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(v1.7.1.9016) only_treatable ab selectors

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dr. M.S. (Matthijs) Berends
2021-07-08 22:23:28 +02:00
parent 625a6fb304
commit b228eb1536
25 changed files with 112 additions and 79 deletions
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docs/404.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR//index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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docs/articles/datasets.html
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@ -39,7 +39,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>
@ -192,7 +192,7 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 class="date">07 July 2021</h4>
<h4 class="date">08 July 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>

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docs/articles/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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docs/authors.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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docs/index.html
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@ -42,7 +42,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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docs/news/index.html
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@ -81,7 +81,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>
@ -236,12 +236,12 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1719015" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9015">
<a href="#amr-1719015" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9015</h1>
<div id="last-updated-7-july-2021" class="section level2">
<div id="amr-1719016" class="section level1">
<h1 class="page-header" data-toc-text="1.7.1.9016">
<a href="#amr-1719016" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.7.1.9016</h1>
<div id="last-updated-8-july-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-7-july-2021" class="anchor"></a><small>Last updated: 7 July 2021</small>
<a href="#last-updated-8-july-2021" class="anchor"></a><small>Last updated: 8 July 2021</small>
</h2>
<div id="changed" class="section level3">
<h3 class="hasAnchor">
@ -249,10 +249,11 @@
<ul>
<li>Antibiotic class selectors (see <code><a href="../reference/antibiotic_class_selectors.html">ab_class()</a></code>)
<ul>
<li>They now finally also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
<li>They now also work in R-3.0 and R-3.1, supporting every version of R since 2013</li>
<li>Added more selectors: <code><a href="../reference/antibiotic_class_selectors.html">aminopenicillins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lincosamides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">lipoglycopeptides()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">polymyxins()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">quinolones()</a></code>, <code><a href="../reference/antibiotic_class_selectors.html">streptogramins()</a></code> and <code><a href="../reference/antibiotic_class_selectors.html">ureidopenicillins()</a></code>
</li>
<li>Fix for using selectors multiple times in one call (e.g., using them in <code><a href="https://dplyr.tidyverse.org/reference/filter.html">dplyr::filter()</a></code> and immediately after in <code><a href="https://dplyr.tidyverse.org/reference/select.html">dplyr::select()</a></code>)</li>
<li>Added argument <code>only_treatable</code>, which defaults to <code>TRUE</code> and will exclude drugs that are only for laboratory tests and not for treating patients (such as imipenem/EDTA and gentamicin-high)</li>
</ul>
</li>
<li>Fix for duplicate ATC codes in the <code>antibiotics</code> data set</li>

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docs/pkgdown.yml
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@ -12,7 +12,7 @@ articles:
datasets: datasets.html
resistance_predict: resistance_predict.html
welcome_to_AMR: welcome_to_AMR.html
last_built: 2021-07-07T18:31Z
last_built: 2021-07-08T20:22Z
urls:
reference: https://msberends.github.io/AMR//reference
article: https://msberends.github.io/AMR//articles

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>
@ -242,15 +242,15 @@
<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class, without the need to define the columns or antibiotic abbreviations.</p>
</div>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>aminopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>betalactams</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>betalactams</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>cephalosporins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@ -278,7 +278,7 @@
<span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>polymyxins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>polymyxins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>streptogramins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
@ -299,6 +299,10 @@
<th>only_rsi_columns</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only columns of class <code>&lt;rsi&gt;</code> must be selected (defaults to <code>FALSE</code>), see <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
</tr>
<tr>
<th>only_treatable</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether agents that are only for laboratory tests should be excluded (defaults to <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>

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docs/survey.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9016</span>
</span>
</div>