212,7 +212,7 @@ <h2 id="toc-title">Table of contents</h2>
 <section id="introduction" class="level2">
 <h2 class="anchored" data-anchor-id="introduction">Introduction</h2>
 <p>When creating ADaM Basic Data Structure (BDS) datasets, we often encounter deriving a new parameter based on the analysis values (e.g., AVAL) of other parameters.</p>
-<p>The <a href="https://pharmaverse.github.io/admiral/cran-release/"><code>admiral</code></a> function <a href="https://pharmaverse.github.io/admiral/cran-release/reference/derive_param_computed.html"><code>derive_param_computed()</code></a> adds a parameter computed from the analysis value of other parameters.</p>
+<p>The <a href="https://pharmaverse.github.io/admiral/"><code>admiral</code></a> function <a href="https://pharmaverse.github.io/admiral/reference/derive_param_computed.html"><code>derive_param_computed()</code></a> adds a parameter computed from the analysis value of other parameters.</p>
 <p>It works like a calculator to derive new records without worrying about merging and combining datasets, all you need is a derivation formula, which also improves the readability of the code.</p>
 </section>
 <section id="example" class="level2">
@@ -248,17 +248,12 @@ <h3 class="anchored" data-anchor-id="derive-new-parameter">Derive New Parameter<
 <span id="cb2-2"><a href="#cb2-2" aria-hidden="true" tabindex="-1"></a>  adex,</span>
 <span id="cb2-3"><a href="#cb2-3" aria-hidden="true" tabindex="-1"></a>  <span class="at">by_vars =</span> <span class="fu">exprs</span>(USUBJID),</span>
 <span id="cb2-4"><a href="#cb2-4" aria-hidden="true" tabindex="-1"></a>  <span class="at">parameters =</span> <span class="fu">c</span>(<span class="st">"TOTDOSE"</span>, <span class="st">"NUMCYC"</span>),</span>
-<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">analysis_value =</span> AVAL.TOTDOSE <span class="sc">/</span> AVAL.NUMCYC,</span>
-<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>  <span class="at">set_values_to =</span> <span class="fu">exprs</span>(</span>
-<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>    <span class="at">PARAMCD =</span> <span class="st">"ADPCYMG"</span>,</span>
-<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>    <span class="at">PARAM =</span> <span class="st">"Actual Dose per Cycle (mg)"</span></span>
+<span id="cb2-5"><a href="#cb2-5" aria-hidden="true" tabindex="-1"></a>  <span class="at">set_values_to =</span> <span class="fu">exprs</span>(</span>
+<span id="cb2-6"><a href="#cb2-6" aria-hidden="true" tabindex="-1"></a>    <span class="at">PARAMCD =</span> <span class="st">"ADPCYMG"</span>,</span>
+<span id="cb2-7"><a href="#cb2-7" aria-hidden="true" tabindex="-1"></a>    <span class="at">PARAM =</span> <span class="st">"Actual Dose per Cycle (mg)"</span>,</span>
+<span id="cb2-8"><a href="#cb2-8" aria-hidden="true" tabindex="-1"></a>    <span class="at">AVAL =</span> AVAL.TOTDOSE <span class="sc">/</span> AVAL.NUMCYC</span>
 <span id="cb2-9"><a href="#cb2-9" aria-hidden="true" tabindex="-1"></a>  )</span>
 <span id="cb2-10"><a href="#cb2-10" aria-hidden="true" tabindex="-1"></a>)</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
-<div class="cell-output cell-output-stderr">
-<pre><code>Warning: The `analysis_value` argument of `derive_param_computed()` is deprecated as
-of admiral 0.12.0.
-ℹ Please use the `set_values_to` argument instead.</code></pre>
-</div>
 </div>
 <div class="cell">
 <div class="cell-output cell-output-stdout">
@@ -275,15 +270,15 @@ <h3 class="anchored" data-anchor-id="derive-new-parameter">Derive New Parameter<
 <h3 class="anchored" data-anchor-id="compare">Compare</h3>
 <p>For validation purpose, the <a href="https://gowerc.github.io/diffdf/reference/diffdf.html">diffdf</a> package is used below to mimic SAS <code>proc compare</code>.</p>
 <div class="cell">
-<div class="sourceCode cell-code" id="cb5"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb5-1"><a href="#cb5-1" aria-hidden="true" tabindex="-1"></a>adex_expected <span class="ot">&lt;-</span> <span class="fu">bind_rows</span>(</span>
-<span id="cb5-2"><a href="#cb5-2" aria-hidden="true" tabindex="-1"></a>  adex,</span>
-<span id="cb5-3"><a href="#cb5-3" aria-hidden="true" tabindex="-1"></a>  <span class="fu">tribble</span>(</span>
-<span id="cb5-4"><a href="#cb5-4" aria-hidden="true" tabindex="-1"></a>    <span class="sc">~</span>USUBJID,  <span class="sc">~</span>PARAMCD,  <span class="sc">~</span>PARAM,                       <span class="sc">~</span>AVAL,</span>
-<span id="cb5-5"><a href="#cb5-5" aria-hidden="true" tabindex="-1"></a>    <span class="st">"101"</span>,     <span class="st">"ADPCYMG"</span>, <span class="st">"Actual Dose per Cycle (mg)"</span>, <span class="dv">60</span></span>
-<span id="cb5-6"><a href="#cb5-6" aria-hidden="true" tabindex="-1"></a>  )</span>
-<span id="cb5-7"><a href="#cb5-7" aria-hidden="true" tabindex="-1"></a>)</span>
-<span id="cb5-8"><a href="#cb5-8" aria-hidden="true" tabindex="-1"></a></span>
-<span id="cb5-9"><a href="#cb5-9" aria-hidden="true" tabindex="-1"></a><span class="fu">diffdf</span>(adex_expected, adex_admiral, <span class="at">keys =</span> <span class="fu">c</span>(<span class="st">"USUBJID"</span>, <span class="st">"PARAMCD"</span>))</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
+<div class="sourceCode cell-code" id="cb4"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb4-1"><a href="#cb4-1" aria-hidden="true" tabindex="-1"></a>adex_expected <span class="ot">&lt;-</span> <span class="fu">bind_rows</span>(</span>
+<span id="cb4-2"><a href="#cb4-2" aria-hidden="true" tabindex="-1"></a>  adex,</span>
+<span id="cb4-3"><a href="#cb4-3" aria-hidden="true" tabindex="-1"></a>  <span class="fu">tribble</span>(</span>
+<span id="cb4-4"><a href="#cb4-4" aria-hidden="true" tabindex="-1"></a>    <span class="sc">~</span>USUBJID,  <span class="sc">~</span>PARAMCD,  <span class="sc">~</span>PARAM,                       <span class="sc">~</span>AVAL,</span>
+<span id="cb4-5"><a href="#cb4-5" aria-hidden="true" tabindex="-1"></a>    <span class="st">"101"</span>,     <span class="st">"ADPCYMG"</span>, <span class="st">"Actual Dose per Cycle (mg)"</span>, <span class="dv">60</span></span>
+<span id="cb4-6"><a href="#cb4-6" aria-hidden="true" tabindex="-1"></a>  )</span>
+<span id="cb4-7"><a href="#cb4-7" aria-hidden="true" tabindex="-1"></a>)</span>
+<span id="cb4-8"><a href="#cb4-8" aria-hidden="true" tabindex="-1"></a></span>
+<span id="cb4-9"><a href="#cb4-9" aria-hidden="true" tabindex="-1"></a><span class="fu">diffdf</span>(adex_expected, adex_admiral, <span class="at">keys =</span> <span class="fu">c</span>(<span class="st">"USUBJID"</span>, <span class="st">"PARAMCD"</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-stdout">
 <pre><code>No issues were found!</code></pre>
 </div>
@@ -302,7 +297,7 @@ <h3 class="anchored" data-anchor-id="compare">Compare</h3>
 
 <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>2023-11-27 19:13:38.746856</p>
+<p>2024-01-04 14:10:03.49332</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>

posts/2023-06-27_hackathon_writeup/index.html

@@ -233,7 +233,7 @@ <h2 class="anchored" data-anchor-id="conclusion">Conclusion</h2>
 
 <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>2023-11-27 19:13:36.963431</p>
+<p>2024-01-04 14:09:46.57635</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>

posts/2023-06-28_welcome/index.html

@@ -231,7 +231,7 @@ <h2 class="anchored" data-anchor-id="how-can-i-make-a-blog-post">How can I make
 
 <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>2023-11-27 19:13:52.942147</p>
+<p>2024-01-04 14:10:01.760098</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>

posts/2023-07-09_falcon/falcon.html

@@ -196,7 +196,7 @@ <h2 class="anchored" data-anchor-id="next-steps-vision">Next steps &amp; vision<
 
 <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>2023-11-27 19:13:40.019302</p>
+<p>2024-01-04 14:09:41.635064</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>

posts/2023-07-10_blanks_and_nas/blanks_and_nas.html

@@ -206,7 +206,7 @@ <h2 id="toc-title">Table of contents</h2>
 <!--------------- post begins here ----------------->
 <p>Reading in SAS-based datasets (<code>.sas7bdat</code> or <code>xpt</code>) into R has users calling the R package <a href="https://haven.tidyverse.org/">haven</a>. A typical call might invoke <code>read_sas()</code> or <code>read_xpt()</code> to bring in your source data to construct your ADaMs or SDTMs.</p>
 <p>Unfortunately, while using <a href="https://haven.tidyverse.org/">haven</a> the character blanks (missing data) found in a typical SAS-based dataset are left as blanks. These blanks will typically prove problematic while using functions like <code>is.na</code> in combination with <code>dplyr::filter()</code> to subset data. Check out <a href="https://bayer-group.github.io/sas2r/r-and-sas-syntax.html#handling-of-missing-values">Bayer’s SAS2R catalog: handling-of-missing-values</a> for more discussion on missing values and <code>NAs</code>.</p>
-<p>In the <a href="https://pharmaverse.github.io/admiral/cran-release/">admiral</a> package, we have built a simple function called <code>convert_blanks_to_na()</code> to help us quickly remedy this problem. You can supply an entire dataframe to this function and it will convert any character blanks to <code>NA_character_</code></p>
+<p>In the <a href="https://pharmaverse.github.io/admiral/">admiral</a> package, we have built a simple function called <code>convert_blanks_to_na()</code> to help us quickly remedy this problem. You can supply an entire dataframe to this function and it will convert any character blanks to <code>NA_character_</code></p>
 <section id="loading-packages-and-making-dummy-data" class="level2">
 <h2 class="anchored" data-anchor-id="loading-packages-and-making-dummy-data">Loading Packages and Making Dummy Data</h2>
 <div class="cell">
@@ -269,7 +269,7 @@ <h2 class="anchored" data-anchor-id="a-simple-conversion">A simple conversion</h
 </section>
 <section id="thats-it" class="level2">
 <h2 class="anchored" data-anchor-id="thats-it">That’s it!</h2>
-<p>A simple call to this function can make your derivation life so much easier while working in R if working with SAS-based datasets. In <a href="https://pharmaverse.github.io/admiral/cran-release/">admiral</a>, we make use of this function at the start of all ADaM templates for common ADaM datasets. You can use the function <code>use_ad_template()</code> to get the full R script for the below ADaMs.</p>
+<p>A simple call to this function can make your derivation life so much easier while working in R if working with SAS-based datasets. In <a href="https://pharmaverse.github.io/admiral/">admiral</a>, we make use of this function at the start of all ADaM templates for common ADaM datasets. You can use the function <code>use_ad_template()</code> to get the full R script for the below ADaMs.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb7"><pre class="sourceCode r code-with-copy"><code class="sourceCode r"><span id="cb7-1"><a href="#cb7-1" aria-hidden="true" tabindex="-1"></a><span class="fu">list_all_templates</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-stdout">
@@ -301,7 +301,7 @@ <h2 class="anchored" data-anchor-id="thats-it">That’s it!</h2>
 
 <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>2023-11-27 19:13:51.677601</p>
+<p>2024-01-04 14:09:40.236251</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>