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(v0.7.1.9024) eucast_rules() fix, new MOs

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dr. M.S. (Matthijs) Berends
2019-08-06 14:39:22 +02:00
parent 85b62aaf8f
commit 3a1f960f89
23 changed files with 252 additions and 411 deletions
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docs/news/index.html
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@ -78,7 +78,7 @@
</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">0.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9024</span>
</span>
</div>
@ -225,9 +225,9 @@
</div>
<div id="amr-0-7-1-9023" class="section level1">
<div id="amr-0-7-1-9024" class="section level1">
<h1 class="page-header">
<a href="#amr-0-7-1-9023" class="anchor"></a>AMR 0.7.1.9023<small> Unreleased </small>
<a href="#amr-0-7-1-9024" class="anchor"></a>AMR 0.7.1.9024<small> Unreleased </small>
</h1>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
@ -273,15 +273,23 @@
<h3 class="hasAnchor">
<a href="#changed" class="anchor"></a>Changed</h3>
<ul>
<li>Fixed a bug in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> that caused an error when the input was a specific kind of <code>tibble</code>
</li>
<li>Removed class <code>atc</code> - using <code><a href="../reference/AMR-deprecated.html">as.atc()</a></code> is now deprecated in favour of <code><a href="../reference/ab_property.html">ab_atc()</a></code> and this will return a character, not the <code>atc</code> class anymore</li>
<li>Removed deprecated functions <code>abname()</code>, <code>ab_official()</code>, <code>atc_name()</code>, <code>atc_official()</code>, <code>atc_property()</code>, <code>atc_tradenames()</code>, <code>atc_trivial_nl()</code>
</li>
<li>Fix and speed improvement for <code><a href="../reference/mo_property.html">mo_shortname()</a></code>
</li>
<li>Fix for <code><a href="../reference/as.mo.html">as.mo()</a></code> where misspelled input would not be understood</li>
<li>Algorithm improvements for <code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul>
<li>Some misspelled input were not understood</li>
<li>These new trivial names known to the field are now understood: meningococcus, gonococcus, pneumococcus</li>
<li>Added support for unknown yeasts and fungi</li>
</ul>
</li>
<li>Added the newest taxonomic data from the IJSEM journal (now up to date until August 2019)</li>
<li>Fix for using <code>mo_*</code> functions where the coercion uncertainties and failures would not be available through <code><a href="../reference/as.mo.html">mo_uncertainties()</a></code> and <code><a href="../reference/as.mo.html">mo_failures()</a></code> anymore</li>
<li>Deprecated the <code>country</code> parameter of <code><a href="../reference/mdro.html">mdro()</a></code> in favour of the already existing <code>guideline</code> parameter to support multiple guidelines within one country</li>
<li>Fix for frequency tables when creating one directly on a group (using <code>group_by()</code>)</li>
<li>The <code>name</code> of <code>RIF</code> is now Rifampicin instead of Rifampin</li>
<li>The <code>antibiotics</code> data set is now sorted by name</li>
<li>Using verbose mode with <code><a href="../reference/eucast_rules.html">eucast_rules(..., verbose = TRUE)</a></code> returns more informative and readable output</li>
@ -1198,7 +1206,7 @@ Using <code><a href="../reference/as.mo.html">as.mo(..., allow_uncertain = 3)</a
<div id="tocnav">
<h2>Contents</h2>
<ul class="nav nav-pills nav-stacked">
<li><a href="#amr-0-7-1-9023">0.7.1.9023</a></li>
<li><a href="#amr-0-7-1-9024">0.7.1.9024</a></li>
<li><a href="#amr-0-7-1">0.7.1</a></li>
<li><a href="#amr-0-7-0">0.7.0</a></li>
<li><a href="#amr-0-6-1">0.6.1</a></li>