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(v1.6.0.9014) as.rsi() for numeric values

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dr. M.S. (Matthijs) Berends
2021-04-30 13:18:48 +02:00
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commit e405de079c
18 changed files with 88 additions and 98 deletions
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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">1.6.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.6.0.9014</span>
</span>
</div>
@ -236,13 +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-1609013" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9013">
<a href="#amr-1609013" class="anchor"></a>AMR 1.6.0.9013<small> Unreleased </small>
</h1>
<div id="last-updated-29-april-2021" class="section level2">
<div id="amr-1609014" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0.9014">
<a href="#amr-1609014" class="anchor"></a><small> Unreleased </small><code>AMR</code> 1.6.0.9014</h1>
<div id="last-updated-30-april-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-29-april-2021" class="anchor"></a><small>Last updated: 29 April 2021</small>
<a href="#last-updated-30-april-2021" class="anchor"></a><small>Last updated: 30 April 2021</small>
</h2>
<div id="new" class="section level3">
<h3 class="hasAnchor">
@ -296,14 +295,15 @@
<li>Fixed an installation error on R-3.0</li>
<li>Added <code>info</code> argument to <code><a href="../reference/as.mo.html">as.mo()</a></code> to turn on/off the progress bar</li>
<li>Fixed a bug that <code>col_mo</code> for some functions (esp. <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> and <code><a href="../reference/mdro.html">mdro()</a></code>) could not be column names of the <code>microorganisms</code> data set as it would throw an error</li>
<li>Fix for transforming numeric values to RSI (<code><a href="../reference/as.rsi.html">as.rsi()</a></code>) when the <code>vctrs</code> package is loaded (i.e., when using tidyverse)</li>
<li>Colour fix for using <code><a href="https://rdrr.io/r/graphics/barplot.html">barplot()</a></code> on an RSI class</li>
</ul>
</div>
</div>
</div>
<div id="amr-160" class="section level1">
<h1 class="page-header" data-toc-text="1.6.0">
<a href="#amr-160" class="anchor"></a>AMR 1.6.0<small> 2021-03-14 </small>
</h1>
<a href="#amr-160" class="anchor"></a><small> 2021-03-14 </small><code>AMR</code> 1.6.0</h1>
<div id="new-1" class="section level3">
<h3 class="hasAnchor">
<a href="#new-1" class="anchor"></a>New</h3>
@ -339,7 +339,7 @@
<span class="co">#&gt; Filtering on oxazolidinones: value in column `LNZ` (linezolid) is either "R", "S" or "I"</span></code></pre></div>
</li>
<li><p>Support for custom MDRO guidelines, using the new <code><a href="../reference/mdro.html">custom_mdro_guideline()</a></code> function, please see <code><a href="../reference/mdro.html">mdro()</a></code> for additional info</p></li>
<li><p><code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li><p><code>ggplot()</code> generics for classes <code>&lt;mic&gt;</code> and <code>&lt;disk&gt;</code></p></li>
<li>
<p>Function <code><a href="../reference/mo_property.html">mo_is_yeast()</a></code>, which determines whether a microorganism is a member of the taxonomic class Saccharomycetes or the taxonomic order Saccharomycetales:</p>
<div class="sourceCode" id="cb3"><pre class="downlit sourceCode r">
@ -396,7 +396,7 @@
<li>Plotting of MIC and disk diffusion values now support interpretation colouring if you supply the microorganism and antimicrobial agent</li>
<li>All colours were updated to colour-blind friendly versions for values R, S and I for all plot methods (also applies to tibble printing)</li>
<li>Interpretation of MIC and disk diffusion values to R/SI will now be translated if the system language is German, Dutch or Spanish (see <code>translate</code>)</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code><a href="https://ggplot2.tidyverse.org/reference/ggplot.html">ggplot()</a></code> on any vector of MIC and disk diffusion values</li>
<li>Plotting is now possible with base R using <code><a href="../reference/plot.html">plot()</a></code> and with ggplot2 using <code>ggplot()</code> on any vector of MIC and disk diffusion values</li>
</ul>
</li>
<li>Updated SNOMED codes to US Edition of SNOMED CT from 1 September 2020 and added the source to the help page of the <code>microorganisms</code> data set</li>
@ -440,8 +440,7 @@
</div>
<div id="amr-150" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0">
<a href="#amr-150" class="anchor"></a>AMR 1.5.0<small> 2021-01-06 </small>
</h1>
<a href="#amr-150" class="anchor"></a><small> 2021-01-06 </small><code>AMR</code> 1.5.0</h1>
<div id="new-2" class="section level3">
<h3 class="hasAnchor">
<a href="#new-2" class="anchor"></a>New</h3>
@ -554,8 +553,7 @@
</div>
<div id="amr-140" class="section level1">
<h1 class="page-header" data-toc-text="1.4.0">
<a href="#amr-140" class="anchor"></a>AMR 1.4.0<small> 2020-10-08 </small>
</h1>
<a href="#amr-140" class="anchor"></a><small> 2020-10-08 </small><code>AMR</code> 1.4.0</h1>
<div id="new-3" class="section level3">
<h3 class="hasAnchor">
<a href="#new-3" class="anchor"></a>New</h3>
@ -658,8 +656,7 @@
</div>
<div id="amr-130" class="section level1">
<h1 class="page-header" data-toc-text="1.3.0">
<a href="#amr-130" class="anchor"></a>AMR 1.3.0<small> 2020-07-31 </small>
</h1>
<a href="#amr-130" class="anchor"></a><small> 2020-07-31 </small><code>AMR</code> 1.3.0</h1>
<div id="new-4" class="section level3">
<h3 class="hasAnchor">
<a href="#new-4" class="anchor"></a>New</h3>
@ -741,8 +738,7 @@
</div>
<div id="amr-120" class="section level1">
<h1 class="page-header" data-toc-text="1.2.0">
<a href="#amr-120" class="anchor"></a>AMR 1.2.0<small> 2020-05-28 </small>
</h1>
<a href="#amr-120" class="anchor"></a><small> 2020-05-28 </small><code>AMR</code> 1.2.0</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -805,8 +801,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-110" class="section level1">
<h1 class="page-header" data-toc-text="1.1.0">
<a href="#amr-110" class="anchor"></a>AMR 1.1.0<small> 2020-04-15 </small>
</h1>
<a href="#amr-110" class="anchor"></a><small> 2020-04-15 </small><code>AMR</code> 1.1.0</h1>
<div id="new-5" class="section level3">
<h3 class="hasAnchor">
<a href="#new-5" class="anchor"></a>New</h3>
@ -847,8 +842,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-101" class="section level1">
<h1 class="page-header" data-toc-text="1.0.1">
<a href="#amr-101" class="anchor"></a>AMR 1.0.1<small> 2020-02-23 </small>
</h1>
<a href="#amr-101" class="anchor"></a><small> 2020-02-23 </small><code>AMR</code> 1.0.1</h1>
<div id="changed-7" class="section level3">
<h3 class="hasAnchor">
<a href="#changed-7" class="anchor"></a>Changed</h3>
@ -872,8 +866,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-100" class="section level1">
<h1 class="page-header" data-toc-text="1.0.0">
<a href="#amr-100" class="anchor"></a>AMR 1.0.0<small> 2020-02-17 </small>
</h1>
<a href="#amr-100" class="anchor"></a><small> 2020-02-17 </small><code>AMR</code> 1.0.0</h1>
<p>This software is now out of beta and considered stable. Nonetheless, this package will be developed continually.</p>
<div id="new-6" class="section level3">
<h3 class="hasAnchor">
@ -951,8 +944,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-090" class="section level1">
<h1 class="page-header" data-toc-text="0.9.0">
<a href="#amr-090" class="anchor"></a>AMR 0.9.0<small> 2019-11-29 </small>
</h1>
<a href="#amr-090" class="anchor"></a><small> 2019-11-29 </small><code>AMR</code> 0.9.0</h1>
<div id="breaking-1" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-1" class="anchor"></a>Breaking</h3>
@ -1059,8 +1051,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-080" class="section level1">
<h1 class="page-header" data-toc-text="0.8.0">
<a href="#amr-080" class="anchor"></a>AMR 0.8.0<small> 2019-10-15 </small>
</h1>
<a href="#amr-080" class="anchor"></a><small> 2019-10-15 </small><code>AMR</code> 0.8.0</h1>
<div id="breaking-2" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking-2" class="anchor"></a>Breaking</h3>
@ -1225,8 +1216,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-071" class="section level1">
<h1 class="page-header" data-toc-text="0.7.1">
<a href="#amr-071" class="anchor"></a>AMR 0.7.1<small> 2019-06-23 </small>
</h1>
<a href="#amr-071" class="anchor"></a><small> 2019-06-23 </small><code>AMR</code> 0.7.1</h1>
<div id="new-9" class="section level4">
<h4 class="hasAnchor">
<a href="#new-9" class="anchor"></a>New</h4>
@ -1310,8 +1300,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-070" class="section level1">
<h1 class="page-header" data-toc-text="0.7.0">
<a href="#amr-070" class="anchor"></a>AMR 0.7.0<small> 2019-06-03 </small>
</h1>
<a href="#amr-070" class="anchor"></a><small> 2019-06-03 </small><code>AMR</code> 0.7.0</h1>
<div id="new-10" class="section level4">
<h4 class="hasAnchor">
<a href="#new-10" class="anchor"></a>New</h4>
@ -1407,8 +1396,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-061" class="section level1">
<h1 class="page-header" data-toc-text="0.6.1">
<a href="#amr-061" class="anchor"></a>AMR 0.6.1<small> 2019-03-29 </small>
</h1>
<a href="#amr-061" class="anchor"></a><small> 2019-03-29 </small><code>AMR</code> 0.6.1</h1>
<div id="changed-11" class="section level4">
<h4 class="hasAnchor">
<a href="#changed-11" class="anchor"></a>Changed</h4>
@ -1421,8 +1409,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-060" class="section level1">
<h1 class="page-header" data-toc-text="0.6.0">
<a href="#amr-060" class="anchor"></a>AMR 0.6.0<small> 2019-03-27 </small>
</h1>
<a href="#amr-060" class="anchor"></a><small> 2019-03-27 </small><code>AMR</code> 0.6.0</h1>
<p><strong>New website!</strong></p>
<p>We’ve got a new website: <a href="https://msberends.gitlab.io/AMR/">https://msberends.gitlab.io/AMR</a> (built with the great <a href="https://pkgdown.r-lib.org/"><code>pkgdown</code></a>)</p>
<ul>
@ -1673,8 +1660,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-050" class="section level1">
<h1 class="page-header" data-toc-text="0.5.0">
<a href="#amr-050" class="anchor"></a>AMR 0.5.0<small> 2018-11-30 </small>
</h1>
<a href="#amr-050" class="anchor"></a><small> 2018-11-30 </small><code>AMR</code> 0.5.0</h1>
<div id="new-12" class="section level4">
<h4 class="hasAnchor">
<a href="#new-12" class="anchor"></a>New</h4>
@ -1797,8 +1783,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-040" class="section level1">
<h1 class="page-header" data-toc-text="0.4.0">
<a href="#amr-040" class="anchor"></a>AMR 0.4.0<small> 2018-10-01 </small>
</h1>
<a href="#amr-040" class="anchor"></a><small> 2018-10-01 </small><code>AMR</code> 0.4.0</h1>
<div id="new-13" class="section level4">
<h4 class="hasAnchor">
<a href="#new-13" class="anchor"></a>New</h4>
@ -1946,8 +1931,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-030" class="section level1">
<h1 class="page-header" data-toc-text="0.3.0">
<a href="#amr-030" class="anchor"></a>AMR 0.3.0<small> 2018-08-14 </small>
</h1>
<a href="#amr-030" class="anchor"></a><small> 2018-08-14 </small><code>AMR</code> 0.3.0</h1>
<div id="new-14" class="section level4">
<h4 class="hasAnchor">
<a href="#new-14" class="anchor"></a>New</h4>
@ -2083,8 +2067,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-020" class="section level1">
<h1 class="page-header" data-toc-text="0.2.0">
<a href="#amr-020" class="anchor"></a>AMR 0.2.0<small> 2018-05-03 </small>
</h1>
<a href="#amr-020" class="anchor"></a><small> 2018-05-03 </small><code>AMR</code> 0.2.0</h1>
<div id="new-15" class="section level4">
<h4 class="hasAnchor">
<a href="#new-15" class="anchor"></a>New</h4>
@ -2141,8 +2124,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-011" class="section level1">
<h1 class="page-header" data-toc-text="0.1.1">
<a href="#amr-011" class="anchor"></a>AMR 0.1.1<small> 2018-03-14 </small>
</h1>
<a href="#amr-011" class="anchor"></a><small> 2018-03-14 </small><code>AMR</code> 0.1.1</h1>
<ul>
<li>
<code>EUCAST_rules</code> applies for amoxicillin even if ampicillin is missing</li>
@ -2154,8 +2136,7 @@ This works for all drug combinations, such as ampicillin/sulbactam, ceftazidime/
</div>
<div id="amr-010" class="section level1">
<h1 class="page-header" data-toc-text="0.1.0">
<a href="#amr-010" class="anchor"></a>AMR 0.1.0<small> 2018-02-22 </small>
</h1>
<a href="#amr-010" class="anchor"></a><small> 2018-02-22 </small><code>AMR</code> 0.1.0</h1>
<ul>
<li>First submission to CRAN.</li>
</ul>