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(v1.5.0.9001) more informative argument errors

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dr. M.S. (Matthijs) Berends
2021-01-14 14:41:44 +01:00
parent d014955ce0
commit bc00470dca
30 changed files with 126 additions and 74 deletions
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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">1.5.0.9000</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9001</span>
</span>
</div>
@ -236,22 +236,21 @@
<small>Source: <a href='https://github.com/msberends/AMR/blob/master/NEWS.md'><code>NEWS.md</code></a></small>
</div>
<div id="amr-1509000" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9000">
<a href="#amr-1509000" class="anchor"></a>AMR 1.5.0.9000<small> Unreleased </small>
<div id="amr-1509001" class="section level1">
<h1 class="page-header" data-toc-text="1.5.0.9001">
<a href="#amr-1509001" class="anchor"></a>AMR 1.5.0.9001<small> Unreleased </small>
</h1>
<div id="last-updated-12-january-2021" class="section level2">
<div id="last-updated-14-january-2021" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-12-january-2021" class="anchor"></a><small>Last updated: 12 January 2021</small>
<a href="#last-updated-14-january-2021" class="anchor"></a><small>Last updated: 14 January 2021</small>
</h2>
<p><em>Note: the rules of ‘EUCAST Clinical Breakpoints v11.0 (2021)’ will also be added in this next release, to be expected in February/March 2021.</em></p>
<div id="new" class="section level3">
<h3 class="hasAnchor">
<a href="#new" class="anchor"></a>New</h3>
<ul>
<li><p>Support for EUCAST Clinical Breakpoints v11.0 (2021), effective in the <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> function and in <code><a href="../reference/as.rsi.html">as.rsi()</a></code> to interpret MIC and disk diffusion values. This is now the default guideline in this package.</p></li>
<li><p>Function <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> to to get advised dosages of a certain bug-drug combination based on EUCAST dosage data</p></li>
<li><p>Data set <code>dosage</code> to fuel the new <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> function and to make this data available in a structured way</p></li>
<li><p>Function <code><a href="../reference/eucast_rules.html">eucast_dosage()</a></code> to get a <code>data.frame</code> with advised dosages of a certain bug-drug combination, which is based on the new <code>dosage</code> data set</p></li>
<li><p>Function <code><a href="../reference/isolate_identifier.html">isolate_identifier()</a></code>, which will paste a microorganism code with all antimicrobial results of a data set into one string for each row. This is useful to compare isolates, e.g. between institutions or regions, when there is no genotyping available.</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>
@ -284,6 +283,7 @@
<li>Updated the data set <code>microorganisms.codes</code> (which contains popular LIS and WHONET codes for microorganisms) for some species of <em>Mycobacterium</em> that previously incorrectly returned <em>M. africanum</em>
</li>
<li>Added Pretomanid (PMD, J04AK08) to the <code>antibiotics</code> data set</li>
<li>WHONET code <code>"PNV"</code> will now correctly be interpreted as <code>PHN</code>, the antibiotic code for phenoxymethylpenicillin (‘peni V’)</li>
</ul>
</div>
</div>