diff --git a/404.html b/404.html
index 4ee1c42..596e640 100644
--- a/404.html
+++ b/404.html
@@ -70,7 +70,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE-text.html b/LICENSE-text.html
index e3fc406..006eb6f 100644
--- a/LICENSE-text.html
+++ b/LICENSE-text.html
@@ -52,7 +52,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/LICENSE.html b/LICENSE.html
index d0dc635..f8e68aa 100644
--- a/LICENSE.html
+++ b/LICENSE.html
@@ -56,7 +56,7 @@
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/authors.html b/authors.html
index 53e34e2..ad9fbf8 100644
--- a/authors.html
+++ b/authors.html
@@ -54,6 +54,10 @@ <h2>Authors</h2>
           <p><strong>Mike Stackhouse</strong>. Author. <a href="https://orcid.org/0000-0001-6030-723X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a>
           </p>
         </li>
+        <li>
+          <p><strong>Jana Stoilova</strong>. Author. 
+          </p>
+        </li>
         <li>
           <p><strong>GlaxoSmithKline LLC</strong>. Copyright holder, funder. 
           </p>
@@ -72,16 +76,18 @@ <h2>Authors</h2>
       <h2 id="citation">Citation</h2>
       <p><small class="dont-index">Source: <a href="https://github.com/pharmaverse/metatools/blob/HEAD/DESCRIPTION" class="external-link"><code>DESCRIPTION</code></a></small></p>
 
-      <p>Fillmore C, Stackhouse M (2024).
+      <p>Fillmore C, Stackhouse M, Stoilova J (2024).
 <em>metatools: Enable the Use of 'metacore' to Help Create and Check Dataset</em>.
-R package version 0.1.5.9000, <a href="https://pharmaverse.github.io/metatools/">https://pharmaverse.github.io/metatools/</a>. 
+R package version 0.1.5.9000, 
+https://pharmaverse.github.io/metatools/, <a href="https://github.com/pharmaverse/metatools" class="external-link">https://github.com/pharmaverse/metatools</a>. 
 </p>
       <pre>@Manual{,
   title = {metatools: Enable the Use of 'metacore' to Help Create and Check Dataset},
-  author = {Christina Fillmore and Mike Stackhouse},
+  author = {Christina Fillmore and Mike Stackhouse and Jana Stoilova},
   year = {2024},
-  note = {R package version 0.1.5.9000},
-  url = {https://pharmaverse.github.io/metatools/},
+  note = {R package version 0.1.5.9000, 
+https://pharmaverse.github.io/metatools/},
+  url = {https://github.com/pharmaverse/metatools},
 }</pre>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -89,7 +95,7 @@ <h2 id="citation">Citation</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/index.html b/index.html
index 441a9e5..80e95ad 100644
--- a/index.html
+++ b/index.html
@@ -82,7 +82,7 @@ <h2 id="example">Example<a class="anchor" aria-label="anchor" href="#example"></
 </h2>
 <p>Here is a basic example of some functions to build datasets and create new columns.</p>
 <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
-<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://pharmaverse.github.io/metatools/">metatools</a></span><span class="op">)</span></span>
+<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/pharmaverse/metatools" class="external-link">metatools</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://atorus-research.github.io/metacore/" class="external-link">metacore</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span></span>
 <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
@@ -217,6 +217,7 @@ <h2 data-toc-skip>Developers</h2>
 <ul class="list-unstyled">
 <li>Christina Fillmore <br><small class="roles"> Author, maintainer </small> <a href="https://orcid.org/0000-0003-0595-2302" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
 <li>Mike Stackhouse <br><small class="roles"> Author </small> <a href="https://orcid.org/0000-0001-6030-723X" target="orcid.widget" aria-label="ORCID" class="external-link"><span class="fab fa-orcid orcid" aria-hidden="true"></span></a> </li>
+<li>Jana Stoilova <br><small class="roles"> Author </small>  </li>
 <li>GlaxoSmithKline LLC <br><small class="roles"> Copyright holder, funder </small>  </li>
 <li>F. Hoffmann-La Roche AG <br><small class="roles"> Copyright holder, funder </small>  </li>
 <li>Atorus Research LLC <br><small class="roles"> Copyright holder, funder </small>  </li>
@@ -240,7 +241,7 @@ <h2 data-toc-skip>Dev status</h2>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/news/index.html b/news/index.html
index 87d9a78..1ca0b08 100644
--- a/news/index.html
+++ b/news/index.html
@@ -50,6 +50,7 @@ <h2 class="pkg-version" data-toc-text="0.1.5.9000" id="metatools-0159000">metato
 <li>
 <code><a href="../reference/combine_supp.html">combine_supp()</a></code> now allows multiple <code>QNAM</code> values to go to the same <code>IDVAR</code> (<a href="https://github.com/pharmaverse/metatools/issues/63" class="external-link">#63</a>)</li>
 <li>Allow supp data to be zero-row with <code><a href="../reference/combine_supp.html">combine_supp()</a></code> (<a href="https://github.com/pharmaverse/metatools/issues/45" class="external-link">#45</a>)</li>
+<li>Enhance <code><a href="../reference/check_ct_data.html">check_ct_data()</a></code> so that <code>na_acceptable</code> can now accept a vector of variables. Also add new argument <code>omit_vars</code> to control if any variables should be skipped when doing controlled terminology checks (<a href="https://github.com/pharmaverse/metatools/issues/57" class="external-link">#57</a>).</li>
 </ul></div>
     <div class="section level2">
 <h2 class="pkg-version" data-toc-text="0.1.4" id="metatools-014">metatools 0.1.4<a class="anchor" aria-label="anchor" href="#metatools-014"></a></h2><p class="text-muted">CRAN release: 2023-02-13</p>
@@ -80,7 +81,7 @@ <h2 class="pkg-version" data-toc-text="0.1.1" id="metatools-011">metatools 0.1.1
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/pkgdown.yml b/pkgdown.yml
index 6d88d6e..e1cd4e9 100644
--- a/pkgdown.yml
+++ b/pkgdown.yml
@@ -2,7 +2,7 @@ pandoc: 3.1.11
 pkgdown: 2.0.9
 pkgdown_sha: ~
 articles: {}
-last_built: 2024-04-19T12:17Z
+last_built: 2024-04-26T07:45Z
 urls:
   reference: https://pharmaverse.github.io/metatools/reference
   article: https://pharmaverse.github.io/metatools/articles
diff --git a/reference/add_labels.html b/reference/add_labels.html
index 84dbb65..2115e9d 100644
--- a/reference/add_labels.html
+++ b/reference/add_labels.html
@@ -119,7 +119,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/add_variables.html b/reference/add_variables.html
index 94be6a1..12d1b47 100644
--- a/reference/add_variables.html
+++ b/reference/add_variables.html
@@ -132,7 +132,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/build_from_derived.html b/reference/build_from_derived.html
index 8d0b4f6..4a9b59f 100644
--- a/reference/build_from_derived.html
+++ b/reference/build_from_derived.html
@@ -143,7 +143,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/build_qnam.html b/reference/build_qnam.html
index 9388fc6..4dd0349 100644
--- a/reference/build_qnam.html
+++ b/reference/build_qnam.html
@@ -92,7 +92,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/check_ct_col.html b/reference/check_ct_col.html
index 5576c1e..853dbe1 100644
--- a/reference/check_ct_col.html
+++ b/reference/check_ct_col.html
@@ -146,7 +146,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/check_ct_data.html b/reference/check_ct_data.html
index 8fde6b7..acc7164 100644
--- a/reference/check_ct_data.html
+++ b/reference/check_ct_data.html
@@ -54,7 +54,7 @@
 
     <div class="section level2">
     <h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
-    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">metacore</span>, na_acceptable <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">metacore</span>, na_acceptable <span class="op">=</span> <span class="cn">NULL</span>, omit_vars <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
     </div>
 
     <div class="section level2">
@@ -71,11 +71,18 @@ <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#argumen
 
 
 <dt>na_acceptable</dt>
-<dd><p>Logical value, set to `NULL` by default, so the
-acceptability of missing values is based on if the core for the variable is
-"Required" in the `metacore` object. If set to `TRUE` then will
+<dd><p>`logical` value or `character` vector, set to `NULL` by default.
+`NULL` sets the acceptability of missing values based on if the core for
+the variable is "Required" in the `metacore` object. If set to `TRUE` then will
 pass check if values are in the control terminology or are missing. If set
-to `FALSE`then NA will not be acceptable.</p></dd>
+to `FALSE` then NA will not be acceptable. If set to a `character` vector then
+only the specified variables may contain NA values.</p></dd>
+
+
+<dt>omit_vars</dt>
+<dd><p>`character` vector indicating which variables should be skipped
+when doing the controlled terminology checks. Internally, `omit_vars` is
+evaluated before `na_acceptable`.</p></dd>
 
 </dl></div>
     <div class="section level2">
@@ -93,6 +100,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/load.html" class="external-link">load</a></span><span class="op">(</span><span class="fu"><a href="https://atorus-research.github.io/metacore/reference/metacore_example.html" class="external-link">metacore_example</a></span><span class="op">(</span><span class="st">"pilot_ADaM.rda"</span><span class="op">)</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">spec</span> <span class="op">&lt;-</span> <span class="va">metacore</span> <span class="op"><a href="pipe.html">%&gt;%</a></span> <span class="fu"><a href="https://atorus-research.github.io/metacore/reference/select_dataset.html" class="external-link">select_dataset</a></span><span class="op">(</span><span class="st">"ADSL"</span><span class="op">)</span></span></span>
 <span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">read_xpt</a></span><span class="op">(</span><span class="fu"><a href="metatools_example.html">metatools_example</a></span><span class="op">(</span><span class="st">"adsl.xpt"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span><span class="op">)</span></span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 254 × 49</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN</span>
@@ -114,6 +122,12 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   ITTFL &lt;chr&gt;, EFFFL &lt;chr&gt;, COMP8FL &lt;chr&gt;, COMP16FL &lt;chr&gt;, COMP24FL &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   DISCONFL &lt;chr&gt;, DSRAEFL &lt;chr&gt;, DTHFL &lt;chr&gt;, BMIBL &lt;dbl&gt;, BMIBLGR1 &lt;chr&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   HEIGHTBL &lt;dbl&gt;, WEIGHTBL &lt;dbl&gt;, EDUCLVL &lt;dbl&gt;, DISONSDT &lt;date&gt;, …</span></span>
+<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="cn">FALSE</span><span class="op">)</span> <span class="op">{</span></span></span>
+<span class="r-in"><span><span class="co"># These examples produce errors:</span></span></span>
+<span class="r-in"><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span>, na_acceptable <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span>, na_acceptable <span class="op">=</span> <span class="cn">FALSE</span>, omit_vars <span class="op">=</span> <span class="st">"DISCONFL"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">check_ct_data</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span>, na_acceptable <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"DSRAEFL"</span>, <span class="st">"DCSREAS"</span><span class="op">)</span>, omit_vars <span class="op">=</span> <span class="st">"DISCONFL"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="op">}</span></span></span>
 </code></pre></div>
     </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
@@ -121,7 +135,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/check_variables.html b/reference/check_variables.html
index 04a8b6b..de726ee 100644
--- a/reference/check_variables.html
+++ b/reference/check_variables.html
@@ -123,7 +123,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/combine_supp.html b/reference/combine_supp.html
index 3b82568..cb0b924 100644
--- a/reference/combine_supp.html
+++ b/reference/combine_supp.html
@@ -103,7 +103,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/convert_var_to_fct.html b/reference/convert_var_to_fct.html
index 81125a0..fb82e2d 100644
--- a/reference/convert_var_to_fct.html
+++ b/reference/convert_var_to_fct.html
@@ -137,7 +137,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/create_cat_var.html b/reference/create_cat_var.html
index e728077..417ab0e 100644
--- a/reference/create_cat_var.html
+++ b/reference/create_cat_var.html
@@ -141,7 +141,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/create_subgrps.html b/reference/create_subgrps.html
index e1325db..4453f00 100644
--- a/reference/create_subgrps.html
+++ b/reference/create_subgrps.html
@@ -87,7 +87,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/create_var_from_codelist.html b/reference/create_var_from_codelist.html
index a32bc5c..2d22725 100644
--- a/reference/create_var_from_codelist.html
+++ b/reference/create_var_from_codelist.html
@@ -148,7 +148,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/drop_unspec_vars.html b/reference/drop_unspec_vars.html
index 664a7ca..585f567 100644
--- a/reference/drop_unspec_vars.html
+++ b/reference/drop_unspec_vars.html
@@ -114,7 +114,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/get_bad_ct.html b/reference/get_bad_ct.html
index dbefc8e..2afaad6 100644
--- a/reference/get_bad_ct.html
+++ b/reference/get_bad_ct.html
@@ -91,12 +91,27 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 <p>vector</p>
     </div>
 
+    <div class="section level2">
+    <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
+    <div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://haven.tidyverse.org" class="external-link">haven</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://atorus-research.github.io/metacore/" class="external-link">metacore</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://magrittr.tidyverse.org" class="external-link">magrittr</a></span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/load.html" class="external-link">load</a></span><span class="op">(</span><span class="fu"><a href="https://atorus-research.github.io/metacore/reference/metacore_example.html" class="external-link">metacore_example</a></span><span class="op">(</span><span class="st">"pilot_ADaM.rda"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">spec</span> <span class="op">&lt;-</span> <span class="va">metacore</span> <span class="op"><a href="pipe.html">%&gt;%</a></span> <span class="fu"><a href="https://atorus-research.github.io/metacore/reference/select_dataset.html" class="external-link">select_dataset</a></span><span class="op">(</span><span class="st">"ADSL"</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="va">data</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://haven.tidyverse.org/reference/read_xpt.html" class="external-link">read_xpt</a></span><span class="op">(</span><span class="fu"><a href="metatools_example.html">metatools_example</a></span><span class="op">(</span><span class="st">"adsl.xpt"</span><span class="op">)</span><span class="op">)</span></span></span>
+<span class="r-in"><span><span class="fu">get_bad_ct</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span>, <span class="st">"DISCONFL"</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> character(0)</span>
+<span class="r-in"><span><span class="fu">get_bad_ct</span><span class="op">(</span><span class="va">data</span>, <span class="va">spec</span>, <span class="st">"DISCONFL"</span>, na_acceptable <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> [1] ""</span>
+<span class="r-in"><span></span></span>
+</code></pre></div>
+    </div>
   </main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
     </nav></aside></div>
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/index.html b/reference/index.html
index 89a785a..a79faaf 100644
--- a/reference/index.html
+++ b/reference/index.html
@@ -159,7 +159,7 @@ <h2 id="all-functions">All functions<a class="anchor" aria-label="anchor" href="
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/make_supp_qual.html b/reference/make_supp_qual.html
index 54669d7..ecbac18 100644
--- a/reference/make_supp_qual.html
+++ b/reference/make_supp_qual.html
@@ -107,7 +107,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/metatools_example.html b/reference/metatools_example.html
index 2071de9..147b4af 100644
--- a/reference/metatools_example.html
+++ b/reference/metatools_example.html
@@ -77,7 +77,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/order_cols.html b/reference/order_cols.html
index f77d15d..8319304 100644
--- a/reference/order_cols.html
+++ b/reference/order_cols.html
@@ -116,7 +116,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/pipe.html b/reference/pipe.html
index 4bd6e6f..96cf05a 100644
--- a/reference/pipe.html
+++ b/reference/pipe.html
@@ -76,7 +76,7 @@ <h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/remove_labels.html b/reference/remove_labels.html
index 8d55886..885b71c 100644
--- a/reference/remove_labels.html
+++ b/reference/remove_labels.html
@@ -100,7 +100,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/set_variable_labels.html b/reference/set_variable_labels.html
index f32f83e..e341799 100644
--- a/reference/set_variable_labels.html
+++ b/reference/set_variable_labels.html
@@ -117,7 +117,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/reference/sort_by_key.html b/reference/sort_by_key.html
index b92a72e..299e1a0 100644
--- a/reference/sort_by_key.html
+++ b/reference/sort_by_key.html
@@ -116,7 +116,7 @@ <h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-e
 
 
     <footer><div class="pkgdown-footer-left">
-  <p>Developed by Christina Fillmore, Mike Stackhouse, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
+  <p>Developed by Christina Fillmore, Mike Stackhouse, Jana Stoilova, GlaxoSmithKline LLC, F. Hoffmann-La Roche AG, Atorus Research LLC.</p>
 </div>
 
 <div class="pkgdown-footer-right">
diff --git a/search.json b/search.json
index c65a2d7..9f18273 100644
--- a/search.json
+++ b/search.json
@@ -1 +1 @@
-[{"path":"https://pharmaverse.github.io/metatools/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 metatools authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://pharmaverse.github.io/metatools/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Christina Fillmore. Author, maintainer. Mike Stackhouse. Author. GlaxoSmithKline LLC. Copyright holder, funder. F. Hoffmann-La Roche AG. Copyright holder, funder. Atorus Research LLC. Copyright holder, funder.","code":""},{"path":"https://pharmaverse.github.io/metatools/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Fillmore C, Stackhouse M (2024). metatools: Enable Use 'metacore' Help Create Check Dataset. R package version 0.1.5.9000, https://pharmaverse.github.io/metatools/.","code":"@Manual{,   title = {metatools: Enable the Use of 'metacore' to Help Create and Check Dataset},   author = {Christina Fillmore and Mike Stackhouse},   year = {2024},   note = {R package version 0.1.5.9000},   url = {https://pharmaverse.github.io/metatools/}, }"},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"metatools-","dir":"","previous_headings":"","what":"Enable the Use of metacore to Help Create and Check Dataset","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"goal metatools enable use metacore objects. Metatools can used build datasets enhance columns existing datasets well checking datasets metadata metacore.","code":""},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"can install latest released version metatools CRAN : current development version GitHub :","code":"install.packages(\"metatools\") devtools::install_github(\"pharmaverse/metatools\")"},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"basic example functions build datasets create new columns. Metatools can also used run checks","code":"library(metatools) library(metacore) library(haven) library(dplyr) #>  #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #>  #>     filter, lag #> The following objects are masked from 'package:base': #>  #>     intersect, setdiff, setequal, union load(metacore_example(\"pilot_ADaM.rda\")) metacore <- metacore %>%   select_dataset(\"ADSL\") ds_list <- list(DM = read_xpt(metatools_example(\"dm.xpt\"))) # Pull in columns from DM to be in ADSL adsl <- build_from_derived(metacore, ds_list, predecessor_only = FALSE)  adsl  #> # A tibble: 306 × 13 #>    STUDYID     USUBJID SUBJID SITEID TRT01P   AGE AGEU  RACE  SEX   ETHNIC DTHFL #>    <chr>       <chr>   <chr>  <chr>  <chr>  <dbl> <chr> <chr> <chr> <chr>  <chr> #>  1 CDISCPILOT… 01-701… 1015   701    Place…    63 YEARS WHITE F     HISPA… \"\"    #>  2 CDISCPILOT… 01-701… 1023   701    Place…    64 YEARS WHITE M     HISPA… \"\"    #>  3 CDISCPILOT… 01-701… 1028   701    Xanom…    71 YEARS WHITE M     NOT H… \"\"    #>  4 CDISCPILOT… 01-701… 1033   701    Xanom…    74 YEARS WHITE M     NOT H… \"\"    #>  5 CDISCPILOT… 01-701… 1034   701    Xanom…    77 YEARS WHITE F     NOT H… \"\"    #>  6 CDISCPILOT… 01-701… 1047   701    Place…    85 YEARS WHITE F     NOT H… \"\"    #>  7 CDISCPILOT… 01-701… 1057   701    Scree…    59 YEARS WHITE F     HISPA… \"\"    #>  8 CDISCPILOT… 01-701… 1097   701    Xanom…    68 YEARS WHITE M     NOT H… \"\"    #>  9 CDISCPILOT… 01-701… 1111   701    Xanom…    81 YEARS WHITE F     NOT H… \"\"    #> 10 CDISCPILOT… 01-701… 1115   701    Xanom…    84 YEARS WHITE M     NOT H… \"\"    #> # … with 296 more rows, and 2 more variables: RFSTDTC <chr>, RFENDTC <chr>  # Now we can make some new columns and converting columns into factors adsl %>%    select(USUBJID, AGE, ETHNIC) %>%     create_cat_var(metacore, AGE, AGEGR1, AGEGR1N) %>% #Add an AGEGR1 and AGEGR1N column    convert_var_to_fct(metacore, ETHNIC) # Change ETHNIC to as factor  #> # A tibble: 306 × 5 #>    USUBJID       AGE ETHNIC                 AGEGR1 AGEGR1N #>    <chr>       <dbl> <fct>                  <chr>    <dbl> #>  1 01-701-1015    63 HISPANIC OR LATINO     <65          1 #>  2 01-701-1023    64 HISPANIC OR LATINO     <65          1 #>  3 01-701-1028    71 NOT HISPANIC OR LATINO 65-80        2 #>  4 01-701-1033    74 NOT HISPANIC OR LATINO 65-80        2 #>  5 01-701-1034    77 NOT HISPANIC OR LATINO 65-80        2 #>  6 01-701-1047    85 NOT HISPANIC OR LATINO >80          3 #>  7 01-701-1057    59 HISPANIC OR LATINO     <65          1 #>  8 01-701-1097    68 NOT HISPANIC OR LATINO 65-80        2 #>  9 01-701-1111    81 NOT HISPANIC OR LATINO >80          3 #> 10 01-701-1115    84 NOT HISPANIC OR LATINO >80          3 #> # … with 296 more rows data <- read_xpt(metatools_example(\"adsl.xpt\"))  # Checks can be run on a single column check_ct_col(data, metacore, TRT01PN) # Checks column only contains control terminology #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # … with 244 more rows, and 39 more variables: TRTSDT <date>, TRTEDT <date>, #> #   TRTDURD <dbl>, AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, … # Or across all the columns  check_ct_data(data, metacore) %>%  # Checks control terminology for all columns  check_variables(metacore) # Check all variables in the metadata are in the dataset and there aren't any extra columns  #> No missing or extra variables #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # … with 244 more rows, and 39 more variables: TRTSDT <date>, TRTEDT <date>, #> #   TRTDURD <dbl>, AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply labels to multiple variables on a data frame — add_labels","title":"Apply labels to multiple variables on a data frame — add_labels","text":"function allows user apply several labels dataframe .","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply labels to multiple variables on a data frame — add_labels","text":"","code":"add_labels(data, ...)"},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply labels to multiple variables on a data frame — add_labels","text":"data data.frame tibble ... Named parameters form variable = 'label'","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply labels to multiple variables on a data frame — add_labels","text":"data variable labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply labels to multiple variables on a data frame — add_labels","text":"","code":"add_labels(     mtcars,     mpg = \"Miles Per Gallon\",     cyl = \"Cylinders\"   ) #>                      mpg cyl  disp  hp drat    wt  qsec vs am gear carb #> Mazda RX4           21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4 #> Mazda RX4 Wag       21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4 #> Datsun 710          22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1 #> Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1 #> Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2 #> Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1 #> Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4 #> Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2 #> Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2 #> Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4 #> Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4 #> Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3 #> Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3 #> Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3 #> Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4 #> Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4 #> Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4 #> Fiat 128            32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1 #> Honda Civic         30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2 #> Toyota Corolla      33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1 #> Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1 #> Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2 #> AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2 #> Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4 #> Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2 #> Fiat X1-9           27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1 #> Porsche 914-2       26.0   4 120.3  91 4.43 2.140 16.70  0  1    5    2 #> Lotus Europa        30.4   4  95.1 113 3.77 1.513 16.90  1  1    5    2 #> Ford Pantera L      15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4 #> Ferrari Dino        19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6 #> Maserati Bora       15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8 #> Volvo 142E          21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2"},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Variables — add_variables","title":"Add Missing Variables — add_variables","text":"function adds missing columns according type set metacore object. values new columns missing, typed correctly. unable recognize type metacore object return logical type.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Variables — add_variables","text":"","code":"add_variables(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Variables — add_variables","text":"dataset Dataset add columns . variables present columns added. metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Variables — add_variables","text":"given dataset additional columns added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Missing Variables — add_variables","text":"","code":"library(metacore) library(haven) library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) %>%    select(-TRTSDT, -TRT01P, -TRT01PN) add_variables(data, spec) #> # A tibble: 254 × 49 #>    STUDYID USUBJID SUBJID SITEID SITEGR1 ARM   TRT01A TRT01AN TRTEDT     TRTDURD #>    <chr>   <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <date>       <dbl> #>  1 CDISCP… 01-701… 1015   701    701     Plac… Place…       0 2014-07-02     182 #>  2 CDISCP… 01-701… 1023   701    701     Plac… Place…       0 2012-09-01      28 #>  3 CDISCP… 01-701… 1028   701    701     Xano… Xanom…      81 2014-01-14     180 #>  4 CDISCP… 01-701… 1033   701    701     Xano… Xanom…      54 2014-03-31      14 #>  5 CDISCP… 01-701… 1034   701    701     Xano… Xanom…      81 2014-12-30     183 #>  6 CDISCP… 01-701… 1047   701    701     Plac… Place…       0 2013-03-09      26 #>  7 CDISCP… 01-701… 1097   701    701     Xano… Xanom…      54 2014-07-09     190 #>  8 CDISCP… 01-701… 1111   701    701     Xano… Xanom…      54 2012-09-16      10 #>  9 CDISCP… 01-701… 1115   701    701     Xano… Xanom…      54 2013-01-23      55 #> 10 CDISCP… 01-701… 1118   701    701     Plac… Place…       0 2014-09-09     182 #> # ℹ 244 more rows #> # ℹ 39 more variables: AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a dataset from derived — build_from_derived","title":"Build a dataset from derived — build_from_derived","text":"function builds dataset columns just need pulled . variable derivation format 'dataset.variable' pulled create new dataset. multiple datasets present, joined shared `key_seq` variables. columns often called 'Predecessors' ADaM, universal optional specify.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a dataset from derived — build_from_derived","text":"","code":"build_from_derived(   metacore,   ds_list,   dataset_name = NULL,   predecessor_only = TRUE,   keep = FALSE )"},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a dataset from derived — build_from_derived","text":"metacore metacore object contains specifications dataset interest. ds_list Named list datasets needed build dataset_name Optional string specify dataset built. needed metacore object provided already subsetted. predecessor_only default `FALSE`, `TRUE` use derivations origin 'Predecessor' keep Boolean determine original columns kept. default `FALSE`, ADaM columns kept. `TRUE` resulting dataset ADaM columns well SDTM column renamed ADaM (.e `ARM` `TRT01P` resulting dataset)","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a dataset from derived — build_from_derived","text":"dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build a dataset from derived — build_from_derived","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") ds_list <- list(DM = read_xpt(metatools_example(\"dm.xpt\"))) build_from_derived(spec, ds_list, predecessor_only = FALSE) #> # A tibble: 306 × 13 #>    STUDYID     USUBJID SUBJID SITEID TRT01P   AGE AGEU  RACE  SEX   ETHNIC DTHFL #>    <chr>       <chr>   <chr>  <chr>  <chr>  <dbl> <chr> <chr> <chr> <chr>  <chr> #>  1 CDISCPILOT… 01-701… 1015   701    Place…    63 YEARS WHITE F     HISPA… \"\"    #>  2 CDISCPILOT… 01-701… 1023   701    Place…    64 YEARS WHITE M     HISPA… \"\"    #>  3 CDISCPILOT… 01-701… 1028   701    Xanom…    71 YEARS WHITE M     NOT H… \"\"    #>  4 CDISCPILOT… 01-701… 1033   701    Xanom…    74 YEARS WHITE M     NOT H… \"\"    #>  5 CDISCPILOT… 01-701… 1034   701    Xanom…    77 YEARS WHITE F     NOT H… \"\"    #>  6 CDISCPILOT… 01-701… 1047   701    Place…    85 YEARS WHITE F     NOT H… \"\"    #>  7 CDISCPILOT… 01-701… 1057   701    Scree…    59 YEARS WHITE F     HISPA… \"\"    #>  8 CDISCPILOT… 01-701… 1097   701    Xanom…    68 YEARS WHITE M     NOT H… \"\"    #>  9 CDISCPILOT… 01-701… 1111   701    Xanom…    81 YEARS WHITE F     NOT H… \"\"    #> 10 CDISCPILOT… 01-701… 1115   701    Xanom…    84 YEARS WHITE M     NOT H… \"\"    #> # ℹ 296 more rows #> # ℹ 2 more variables: RFSTDTC <chr>, RFENDTC <chr>"},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":null,"dir":"Reference","previous_headings":"","what":"Build the observations for a single QNAM — build_qnam","title":"Build the observations for a single QNAM — build_qnam","text":"Build observations single QNAM","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build the observations for a single QNAM — build_qnam","text":"","code":"build_qnam(dataset, qnam, qlabel, idvar, qeval, qorig)"},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build the observations for a single QNAM — build_qnam","text":"dataset Input dataset qnam QNAM value qlabel QLABEL value idvar IDVAR variable name (provided string) qeval QEVAL value populated QNAM qorig QORIG value populated QNAM","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build the observations for a single QNAM — build_qnam","text":"Observations structured SUPP format","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Control Terminology for a Single Column — check_ct_col","title":"Check Control Terminology for a Single Column — check_ct_col","text":"function checks column dataset contains control terminology defined metacore specification","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Control Terminology for a Single Column — check_ct_col","text":"","code":"check_ct_col(data, metacore, var, na_acceptable = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Control Terminology for a Single Column — check_ct_col","text":"data Data check metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. var Name variable check na_acceptable Logical value, set `NULL` default, acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE`NA acceptable.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Control Terminology for a Single Column — check_ct_col","text":"Given data column contains control terms. , error   given values column","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Control Terminology for a Single Column — check_ct_col","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) check_ct_col(data, spec, TRT01PN) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, … check_ct_col(data, spec, \"TRT01PN\") #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Control Terminology for a Dataset — check_ct_data","title":"Check Control Terminology for a Dataset — check_ct_data","text":"function checks columns dataset contains control terminology defined metacore specification","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Control Terminology for a Dataset — check_ct_data","text":"","code":"check_ct_data(data, metacore, na_acceptable = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Control Terminology for a Dataset — check_ct_data","text":"data Dataset check metacore metacore object contains specifications dataset interest. variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. na_acceptable Logical value, set `NULL` default, acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE`NA acceptable.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Control Terminology for a Dataset — check_ct_data","text":"Given data columns pass. error otherwise","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Control Terminology for a Dataset — check_ct_data","text":"","code":"library(haven) library(metacore) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) check_ct_data(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Variable Names — check_variables","title":"Check Variable Names — check_variables","text":"function checks variables dataset variables defined metacore specifications. everything matches function return `TRUE` message starting everything expected. additional missing variables error explain discrepancies","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Variable Names — check_variables","text":"","code":"check_variables(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Variable Names — check_variables","text":"data Dataset check metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Variable Names — check_variables","text":"message dataset matches specification dataset, error otherwise","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Variable Names — check_variables","text":"","code":"library(haven) library(metacore) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) check_variables(data, spec) #> No missing or extra variables #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine the Domain and Supplemental Qualifier — combine_supp","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"Combine Domain Supplemental Qualifier","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"","code":"combine_supp(dataset, supp)"},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"dataset Domain dataset supp Supplemental Qualifier dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"dataset supp variables added ","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"","code":"library(safetyData) library(tibble) combine_supp(sdtm_ae, sdtm_suppae)  %>% as_tibble() #> # A tibble: 1,191 × 37 #>    STUDYID DOMAIN USUBJID AESEQ AESPID AETERM AELLT AELLTCD AEDECOD AEPTCD AEHLT #>    <chr>   <chr>  <chr>   <int> <chr>  <chr>  <chr> <lgl>   <chr>   <lgl>  <chr> #>  1 CDISCP… AE     01-701…     1 E07    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  2 CDISCP… AE     01-701…     2 E08    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  3 CDISCP… AE     01-701…     3 E06    DIARR… DIAR… NA      DIARRH… NA     HLT_… #>  4 CDISCP… AE     01-701…     3 E10    ATRIO… AV B… NA      ATRIOV… NA     HLT_… #>  5 CDISCP… AE     01-701…     1 E08    ERYTH… ERYT… NA      ERYTHE… NA     HLT_… #>  6 CDISCP… AE     01-701…     2 E09    ERYTH… LOCA… NA      ERYTHE… NA     HLT_… #>  7 CDISCP… AE     01-701…     4 E08    ERYTH… ERYT… NA      ERYTHE… NA     HLT_… #>  8 CDISCP… AE     01-701…     1 E04    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  9 CDISCP… AE     01-701…     2 E05    APPLI… APPL… NA      APPLIC… NA     HLT_… #> 10 CDISCP… AE     01-701…     1 E08    APPLI… APPL… NA      APPLIC… NA     HLT_… #> # ℹ 1,181 more rows #> # ℹ 26 more variables: AEHLTCD <lgl>, AEHLGT <chr>, AEHLGTCD <lgl>, #> #   AEBODSYS <chr>, AEBDSYCD <lgl>, AESOC <chr>, AESOCCD <lgl>, AESEV <chr>, #> #   AESER <chr>, AEACN <lgl>, AEREL <chr>, AEOUT <chr>, AESCAN <chr>, #> #   AESCONG <chr>, AESDISAB <chr>, AESDTH <chr>, AESHOSP <chr>, AESLIFE <chr>, #> #   AESOD <chr>, AEDTC <chr>, AESTDTC <chr>, AEENDTC <chr>, AESTDY <int>, #> #   AEENDY <int>, IDVARVAL <chr>, AETRTEM <chr>"},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"functions takes dataset, metacore object variable name. looks metacore object control terms given variable uses convert variable factor levels. control terminology code list, code column used. function fails control terminology external library","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"","code":"convert_var_to_fct(data, metacore, var)"},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"data dataset containing variable modified metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package var Name variable change","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"Dataset variable changed factor","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") dm <- read_xpt(metatools_example(\"dm.xpt\")) %>%   select(USUBJID, SEX, ARM) # Variable with codelist control terms convert_var_to_fct(dm, spec, SEX) #> # A tibble: 306 × 3 #>    USUBJID     SEX   ARM                  #>    <chr>       <fct> <chr>                #>  1 01-701-1015 F     Placebo              #>  2 01-701-1023 M     Placebo              #>  3 01-701-1028 M     Xanomeline High Dose #>  4 01-701-1033 M     Xanomeline Low Dose  #>  5 01-701-1034 F     Xanomeline High Dose #>  6 01-701-1047 F     Placebo              #>  7 01-701-1057 F     Screen Failure       #>  8 01-701-1097 M     Xanomeline Low Dose  #>  9 01-701-1111 F     Xanomeline Low Dose  #> 10 01-701-1115 M     Xanomeline Low Dose  #> # ℹ 296 more rows # Variable with permitted value control terms convert_var_to_fct(dm, spec, ARM) #> # A tibble: 306 × 3 #>    USUBJID     SEX   ARM                  #>    <chr>       <chr> <fct>                #>  1 01-701-1015 F     Placebo              #>  2 01-701-1023 M     Placebo              #>  3 01-701-1028 M     Xanomeline High Dose #>  4 01-701-1033 M     Xanomeline Low Dose  #>  5 01-701-1034 F     Xanomeline High Dose #>  6 01-701-1047 F     Placebo              #>  7 01-701-1057 F     NA                   #>  8 01-701-1097 M     Xanomeline Low Dose  #>  9 01-701-1111 F     Xanomeline Low Dose  #> 10 01-701-1115 M     Xanomeline Low Dose  #> # ℹ 296 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Categorical Variable from Codelist — create_cat_var","title":"Create Categorical Variable from Codelist — create_cat_var","text":"Using grouping either `decode_var` `code_var` reference variable (`ref_var`) create categorical variable numeric version categorical variable.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Categorical Variable from Codelist — create_cat_var","text":"","code":"create_cat_var(data, metacore, ref_var, grp_var, num_grp_var = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Categorical Variable from Codelist — create_cat_var","text":"data Dataset reference variable metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. ref_var Name variable used reference .e AGE creating AGEGR1 grp_var Name new grouped variable num_grp_var Name new numeric decode grouped variable. optional value given variable created","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Categorical Variable from Codelist — create_cat_var","text":"dataset new column added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Categorical Variable from Codelist — create_cat_var","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") dm <- read_xpt(metatools_example(\"dm.xpt\")) %>%   select(USUBJID, AGE) # Grouping Column Only create_cat_var(dm, spec, AGE, AGEGR1) #> # A tibble: 306 × 3 #>    USUBJID       AGE AGEGR1 #>    <chr>       <dbl> <chr>  #>  1 01-701-1015    63 <65    #>  2 01-701-1023    64 <65    #>  3 01-701-1028    71 65-80  #>  4 01-701-1033    74 65-80  #>  5 01-701-1034    77 65-80  #>  6 01-701-1047    85 >80    #>  7 01-701-1057    59 <65    #>  8 01-701-1097    68 65-80  #>  9 01-701-1111    81 >80    #> 10 01-701-1115    84 >80    #> # ℹ 296 more rows # Grouping Column and Numeric Decode create_cat_var(dm, spec, AGE, AGEGR1, AGEGR1N) #> # A tibble: 306 × 4 #>    USUBJID       AGE AGEGR1 AGEGR1N #>    <chr>       <dbl> <chr>    <dbl> #>  1 01-701-1015    63 <65          1 #>  2 01-701-1023    64 <65          1 #>  3 01-701-1028    71 65-80        2 #>  4 01-701-1033    74 65-80        2 #>  5 01-701-1034    77 65-80        2 #>  6 01-701-1047    85 >80          3 #>  7 01-701-1057    59 <65          1 #>  8 01-701-1097    68 65-80        2 #>  9 01-701-1111    81 >80          3 #> 10 01-701-1115    84 >80          3 #> # ℹ 296 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Subgroups — create_subgrps","title":"Create Subgroups — create_subgrps","text":"Create Subgroups","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Subgroups — create_subgrps","text":"","code":"create_subgrps(ref_vec, grp_defs)"},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Subgroups — create_subgrps","text":"ref_vec Vector numeric values grp_defs Vector strings groupings defined. Format must either: <00, >=00, 00-00,  00-<00","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Subgroups — create_subgrps","text":"Character vector values subgroups","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Subgroups — create_subgrps","text":"","code":"create_subgrps(c(1:10), c(\"<2\", \"2-5\", \">5\")) #>  [1] \"<2\"  \"2-5\" \"2-5\" \"2-5\" \"2-5\" \">5\"  \">5\"  \">5\"  \">5\"  \">5\"  create_subgrps(c(1:10), c(\"<=2\", \">2-5\", \">5\")) #>  [1] \"<=2\"  \"<=2\"  \">2-5\" \">2-5\" \">2-5\" \">5\"   \">5\"   \">5\"   \">5\"   \">5\"   create_subgrps(c(1:10), c(\"<2\", \"2-<5\", \">=5\")) #>  [1] \"<2\"   \"2-<5\" \"2-<5\" \"2-<5\" \">=5\"  \">=5\"  \">=5\"  \">=5\"  \">=5\"  \">=5\""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Variable from Codelist — create_var_from_codelist","title":"Create Variable from Codelist — create_var_from_codelist","text":"functions uses code/decode pairs metacore object create new variables data","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Variable from Codelist — create_var_from_codelist","text":"","code":"create_var_from_codelist(   data,   metacore,   input_var,   out_var,   decode_to_code = TRUE )"},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Variable from Codelist — create_var_from_codelist","text":"data Dataset contains input variable metacore metacore object get codelist . `out_var` different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. input_var Name variable translated new column out_var Name output variable. Note: grouping always code codelist associates `out_var` decode_to_code Direction translation. default assumes `input_var` decode column codelist. Set `FALSE` `input_var` code column codelist","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Variable from Codelist — create_var_from_codelist","text":"Dataset new column added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Variable from Codelist — create_var_from_codelist","text":"","code":"library(metacore) library(tibble) data <- tribble(   ~USUBJID, ~VAR1, ~VAR2,   1, \"M\", \"Male\",   2, \"F\", \"Female\",   3, \"F\", \"Female\",   4, \"U\", \"Unknown\",   5, \"M\", \"Male\", ) spec <- spec_to_metacore(metacore_example(\"p21_mock.xlsx\"), quiet = TRUE) #>  #>  Metadata successfully imported #> Loading in metacore object with suppressed warnings create_var_from_codelist(data, spec, VAR2, SEX) #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX   #>     <dbl> <chr> <chr>   <chr> #> 1       1 M     Male    M     #> 2       2 F     Female  F     #> 3       3 F     Female  F     #> 4       4 U     Unknown U     #> 5       5 M     Male    M     create_var_from_codelist(data, spec, \"VAR2\", \"SEX\") #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX   #>     <dbl> <chr> <chr>   <chr> #> 1       1 M     Male    M     #> 2       2 F     Female  F     #> 3       3 F     Female  F     #> 4       4 U     Unknown U     #> 5       5 M     Male    M     create_var_from_codelist(data, spec, VAR1, SEX, decode_to_code = FALSE) #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX     #>     <dbl> <chr> <chr>   <chr>   #> 1       1 M     Male    Male    #> 2       2 F     Female  Female  #> 3       3 F     Female  Female  #> 4       4 U     Unknown Unknown #> 5       5 M     Male    Male"},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop Unspecified Variables — drop_unspec_vars","title":"Drop Unspecified Variables — drop_unspec_vars","text":"function drops unspecified variables. throw error dataset contain expected variables.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop Unspecified Variables — drop_unspec_vars","text":"","code":"drop_unspec_vars(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop Unspecified Variables — drop_unspec_vars","text":"dataset Dataset change metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop Unspecified Variables — drop_unspec_vars","text":"Dataset specified columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Drop Unspecified Variables — drop_unspec_vars","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) %>%   select(USUBJID, SITEID) %>%   mutate(foo = \"Hello\") drop_unspec_vars(data, spec) #> The following variable(s) were dropped: #>   foo #> # A tibble: 254 × 2 #>    USUBJID     SITEID #>    <chr>       <chr>  #>  1 01-701-1015 701    #>  2 01-701-1023 701    #>  3 01-701-1028 701    #>  4 01-701-1033 701    #>  5 01-701-1034 701    #>  6 01-701-1047 701    #>  7 01-701-1097 701    #>  8 01-701-1111 701    #>  9 01-701-1115 701    #> 10 01-701-1118 701    #> # ℹ 244 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets vector of control terminology which should be there — get_bad_ct","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"function checks column dataset contains control terminology defined metacore specification. return values found control terminology","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"","code":"get_bad_ct(data, metacore, var, na_acceptable = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"data Data check metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. var Name variable check na_acceptable Logical value, set `NULL` default, acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE`NA acceptable.e","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"vector","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":null,"dir":"Reference","previous_headings":"","what":"Make Supplemental Qualifier — make_supp_qual","title":"Make Supplemental Qualifier — make_supp_qual","text":"Make Supplemental Qualifier","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make Supplemental Qualifier — make_supp_qual","text":"","code":"make_supp_qual(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make Supplemental Qualifier — make_supp_qual","text":"dataset dataset supp pulled metacore subsetted metacore object get supp information . already subsetted `dataset_name` need provided dataset_name optional name dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make Supplemental Qualifier — make_supp_qual","text":"CDISC formatted SUPP dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make Supplemental Qualifier — make_supp_qual","text":"","code":"library(metacore) library(safetyData) library(tibble) load(metacore_example(\"pilot_SDTM.rda\")) spec <- metacore %>% select_dataset(\"AE\") ae <- combine_supp(sdtm_ae, sdtm_suppae) make_supp_qual(ae, spec) %>% as_tibble() #> # A tibble: 1,191 × 10 #>    STUDYID      RDOMAIN USUBJID    IDVAR IDVARVAL QNAM  QLABEL QVAL  QORIG QEVAL #>    <chr>        <chr>   <chr>      <chr>    <int> <chr> <chr>  <chr> <chr> <chr> #>  1 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  2 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #>  3 CDISCPILOT01 AE      01-701-10… AESEQ        3 AETR… TREAT… Y     DERI… CLIN… #>  4 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  5 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #>  6 CDISCPILOT01 AE      01-701-10… AESEQ        3 AETR… TREAT… Y     DERI… CLIN… #>  7 CDISCPILOT01 AE      01-701-10… AESEQ        4 AETR… TREAT… Y     DERI… CLIN… #>  8 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  9 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #> 10 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #> # ℹ 1,181 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Get path to pkg example — metatools_example","title":"Get path to pkg example — metatools_example","text":"pkg comes bundled number sample files `inst/extdata` directory. function make easy access","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get path to pkg example — metatools_example","text":"","code":"metatools_example(file = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get path to pkg example — metatools_example","text":"file Name file. `NULL`, example files listed.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get path to pkg example — metatools_example","text":"","code":"metatools_example() #> [1] \"adsl.xpt\" \"dm.xpt\"   metatools_example(\"dm.xpt\") #> [1] \"/home/runner/work/_temp/Library/metatools/extdata/dm.xpt\""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort Columns by Order — order_cols","title":"Sort Columns by Order — order_cols","text":"function sorts dataset according order found metacore object.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort Columns by Order — order_cols","text":"","code":"order_cols(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort Columns by Order — order_cols","text":"data Dataset sort metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort Columns by Order — order_cols","text":"dataset ordered columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort Columns by Order — order_cols","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) order_cols(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove labels to multiple variables on a data frame — remove_labels","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"function allows user removes labels dataframe .","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"","code":"remove_labels(data)"},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"data data.frame tibble","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"data variable labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"","code":"library(haven) data <- read_xpt(metatools_example(\"adsl.xpt\")) remove_labels(data) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply labels to a data frame using a metacore object — set_variable_labels","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"function leverages metadata available metacore object apply labels data frame.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"","code":"set_variable_labels(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"data dataframe tibble upon labels applied metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"Dataframe labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"","code":"mc <- metacore::spec_to_metacore(         metacore::metacore_example(\"p21_mock.xlsx\"),         quiet=TRUE         ) #>  #>  Metadata successfully imported #> Loading in metacore object with suppressed warnings dm <- haven::read_xpt(metatools_example(\"dm.xpt\")) set_variable_labels(dm, mc, dataset_name = \"DM\") #> # A tibble: 306 × 25 #>    STUDYID      DOMAIN USUBJID  SUBJID RFSTDTC RFENDTC RFXSTDTC RFXENDTC RFICDTC #>    <chr>        <chr>  <chr>    <chr>  <chr>   <chr>   <chr>    <chr>    <chr>   #>  1 CDISCPILOT01 DM     01-701-… 1015   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  2 CDISCPILOT01 DM     01-701-… 1023   \"2012-… \"2012-… \"2012-0… \"2012-0… \"\"      #>  3 CDISCPILOT01 DM     01-701-… 1028   \"2013-… \"2014-… \"2013-0… \"2014-0… \"\"      #>  4 CDISCPILOT01 DM     01-701-… 1033   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  5 CDISCPILOT01 DM     01-701-… 1034   \"2014-… \"2014-… \"2014-0… \"2014-1… \"\"      #>  6 CDISCPILOT01 DM     01-701-… 1047   \"2013-… \"2013-… \"2013-0… \"2013-0… \"\"      #>  7 CDISCPILOT01 DM     01-701-… 1057   \"\"      \"\"      \"\"       \"\"       \"\"      #>  8 CDISCPILOT01 DM     01-701-… 1097   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  9 CDISCPILOT01 DM     01-701-… 1111   \"2012-… \"2012-… \"2012-0… \"2012-0… \"\"      #> 10 CDISCPILOT01 DM     01-701-… 1115   \"2012-… \"2013-… \"2012-1… \"2013-0… \"\"      #> # ℹ 296 more rows #> # ℹ 16 more variables: RFPENDTC <chr>, DTHDTC <chr>, DTHFL <chr>, SITEID <chr>, #> #   AGE <dbl>, AGEU <chr>, SEX <chr>, RACE <chr>, ETHNIC <chr>, ARMCD <chr>, #> #   ARM <chr>, ACTARMCD <chr>, ACTARM <chr>, COUNTRY <chr>, DMDTC <chr>, #> #   DMDY <dbl>"},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort Rows by Key Sequence — sort_by_key","title":"Sort Rows by Key Sequence — sort_by_key","text":"function sorts dataset according key sequence found metacore object.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort Rows by Key Sequence — sort_by_key","text":"","code":"sort_by_key(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort Rows by Key Sequence — sort_by_key","text":"data Dataset sort metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort Rows by Key Sequence — sort_by_key","text":"dataset ordered columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort Rows by Key Sequence — sort_by_key","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) sort_by_key(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-0159000","dir":"Changelog","previous_headings":"","what":"metatools 0.1.5.9000","title":"metatools 0.1.5.9000","text":"Breaking change: combine_supp() requires QNAM columns source dataset (#64) combine_supp() now allows multiple QNAM values go IDVAR (#63) Allow supp data zero-row combine_supp() (#45)","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-014","dir":"Changelog","previous_headings":"","what":"metatools 0.1.4","title":"metatools 0.1.4","text":"CRAN release: 2023-02-13 correct bug combine_supp() data supp white space. Now trimmed attempting merge Updates made work newest version dplyr","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-013","dir":"Changelog","previous_headings":"","what":"metatools 0.1.3","title":"metatools 0.1.3","text":"CRAN release: 2022-10-06 correct bug build_from_derived() prevented multiple combined removed library calls tests remove floating_pt_correction combine_supp() best never change type main dataset Add message drop_unspec_vars explain variables dropped Correct bug order_cols, still work columns present","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-012","dir":"Changelog","previous_headings":"","what":"metatools 0.1.2","title":"metatools 0.1.2","text":"correct bug combine_supp() data supp different classes IDVARVAL add error combine_supp() report rows supp merged add floating_pt_correction argument combine_supp() used floating point errors IDVARVAL","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-011","dir":"Changelog","previous_headings":"","what":"metatools 0.1.1","title":"metatools 0.1.1","text":"CRAN release: 2022-04-20 Based tester feedback, remove row supplemental qualifiers empty rearranged columns","code":""}]
+[{"path":"https://pharmaverse.github.io/metatools/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"MIT License","title":"MIT License","text":"Copyright (c) 2022 metatools authors Permission hereby granted, free charge, person obtaining copy software associated documentation files (“Software”), deal Software without restriction, including without limitation rights use, copy, modify, merge, publish, distribute, sublicense, /sell copies Software, permit persons Software furnished , subject following conditions: copyright notice permission notice shall included copies substantial portions Software. SOFTWARE PROVIDED “”, WITHOUT WARRANTY KIND, EXPRESS IMPLIED, INCLUDING LIMITED WARRANTIES MERCHANTABILITY, FITNESS PARTICULAR PURPOSE NONINFRINGEMENT. EVENT SHALL AUTHORS COPYRIGHT HOLDERS LIABLE CLAIM, DAMAGES LIABILITY, WHETHER ACTION CONTRACT, TORT OTHERWISE, ARISING , CONNECTION SOFTWARE USE DEALINGS SOFTWARE.","code":""},{"path":"https://pharmaverse.github.io/metatools/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Christina Fillmore. Author, maintainer. Mike Stackhouse. Author. Jana Stoilova. Author. GlaxoSmithKline LLC. Copyright holder, funder. F. Hoffmann-La Roche AG. Copyright holder, funder. Atorus Research LLC. Copyright holder, funder.","code":""},{"path":"https://pharmaverse.github.io/metatools/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Fillmore C, Stackhouse M, Stoilova J (2024). metatools: Enable Use 'metacore' Help Create Check Dataset. R package version 0.1.5.9000,  https://pharmaverse.github.io/metatools/, https://github.com/pharmaverse/metatools.","code":"@Manual{,   title = {metatools: Enable the Use of 'metacore' to Help Create and Check Dataset},   author = {Christina Fillmore and Mike Stackhouse and Jana Stoilova},   year = {2024},   note = {R package version 0.1.5.9000,  https://pharmaverse.github.io/metatools/},   url = {https://github.com/pharmaverse/metatools}, }"},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"metatools-","dir":"","previous_headings":"","what":"Enable the Use of metacore to Help Create and Check Dataset","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"goal metatools enable use metacore objects. Metatools can used build datasets enhance columns existing datasets well checking datasets metadata metacore.","code":""},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"can install latest released version metatools CRAN : current development version GitHub :","code":"install.packages(\"metatools\") devtools::install_github(\"pharmaverse/metatools\")"},{"path":"https://pharmaverse.github.io/metatools/index.html","id":"example","dir":"","previous_headings":"","what":"Example","title":"Enable the Use of metacore to Help Create and Check Dataset","text":"basic example functions build datasets create new columns. Metatools can also used run checks","code":"library(metatools) library(metacore) library(haven) library(dplyr) #>  #> Attaching package: 'dplyr' #> The following objects are masked from 'package:stats': #>  #>     filter, lag #> The following objects are masked from 'package:base': #>  #>     intersect, setdiff, setequal, union load(metacore_example(\"pilot_ADaM.rda\")) metacore <- metacore %>%   select_dataset(\"ADSL\") ds_list <- list(DM = read_xpt(metatools_example(\"dm.xpt\"))) # Pull in columns from DM to be in ADSL adsl <- build_from_derived(metacore, ds_list, predecessor_only = FALSE)  adsl  #> # A tibble: 306 × 13 #>    STUDYID     USUBJID SUBJID SITEID TRT01P   AGE AGEU  RACE  SEX   ETHNIC DTHFL #>    <chr>       <chr>   <chr>  <chr>  <chr>  <dbl> <chr> <chr> <chr> <chr>  <chr> #>  1 CDISCPILOT… 01-701… 1015   701    Place…    63 YEARS WHITE F     HISPA… \"\"    #>  2 CDISCPILOT… 01-701… 1023   701    Place…    64 YEARS WHITE M     HISPA… \"\"    #>  3 CDISCPILOT… 01-701… 1028   701    Xanom…    71 YEARS WHITE M     NOT H… \"\"    #>  4 CDISCPILOT… 01-701… 1033   701    Xanom…    74 YEARS WHITE M     NOT H… \"\"    #>  5 CDISCPILOT… 01-701… 1034   701    Xanom…    77 YEARS WHITE F     NOT H… \"\"    #>  6 CDISCPILOT… 01-701… 1047   701    Place…    85 YEARS WHITE F     NOT H… \"\"    #>  7 CDISCPILOT… 01-701… 1057   701    Scree…    59 YEARS WHITE F     HISPA… \"\"    #>  8 CDISCPILOT… 01-701… 1097   701    Xanom…    68 YEARS WHITE M     NOT H… \"\"    #>  9 CDISCPILOT… 01-701… 1111   701    Xanom…    81 YEARS WHITE F     NOT H… \"\"    #> 10 CDISCPILOT… 01-701… 1115   701    Xanom…    84 YEARS WHITE M     NOT H… \"\"    #> # … with 296 more rows, and 2 more variables: RFSTDTC <chr>, RFENDTC <chr>  # Now we can make some new columns and converting columns into factors adsl %>%    select(USUBJID, AGE, ETHNIC) %>%     create_cat_var(metacore, AGE, AGEGR1, AGEGR1N) %>% #Add an AGEGR1 and AGEGR1N column    convert_var_to_fct(metacore, ETHNIC) # Change ETHNIC to as factor  #> # A tibble: 306 × 5 #>    USUBJID       AGE ETHNIC                 AGEGR1 AGEGR1N #>    <chr>       <dbl> <fct>                  <chr>    <dbl> #>  1 01-701-1015    63 HISPANIC OR LATINO     <65          1 #>  2 01-701-1023    64 HISPANIC OR LATINO     <65          1 #>  3 01-701-1028    71 NOT HISPANIC OR LATINO 65-80        2 #>  4 01-701-1033    74 NOT HISPANIC OR LATINO 65-80        2 #>  5 01-701-1034    77 NOT HISPANIC OR LATINO 65-80        2 #>  6 01-701-1047    85 NOT HISPANIC OR LATINO >80          3 #>  7 01-701-1057    59 HISPANIC OR LATINO     <65          1 #>  8 01-701-1097    68 NOT HISPANIC OR LATINO 65-80        2 #>  9 01-701-1111    81 NOT HISPANIC OR LATINO >80          3 #> 10 01-701-1115    84 NOT HISPANIC OR LATINO >80          3 #> # … with 296 more rows data <- read_xpt(metatools_example(\"adsl.xpt\"))  # Checks can be run on a single column check_ct_col(data, metacore, TRT01PN) # Checks column only contains control terminology #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # … with 244 more rows, and 39 more variables: TRTSDT <date>, TRTEDT <date>, #> #   TRTDURD <dbl>, AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, … # Or across all the columns  check_ct_data(data, metacore) %>%  # Checks control terminology for all columns  check_variables(metacore) # Check all variables in the metadata are in the dataset and there aren't any extra columns  #> No missing or extra variables #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # … with 244 more rows, and 39 more variables: TRTSDT <date>, TRTEDT <date>, #> #   TRTDURD <dbl>, AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply labels to multiple variables on a data frame — add_labels","title":"Apply labels to multiple variables on a data frame — add_labels","text":"function allows user apply several labels dataframe .","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply labels to multiple variables on a data frame — add_labels","text":"","code":"add_labels(data, ...)"},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply labels to multiple variables on a data frame — add_labels","text":"data data.frame tibble ... Named parameters form variable = 'label'","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply labels to multiple variables on a data frame — add_labels","text":"data variable labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply labels to multiple variables on a data frame — add_labels","text":"","code":"add_labels(     mtcars,     mpg = \"Miles Per Gallon\",     cyl = \"Cylinders\"   ) #>                      mpg cyl  disp  hp drat    wt  qsec vs am gear carb #> Mazda RX4           21.0   6 160.0 110 3.90 2.620 16.46  0  1    4    4 #> Mazda RX4 Wag       21.0   6 160.0 110 3.90 2.875 17.02  0  1    4    4 #> Datsun 710          22.8   4 108.0  93 3.85 2.320 18.61  1  1    4    1 #> Hornet 4 Drive      21.4   6 258.0 110 3.08 3.215 19.44  1  0    3    1 #> Hornet Sportabout   18.7   8 360.0 175 3.15 3.440 17.02  0  0    3    2 #> Valiant             18.1   6 225.0 105 2.76 3.460 20.22  1  0    3    1 #> Duster 360          14.3   8 360.0 245 3.21 3.570 15.84  0  0    3    4 #> Merc 240D           24.4   4 146.7  62 3.69 3.190 20.00  1  0    4    2 #> Merc 230            22.8   4 140.8  95 3.92 3.150 22.90  1  0    4    2 #> Merc 280            19.2   6 167.6 123 3.92 3.440 18.30  1  0    4    4 #> Merc 280C           17.8   6 167.6 123 3.92 3.440 18.90  1  0    4    4 #> Merc 450SE          16.4   8 275.8 180 3.07 4.070 17.40  0  0    3    3 #> Merc 450SL          17.3   8 275.8 180 3.07 3.730 17.60  0  0    3    3 #> Merc 450SLC         15.2   8 275.8 180 3.07 3.780 18.00  0  0    3    3 #> Cadillac Fleetwood  10.4   8 472.0 205 2.93 5.250 17.98  0  0    3    4 #> Lincoln Continental 10.4   8 460.0 215 3.00 5.424 17.82  0  0    3    4 #> Chrysler Imperial   14.7   8 440.0 230 3.23 5.345 17.42  0  0    3    4 #> Fiat 128            32.4   4  78.7  66 4.08 2.200 19.47  1  1    4    1 #> Honda Civic         30.4   4  75.7  52 4.93 1.615 18.52  1  1    4    2 #> Toyota Corolla      33.9   4  71.1  65 4.22 1.835 19.90  1  1    4    1 #> Toyota Corona       21.5   4 120.1  97 3.70 2.465 20.01  1  0    3    1 #> Dodge Challenger    15.5   8 318.0 150 2.76 3.520 16.87  0  0    3    2 #> AMC Javelin         15.2   8 304.0 150 3.15 3.435 17.30  0  0    3    2 #> Camaro Z28          13.3   8 350.0 245 3.73 3.840 15.41  0  0    3    4 #> Pontiac Firebird    19.2   8 400.0 175 3.08 3.845 17.05  0  0    3    2 #> Fiat X1-9           27.3   4  79.0  66 4.08 1.935 18.90  1  1    4    1 #> Porsche 914-2       26.0   4 120.3  91 4.43 2.140 16.70  0  1    5    2 #> Lotus Europa        30.4   4  95.1 113 3.77 1.513 16.90  1  1    5    2 #> Ford Pantera L      15.8   8 351.0 264 4.22 3.170 14.50  0  1    5    4 #> Ferrari Dino        19.7   6 145.0 175 3.62 2.770 15.50  0  1    5    6 #> Maserati Bora       15.0   8 301.0 335 3.54 3.570 14.60  0  1    5    8 #> Volvo 142E          21.4   4 121.0 109 4.11 2.780 18.60  1  1    4    2"},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Add Missing Variables — add_variables","title":"Add Missing Variables — add_variables","text":"function adds missing columns according type set metacore object. values new columns missing, typed correctly. unable recognize type metacore object return logical type.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add Missing Variables — add_variables","text":"","code":"add_variables(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add Missing Variables — add_variables","text":"dataset Dataset add columns . variables present columns added. metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add Missing Variables — add_variables","text":"given dataset additional columns added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/add_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add Missing Variables — add_variables","text":"","code":"library(metacore) library(haven) library(dplyr) #>  #> Attaching package: ‘dplyr’ #> The following objects are masked from ‘package:stats’: #>  #>     filter, lag #> The following objects are masked from ‘package:base’: #>  #>     intersect, setdiff, setequal, union load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) %>%    select(-TRTSDT, -TRT01P, -TRT01PN) add_variables(data, spec) #> # A tibble: 254 × 49 #>    STUDYID USUBJID SUBJID SITEID SITEGR1 ARM   TRT01A TRT01AN TRTEDT     TRTDURD #>    <chr>   <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <date>       <dbl> #>  1 CDISCP… 01-701… 1015   701    701     Plac… Place…       0 2014-07-02     182 #>  2 CDISCP… 01-701… 1023   701    701     Plac… Place…       0 2012-09-01      28 #>  3 CDISCP… 01-701… 1028   701    701     Xano… Xanom…      81 2014-01-14     180 #>  4 CDISCP… 01-701… 1033   701    701     Xano… Xanom…      54 2014-03-31      14 #>  5 CDISCP… 01-701… 1034   701    701     Xano… Xanom…      81 2014-12-30     183 #>  6 CDISCP… 01-701… 1047   701    701     Plac… Place…       0 2013-03-09      26 #>  7 CDISCP… 01-701… 1097   701    701     Xano… Xanom…      54 2014-07-09     190 #>  8 CDISCP… 01-701… 1111   701    701     Xano… Xanom…      54 2012-09-16      10 #>  9 CDISCP… 01-701… 1115   701    701     Xano… Xanom…      54 2013-01-23      55 #> 10 CDISCP… 01-701… 1118   701    701     Plac… Place…       0 2014-09-09     182 #> # ℹ 244 more rows #> # ℹ 39 more variables: AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, #> #   AGEGR1N <dbl>, AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, #> #   ETHNIC <chr>, SAFFL <chr>, ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, #> #   COMP16FL <chr>, COMP24FL <chr>, DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, #> #   BMIBL <dbl>, BMIBLGR1 <chr>, HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, #> #   DISONSDT <date>, DURDIS <dbl>, DURDSGR1 <chr>, VISIT1DT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":null,"dir":"Reference","previous_headings":"","what":"Build a dataset from derived — build_from_derived","title":"Build a dataset from derived — build_from_derived","text":"function builds dataset columns just need pulled . variable derivation format 'dataset.variable' pulled create new dataset. multiple datasets present, joined shared `key_seq` variables. columns often called 'Predecessors' ADaM, universal optional specify.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build a dataset from derived — build_from_derived","text":"","code":"build_from_derived(   metacore,   ds_list,   dataset_name = NULL,   predecessor_only = TRUE,   keep = FALSE )"},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build a dataset from derived — build_from_derived","text":"metacore metacore object contains specifications dataset interest. ds_list Named list datasets needed build dataset_name Optional string specify dataset built. needed metacore object provided already subsetted. predecessor_only default `FALSE`, `TRUE` use derivations origin 'Predecessor' keep Boolean determine original columns kept. default `FALSE`, ADaM columns kept. `TRUE` resulting dataset ADaM columns well SDTM column renamed ADaM (.e `ARM` `TRT01P` resulting dataset)","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build a dataset from derived — build_from_derived","text":"dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_from_derived.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Build a dataset from derived — build_from_derived","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") ds_list <- list(DM = read_xpt(metatools_example(\"dm.xpt\"))) build_from_derived(spec, ds_list, predecessor_only = FALSE) #> # A tibble: 306 × 13 #>    STUDYID     USUBJID SUBJID SITEID TRT01P   AGE AGEU  RACE  SEX   ETHNIC DTHFL #>    <chr>       <chr>   <chr>  <chr>  <chr>  <dbl> <chr> <chr> <chr> <chr>  <chr> #>  1 CDISCPILOT… 01-701… 1015   701    Place…    63 YEARS WHITE F     HISPA… \"\"    #>  2 CDISCPILOT… 01-701… 1023   701    Place…    64 YEARS WHITE M     HISPA… \"\"    #>  3 CDISCPILOT… 01-701… 1028   701    Xanom…    71 YEARS WHITE M     NOT H… \"\"    #>  4 CDISCPILOT… 01-701… 1033   701    Xanom…    74 YEARS WHITE M     NOT H… \"\"    #>  5 CDISCPILOT… 01-701… 1034   701    Xanom…    77 YEARS WHITE F     NOT H… \"\"    #>  6 CDISCPILOT… 01-701… 1047   701    Place…    85 YEARS WHITE F     NOT H… \"\"    #>  7 CDISCPILOT… 01-701… 1057   701    Scree…    59 YEARS WHITE F     HISPA… \"\"    #>  8 CDISCPILOT… 01-701… 1097   701    Xanom…    68 YEARS WHITE M     NOT H… \"\"    #>  9 CDISCPILOT… 01-701… 1111   701    Xanom…    81 YEARS WHITE F     NOT H… \"\"    #> 10 CDISCPILOT… 01-701… 1115   701    Xanom…    84 YEARS WHITE M     NOT H… \"\"    #> # ℹ 296 more rows #> # ℹ 2 more variables: RFSTDTC <chr>, RFENDTC <chr>"},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":null,"dir":"Reference","previous_headings":"","what":"Build the observations for a single QNAM — build_qnam","title":"Build the observations for a single QNAM — build_qnam","text":"Build observations single QNAM","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Build the observations for a single QNAM — build_qnam","text":"","code":"build_qnam(dataset, qnam, qlabel, idvar, qeval, qorig)"},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Build the observations for a single QNAM — build_qnam","text":"dataset Input dataset qnam QNAM value qlabel QLABEL value idvar IDVAR variable name (provided string) qeval QEVAL value populated QNAM qorig QORIG value populated QNAM","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/build_qnam.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Build the observations for a single QNAM — build_qnam","text":"Observations structured SUPP format","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Control Terminology for a Single Column — check_ct_col","title":"Check Control Terminology for a Single Column — check_ct_col","text":"function checks column dataset contains control terminology defined metacore specification","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Control Terminology for a Single Column — check_ct_col","text":"","code":"check_ct_col(data, metacore, var, na_acceptable = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Control Terminology for a Single Column — check_ct_col","text":"data Data check metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. var Name variable check na_acceptable Logical value, set `NULL` default, acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE`NA acceptable.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Control Terminology for a Single Column — check_ct_col","text":"Given data column contains control terms. , error   given values column","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_col.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Control Terminology for a Single Column — check_ct_col","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) check_ct_col(data, spec, TRT01PN) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, … check_ct_col(data, spec, \"TRT01PN\") #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Control Terminology for a Dataset — check_ct_data","title":"Check Control Terminology for a Dataset — check_ct_data","text":"function checks columns dataset contains control terminology defined metacore specification","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Control Terminology for a Dataset — check_ct_data","text":"","code":"check_ct_data(data, metacore, na_acceptable = NULL, omit_vars = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Control Terminology for a Dataset — check_ct_data","text":"data Dataset check metacore metacore object contains specifications dataset interest. variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. na_acceptable `logical` value `character` vector, set `NULL` default. `NULL` sets acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE` NA acceptable. set `character` vector specified variables may contain NA values. omit_vars `character` vector indicating variables skipped controlled terminology checks. Internally, `omit_vars` evaluated `na_acceptable`.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Control Terminology for a Dataset — check_ct_data","text":"Given data columns pass. error otherwise","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_ct_data.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Control Terminology for a Dataset — check_ct_data","text":"","code":"library(haven) library(metacore) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\"))  check_ct_data(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, … if (FALSE) { # These examples produce errors: check_ct_data(data, spec, na_acceptable = FALSE) check_ct_data(data, spec, na_acceptable = FALSE, omit_vars = \"DISCONFL\") check_ct_data(data, spec, na_acceptable = c(\"DSRAEFL\", \"DCSREAS\"), omit_vars = \"DISCONFL\") }"},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":null,"dir":"Reference","previous_headings":"","what":"Check Variable Names — check_variables","title":"Check Variable Names — check_variables","text":"function checks variables dataset variables defined metacore specifications. everything matches function return `TRUE` message starting everything expected. additional missing variables error explain discrepancies","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Check Variable Names — check_variables","text":"","code":"check_variables(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Check Variable Names — check_variables","text":"data Dataset check metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Check Variable Names — check_variables","text":"message dataset matches specification dataset, error otherwise","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/check_variables.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Check Variable Names — check_variables","text":"","code":"library(haven) library(metacore) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) check_variables(data, spec) #> No missing or extra variables #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":null,"dir":"Reference","previous_headings":"","what":"Combine the Domain and Supplemental Qualifier — combine_supp","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"Combine Domain Supplemental Qualifier","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"","code":"combine_supp(dataset, supp)"},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"dataset Domain dataset supp Supplemental Qualifier dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"dataset supp variables added ","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/combine_supp.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Combine the Domain and Supplemental Qualifier — combine_supp","text":"","code":"library(safetyData) library(tibble) combine_supp(sdtm_ae, sdtm_suppae)  %>% as_tibble() #> # A tibble: 1,191 × 37 #>    STUDYID DOMAIN USUBJID AESEQ AESPID AETERM AELLT AELLTCD AEDECOD AEPTCD AEHLT #>    <chr>   <chr>  <chr>   <int> <chr>  <chr>  <chr> <lgl>   <chr>   <lgl>  <chr> #>  1 CDISCP… AE     01-701…     1 E07    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  2 CDISCP… AE     01-701…     2 E08    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  3 CDISCP… AE     01-701…     3 E06    DIARR… DIAR… NA      DIARRH… NA     HLT_… #>  4 CDISCP… AE     01-701…     3 E10    ATRIO… AV B… NA      ATRIOV… NA     HLT_… #>  5 CDISCP… AE     01-701…     1 E08    ERYTH… ERYT… NA      ERYTHE… NA     HLT_… #>  6 CDISCP… AE     01-701…     2 E09    ERYTH… LOCA… NA      ERYTHE… NA     HLT_… #>  7 CDISCP… AE     01-701…     4 E08    ERYTH… ERYT… NA      ERYTHE… NA     HLT_… #>  8 CDISCP… AE     01-701…     1 E04    APPLI… APPL… NA      APPLIC… NA     HLT_… #>  9 CDISCP… AE     01-701…     2 E05    APPLI… APPL… NA      APPLIC… NA     HLT_… #> 10 CDISCP… AE     01-701…     1 E08    APPLI… APPL… NA      APPLIC… NA     HLT_… #> # ℹ 1,181 more rows #> # ℹ 26 more variables: AEHLTCD <lgl>, AEHLGT <chr>, AEHLGTCD <lgl>, #> #   AEBODSYS <chr>, AEBDSYCD <lgl>, AESOC <chr>, AESOCCD <lgl>, AESEV <chr>, #> #   AESER <chr>, AEACN <lgl>, AEREL <chr>, AEOUT <chr>, AESCAN <chr>, #> #   AESCONG <chr>, AESDISAB <chr>, AESDTH <chr>, AESHOSP <chr>, AESLIFE <chr>, #> #   AESOD <chr>, AEDTC <chr>, AESTDTC <chr>, AEENDTC <chr>, AESTDY <int>, #> #   AEENDY <int>, IDVARVAL <chr>, AETRTEM <chr>"},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":null,"dir":"Reference","previous_headings":"","what":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"functions takes dataset, metacore object variable name. looks metacore object control terms given variable uses convert variable factor levels. control terminology code list, code column used. function fails control terminology external library","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"","code":"convert_var_to_fct(data, metacore, var)"},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"data dataset containing variable modified metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package var Name variable change","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"Dataset variable changed factor","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/convert_var_to_fct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Convert Variable to Factor with Levels Set by Control Terms — convert_var_to_fct","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") dm <- read_xpt(metatools_example(\"dm.xpt\")) %>%   select(USUBJID, SEX, ARM) # Variable with codelist control terms convert_var_to_fct(dm, spec, SEX) #> # A tibble: 306 × 3 #>    USUBJID     SEX   ARM                  #>    <chr>       <fct> <chr>                #>  1 01-701-1015 F     Placebo              #>  2 01-701-1023 M     Placebo              #>  3 01-701-1028 M     Xanomeline High Dose #>  4 01-701-1033 M     Xanomeline Low Dose  #>  5 01-701-1034 F     Xanomeline High Dose #>  6 01-701-1047 F     Placebo              #>  7 01-701-1057 F     Screen Failure       #>  8 01-701-1097 M     Xanomeline Low Dose  #>  9 01-701-1111 F     Xanomeline Low Dose  #> 10 01-701-1115 M     Xanomeline Low Dose  #> # ℹ 296 more rows # Variable with permitted value control terms convert_var_to_fct(dm, spec, ARM) #> # A tibble: 306 × 3 #>    USUBJID     SEX   ARM                  #>    <chr>       <chr> <fct>                #>  1 01-701-1015 F     Placebo              #>  2 01-701-1023 M     Placebo              #>  3 01-701-1028 M     Xanomeline High Dose #>  4 01-701-1033 M     Xanomeline Low Dose  #>  5 01-701-1034 F     Xanomeline High Dose #>  6 01-701-1047 F     Placebo              #>  7 01-701-1057 F     NA                   #>  8 01-701-1097 M     Xanomeline Low Dose  #>  9 01-701-1111 F     Xanomeline Low Dose  #> 10 01-701-1115 M     Xanomeline Low Dose  #> # ℹ 296 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Categorical Variable from Codelist — create_cat_var","title":"Create Categorical Variable from Codelist — create_cat_var","text":"Using grouping either `decode_var` `code_var` reference variable (`ref_var`) create categorical variable numeric version categorical variable.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Categorical Variable from Codelist — create_cat_var","text":"","code":"create_cat_var(data, metacore, ref_var, grp_var, num_grp_var = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Categorical Variable from Codelist — create_cat_var","text":"data Dataset reference variable metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. ref_var Name variable used reference .e AGE creating AGEGR1 grp_var Name new grouped variable num_grp_var Name new numeric decode grouped variable. optional value given variable created","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Categorical Variable from Codelist — create_cat_var","text":"dataset new column added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_cat_var.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Categorical Variable from Codelist — create_cat_var","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") dm <- read_xpt(metatools_example(\"dm.xpt\")) %>%   select(USUBJID, AGE) # Grouping Column Only create_cat_var(dm, spec, AGE, AGEGR1) #> # A tibble: 306 × 3 #>    USUBJID       AGE AGEGR1 #>    <chr>       <dbl> <chr>  #>  1 01-701-1015    63 <65    #>  2 01-701-1023    64 <65    #>  3 01-701-1028    71 65-80  #>  4 01-701-1033    74 65-80  #>  5 01-701-1034    77 65-80  #>  6 01-701-1047    85 >80    #>  7 01-701-1057    59 <65    #>  8 01-701-1097    68 65-80  #>  9 01-701-1111    81 >80    #> 10 01-701-1115    84 >80    #> # ℹ 296 more rows # Grouping Column and Numeric Decode create_cat_var(dm, spec, AGE, AGEGR1, AGEGR1N) #> # A tibble: 306 × 4 #>    USUBJID       AGE AGEGR1 AGEGR1N #>    <chr>       <dbl> <chr>    <dbl> #>  1 01-701-1015    63 <65          1 #>  2 01-701-1023    64 <65          1 #>  3 01-701-1028    71 65-80        2 #>  4 01-701-1033    74 65-80        2 #>  5 01-701-1034    77 65-80        2 #>  6 01-701-1047    85 >80          3 #>  7 01-701-1057    59 <65          1 #>  8 01-701-1097    68 65-80        2 #>  9 01-701-1111    81 >80          3 #> 10 01-701-1115    84 >80          3 #> # ℹ 296 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Subgroups — create_subgrps","title":"Create Subgroups — create_subgrps","text":"Create Subgroups","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Subgroups — create_subgrps","text":"","code":"create_subgrps(ref_vec, grp_defs)"},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Subgroups — create_subgrps","text":"ref_vec Vector numeric values grp_defs Vector strings groupings defined. Format must either: <00, >=00, 00-00,  00-<00","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Subgroups — create_subgrps","text":"Character vector values subgroups","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_subgrps.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Subgroups — create_subgrps","text":"","code":"create_subgrps(c(1:10), c(\"<2\", \"2-5\", \">5\")) #>  [1] \"<2\"  \"2-5\" \"2-5\" \"2-5\" \"2-5\" \">5\"  \">5\"  \">5\"  \">5\"  \">5\"  create_subgrps(c(1:10), c(\"<=2\", \">2-5\", \">5\")) #>  [1] \"<=2\"  \"<=2\"  \">2-5\" \">2-5\" \">2-5\" \">5\"   \">5\"   \">5\"   \">5\"   \">5\"   create_subgrps(c(1:10), c(\"<2\", \"2-<5\", \">=5\")) #>  [1] \"<2\"   \"2-<5\" \"2-<5\" \"2-<5\" \">=5\"  \">=5\"  \">=5\"  \">=5\"  \">=5\"  \">=5\""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":null,"dir":"Reference","previous_headings":"","what":"Create Variable from Codelist — create_var_from_codelist","title":"Create Variable from Codelist — create_var_from_codelist","text":"functions uses code/decode pairs metacore object create new variables data","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create Variable from Codelist — create_var_from_codelist","text":"","code":"create_var_from_codelist(   data,   metacore,   input_var,   out_var,   decode_to_code = TRUE )"},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create Variable from Codelist — create_var_from_codelist","text":"data Dataset contains input variable metacore metacore object get codelist . `out_var` different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. input_var Name variable translated new column out_var Name output variable. Note: grouping always code codelist associates `out_var` decode_to_code Direction translation. default assumes `input_var` decode column codelist. Set `FALSE` `input_var` code column codelist","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create Variable from Codelist — create_var_from_codelist","text":"Dataset new column added","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/create_var_from_codelist.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create Variable from Codelist — create_var_from_codelist","text":"","code":"library(metacore) library(tibble) data <- tribble(   ~USUBJID, ~VAR1, ~VAR2,   1, \"M\", \"Male\",   2, \"F\", \"Female\",   3, \"F\", \"Female\",   4, \"U\", \"Unknown\",   5, \"M\", \"Male\", ) spec <- spec_to_metacore(metacore_example(\"p21_mock.xlsx\"), quiet = TRUE) #>  #>  Metadata successfully imported #> Loading in metacore object with suppressed warnings create_var_from_codelist(data, spec, VAR2, SEX) #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX   #>     <dbl> <chr> <chr>   <chr> #> 1       1 M     Male    M     #> 2       2 F     Female  F     #> 3       3 F     Female  F     #> 4       4 U     Unknown U     #> 5       5 M     Male    M     create_var_from_codelist(data, spec, \"VAR2\", \"SEX\") #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX   #>     <dbl> <chr> <chr>   <chr> #> 1       1 M     Male    M     #> 2       2 F     Female  F     #> 3       3 F     Female  F     #> 4       4 U     Unknown U     #> 5       5 M     Male    M     create_var_from_codelist(data, spec, VAR1, SEX, decode_to_code = FALSE) #> # A tibble: 5 × 4 #>   USUBJID VAR1  VAR2    SEX     #>     <dbl> <chr> <chr>   <chr>   #> 1       1 M     Male    Male    #> 2       2 F     Female  Female  #> 3       3 F     Female  Female  #> 4       4 U     Unknown Unknown #> 5       5 M     Male    Male"},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":null,"dir":"Reference","previous_headings":"","what":"Drop Unspecified Variables — drop_unspec_vars","title":"Drop Unspecified Variables — drop_unspec_vars","text":"function drops unspecified variables. throw error dataset contain expected variables.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Drop Unspecified Variables — drop_unspec_vars","text":"","code":"drop_unspec_vars(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Drop Unspecified Variables — drop_unspec_vars","text":"dataset Dataset change metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Drop Unspecified Variables — drop_unspec_vars","text":"Dataset specified columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/drop_unspec_vars.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Drop Unspecified Variables — drop_unspec_vars","text":"","code":"library(metacore) library(haven) library(dplyr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) %>%   select(USUBJID, SITEID) %>%   mutate(foo = \"Hello\") drop_unspec_vars(data, spec) #> The following variable(s) were dropped: #>   foo #> # A tibble: 254 × 2 #>    USUBJID     SITEID #>    <chr>       <chr>  #>  1 01-701-1015 701    #>  2 01-701-1023 701    #>  3 01-701-1028 701    #>  4 01-701-1033 701    #>  5 01-701-1034 701    #>  6 01-701-1047 701    #>  7 01-701-1097 701    #>  8 01-701-1111 701    #>  9 01-701-1115 701    #> 10 01-701-1118 701    #> # ℹ 244 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":null,"dir":"Reference","previous_headings":"","what":"Gets vector of control terminology which should be there — get_bad_ct","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"function checks column dataset contains control terminology defined metacore specification. return values found control terminology","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"","code":"get_bad_ct(data, metacore, var, na_acceptable = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"data Data check metacore metacore object get codelist . variable different codelists different datasets metacore object need subsetted using `select_dataset` metacore package. var Name variable check na_acceptable Logical value, set `NULL` default, acceptability missing values based core variable \"Required\" `metacore` object. set `TRUE` pass check values control terminology missing. set `FALSE`NA acceptable.e","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"vector","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/get_bad_ct.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Gets vector of control terminology which should be there — get_bad_ct","text":"","code":"library(haven) library(metacore) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) get_bad_ct(data, spec, \"DISCONFL\") #> character(0) get_bad_ct(data, spec, \"DISCONFL\", na_acceptable = FALSE) #> [1] \"\""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":null,"dir":"Reference","previous_headings":"","what":"Make Supplemental Qualifier — make_supp_qual","title":"Make Supplemental Qualifier — make_supp_qual","text":"Make Supplemental Qualifier","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Make Supplemental Qualifier — make_supp_qual","text":"","code":"make_supp_qual(dataset, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Make Supplemental Qualifier — make_supp_qual","text":"dataset dataset supp pulled metacore subsetted metacore object get supp information . already subsetted `dataset_name` need provided dataset_name optional name dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Make Supplemental Qualifier — make_supp_qual","text":"CDISC formatted SUPP dataset","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/make_supp_qual.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Make Supplemental Qualifier — make_supp_qual","text":"","code":"library(metacore) library(safetyData) library(tibble) load(metacore_example(\"pilot_SDTM.rda\")) spec <- metacore %>% select_dataset(\"AE\") ae <- combine_supp(sdtm_ae, sdtm_suppae) make_supp_qual(ae, spec) %>% as_tibble() #> # A tibble: 1,191 × 10 #>    STUDYID      RDOMAIN USUBJID    IDVAR IDVARVAL QNAM  QLABEL QVAL  QORIG QEVAL #>    <chr>        <chr>   <chr>      <chr>    <int> <chr> <chr>  <chr> <chr> <chr> #>  1 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  2 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #>  3 CDISCPILOT01 AE      01-701-10… AESEQ        3 AETR… TREAT… Y     DERI… CLIN… #>  4 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  5 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #>  6 CDISCPILOT01 AE      01-701-10… AESEQ        3 AETR… TREAT… Y     DERI… CLIN… #>  7 CDISCPILOT01 AE      01-701-10… AESEQ        4 AETR… TREAT… Y     DERI… CLIN… #>  8 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #>  9 CDISCPILOT01 AE      01-701-10… AESEQ        2 AETR… TREAT… Y     DERI… CLIN… #> 10 CDISCPILOT01 AE      01-701-10… AESEQ        1 AETR… TREAT… Y     DERI… CLIN… #> # ℹ 1,181 more rows"},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":null,"dir":"Reference","previous_headings":"","what":"Get path to pkg example — metatools_example","title":"Get path to pkg example — metatools_example","text":"pkg comes bundled number sample files `inst/extdata` directory. function make easy access","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Get path to pkg example — metatools_example","text":"","code":"metatools_example(file = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Get path to pkg example — metatools_example","text":"file Name file. `NULL`, example files listed.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/metatools_example.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Get path to pkg example — metatools_example","text":"","code":"metatools_example() #> [1] \"adsl.xpt\" \"dm.xpt\"   metatools_example(\"dm.xpt\") #> [1] \"/home/runner/work/_temp/Library/metatools/extdata/dm.xpt\""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort Columns by Order — order_cols","title":"Sort Columns by Order — order_cols","text":"function sorts dataset according order found metacore object.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort Columns by Order — order_cols","text":"","code":"order_cols(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort Columns by Order — order_cols","text":"data Dataset sort metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort Columns by Order — order_cols","text":"dataset ordered columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/order_cols.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort Columns by Order — order_cols","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) order_cols(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":null,"dir":"Reference","previous_headings":"","what":"Pipe operator — %>%","title":"Pipe operator — %>%","text":"See magrittr::%>% details.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Pipe operator — %>%","text":"","code":"lhs %>% rhs"},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Pipe operator — %>%","text":"lhs value magrittr placeholder. rhs function call using magrittr semantics.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/pipe.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Pipe operator — %>%","text":"result calling `rhs(lhs)`.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Remove labels to multiple variables on a data frame — remove_labels","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"function allows user removes labels dataframe .","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"","code":"remove_labels(data)"},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"data data.frame tibble","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"data variable labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/remove_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Remove labels to multiple variables on a data frame — remove_labels","text":"","code":"library(haven) data <- read_xpt(metatools_example(\"adsl.xpt\")) remove_labels(data) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":null,"dir":"Reference","previous_headings":"","what":"Apply labels to a data frame using a metacore object — set_variable_labels","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"function leverages metadata available metacore object apply labels data frame.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"","code":"set_variable_labels(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"data dataframe tibble upon labels applied metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"Dataframe labels applied","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/set_variable_labels.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Apply labels to a data frame using a metacore object — set_variable_labels","text":"","code":"mc <- metacore::spec_to_metacore(         metacore::metacore_example(\"p21_mock.xlsx\"),         quiet=TRUE         ) #>  #>  Metadata successfully imported #> Loading in metacore object with suppressed warnings dm <- haven::read_xpt(metatools_example(\"dm.xpt\")) set_variable_labels(dm, mc, dataset_name = \"DM\") #> # A tibble: 306 × 25 #>    STUDYID      DOMAIN USUBJID  SUBJID RFSTDTC RFENDTC RFXSTDTC RFXENDTC RFICDTC #>    <chr>        <chr>  <chr>    <chr>  <chr>   <chr>   <chr>    <chr>    <chr>   #>  1 CDISCPILOT01 DM     01-701-… 1015   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  2 CDISCPILOT01 DM     01-701-… 1023   \"2012-… \"2012-… \"2012-0… \"2012-0… \"\"      #>  3 CDISCPILOT01 DM     01-701-… 1028   \"2013-… \"2014-… \"2013-0… \"2014-0… \"\"      #>  4 CDISCPILOT01 DM     01-701-… 1033   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  5 CDISCPILOT01 DM     01-701-… 1034   \"2014-… \"2014-… \"2014-0… \"2014-1… \"\"      #>  6 CDISCPILOT01 DM     01-701-… 1047   \"2013-… \"2013-… \"2013-0… \"2013-0… \"\"      #>  7 CDISCPILOT01 DM     01-701-… 1057   \"\"      \"\"      \"\"       \"\"       \"\"      #>  8 CDISCPILOT01 DM     01-701-… 1097   \"2014-… \"2014-… \"2014-0… \"2014-0… \"\"      #>  9 CDISCPILOT01 DM     01-701-… 1111   \"2012-… \"2012-… \"2012-0… \"2012-0… \"\"      #> 10 CDISCPILOT01 DM     01-701-… 1115   \"2012-… \"2013-… \"2012-1… \"2013-0… \"\"      #> # ℹ 296 more rows #> # ℹ 16 more variables: RFPENDTC <chr>, DTHDTC <chr>, DTHFL <chr>, SITEID <chr>, #> #   AGE <dbl>, AGEU <chr>, SEX <chr>, RACE <chr>, ETHNIC <chr>, ARMCD <chr>, #> #   ARM <chr>, ACTARMCD <chr>, ACTARM <chr>, COUNTRY <chr>, DMDTC <chr>, #> #   DMDY <dbl>"},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":null,"dir":"Reference","previous_headings":"","what":"Sort Rows by Key Sequence — sort_by_key","title":"Sort Rows by Key Sequence — sort_by_key","text":"function sorts dataset according key sequence found metacore object.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Sort Rows by Key Sequence — sort_by_key","text":"","code":"sort_by_key(data, metacore, dataset_name = NULL)"},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Sort Rows by Key Sequence — sort_by_key","text":"data Dataset sort metacore metacore object contains specifications dataset interest. dataset_name Optional string specify dataset. needed metacore object provided already subsetted.","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Sort Rows by Key Sequence — sort_by_key","text":"dataset ordered columns","code":""},{"path":"https://pharmaverse.github.io/metatools/reference/sort_by_key.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Sort Rows by Key Sequence — sort_by_key","text":"","code":"library(metacore) library(haven) library(magrittr) load(metacore_example(\"pilot_ADaM.rda\")) spec <- metacore %>% select_dataset(\"ADSL\") data <- read_xpt(metatools_example(\"adsl.xpt\")) sort_by_key(data, spec) #> # A tibble: 254 × 49 #>    STUDYID     USUBJID SUBJID SITEID SITEGR1 ARM   TRT01P TRT01PN TRT01A TRT01AN #>    <chr>       <chr>   <chr>  <chr>  <chr>   <chr> <chr>    <dbl> <chr>    <dbl> #>  1 CDISCPILOT… 01-701… 1015   701    701     Plac… Place…       0 Place…       0 #>  2 CDISCPILOT… 01-701… 1023   701    701     Plac… Place…       0 Place…       0 #>  3 CDISCPILOT… 01-701… 1028   701    701     Xano… Xanom…      81 Xanom…      81 #>  4 CDISCPILOT… 01-701… 1033   701    701     Xano… Xanom…      54 Xanom…      54 #>  5 CDISCPILOT… 01-701… 1034   701    701     Xano… Xanom…      81 Xanom…      81 #>  6 CDISCPILOT… 01-701… 1047   701    701     Plac… Place…       0 Place…       0 #>  7 CDISCPILOT… 01-701… 1097   701    701     Xano… Xanom…      54 Xanom…      54 #>  8 CDISCPILOT… 01-701… 1111   701    701     Xano… Xanom…      54 Xanom…      54 #>  9 CDISCPILOT… 01-701… 1115   701    701     Xano… Xanom…      54 Xanom…      54 #> 10 CDISCPILOT… 01-701… 1118   701    701     Plac… Place…       0 Place…       0 #> # ℹ 244 more rows #> # ℹ 39 more variables: TRTSDT <date>, TRTEDT <date>, TRTDURD <dbl>, #> #   AVGDD <dbl>, CUMDOSE <dbl>, AGE <dbl>, AGEGR1 <chr>, AGEGR1N <dbl>, #> #   AGEU <chr>, RACE <chr>, RACEN <dbl>, SEX <chr>, ETHNIC <chr>, SAFFL <chr>, #> #   ITTFL <chr>, EFFFL <chr>, COMP8FL <chr>, COMP16FL <chr>, COMP24FL <chr>, #> #   DISCONFL <chr>, DSRAEFL <chr>, DTHFL <chr>, BMIBL <dbl>, BMIBLGR1 <chr>, #> #   HEIGHTBL <dbl>, WEIGHTBL <dbl>, EDUCLVL <dbl>, DISONSDT <date>, …"},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-0159000","dir":"Changelog","previous_headings":"","what":"metatools 0.1.5.9000","title":"metatools 0.1.5.9000","text":"Breaking change: combine_supp() requires QNAM columns source dataset (#64) combine_supp() now allows multiple QNAM values go IDVAR (#63) Allow supp data zero-row combine_supp() (#45) Enhance check_ct_data() na_acceptable can now accept vector variables. Also add new argument omit_vars control variables skipped controlled terminology checks (#57).","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-014","dir":"Changelog","previous_headings":"","what":"metatools 0.1.4","title":"metatools 0.1.4","text":"CRAN release: 2023-02-13 correct bug combine_supp() data supp white space. Now trimmed attempting merge Updates made work newest version dplyr","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-013","dir":"Changelog","previous_headings":"","what":"metatools 0.1.3","title":"metatools 0.1.3","text":"CRAN release: 2022-10-06 correct bug build_from_derived() prevented multiple combined removed library calls tests remove floating_pt_correction combine_supp() best never change type main dataset Add message drop_unspec_vars explain variables dropped Correct bug order_cols, still work columns present","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-012","dir":"Changelog","previous_headings":"","what":"metatools 0.1.2","title":"metatools 0.1.2","text":"correct bug combine_supp() data supp different classes IDVARVAL add error combine_supp() report rows supp merged add floating_pt_correction argument combine_supp() used floating point errors IDVARVAL","code":""},{"path":"https://pharmaverse.github.io/metatools/news/index.html","id":"metatools-011","dir":"Changelog","previous_headings":"","what":"metatools 0.1.1","title":"metatools 0.1.1","text":"CRAN release: 2022-04-20 Based tester feedback, remove row supplemental qualifiers empty rearranged columns","code":""}]