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(v1.8.0.9002) as.rsi() cleanup, more informative warnings

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dr. M.S. (Matthijs) Berends
2022-03-02 15:38:55 +01:00
parent 18e8525d10
commit 3b2b2be5f8
35 changed files with 267 additions and 320 deletions
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docs/news/index.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.0.9001</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.0.9002</span>
</span>
</div>
@ -157,13 +157,13 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.0.9001" id="amr-1809001">
<code>AMR</code> 1.8.0.9001<a class="anchor" aria-label="anchor" href="#amr-1809001"></a></h2>
<h2 class="page-header" data-toc-text="1.8.0.9002" id="amr-1809002">
<code>AMR</code> 1.8.0.9002<a class="anchor" aria-label="anchor" href="#amr-1809002"></a></h2>
<div class="section level3">
<h3 id="last-updated-february-1-8-0-9001"><small>Last updated: 26 February 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-february-1-8-0-9001"></a></h3>
<h3 id="last-updated-march-1-8-0-9002"><small>Last updated: 2 March 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-march-1-8-0-9002"></a></h3>
<p>All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
<div class="section level4">
<h4 id="changed-1-8-0-9001">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9001"></a></h4>
<h4 id="changed-1-8-0-9002">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-0-9002"></a></h4>
<ul><li><p>Support for antibiotic interpretations of the MIPS laboratory system: <code>"U"</code> for S (‘susceptible urine’), <code>"D"</code> for I (‘susceptible dose-dependent’)</p></li>
<li>
<p>Improved algorithm of <code><a href="../reference/as.mo.html">as.mo()</a></code>, especially for ignoring non-taxonomic text, such as:</p>
@ -172,9 +172,10 @@
<span class="fu"><a href="../reference/mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"methicillin-resistant S. aureus (MRSA)"</span><span class="op">)</span>
<span class="co">#&gt; [1] "Staphylococcus aureus"</span></code></pre></div>
</li>
<li><p>More informative warning messages</p></li>
</ul></div>
<div class="section level4">
<h4 id="other-1-8-0-9001">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9001"></a></h4>
<h4 id="other-1-8-0-9002">Other<a class="anchor" aria-label="anchor" href="#other-1-8-0-9002"></a></h4>
<ul><li>Fix for unit testing on R 3.3</li>
<li>Fix for size of some image elements, as requested by CRAN</li>
</ul></div>