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(v0.8.0.9033) antivirals data set, cleanup

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dr. M.S. (Matthijs) Berends
2019-11-18 12:10:47 +01:00
parent 67f3f4387b
commit 267320f15f
97 changed files with 1131 additions and 644 deletions
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docs/news/index.html
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@ -84,7 +84,7 @@
</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">0.8.0.9032</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9033</span>
</span>
</div>
@ -231,11 +231,14 @@
</div>
<div id="amr-0-8-0-9032" class="section level1">
<div id="amr-0-8-0-9033" class="section level1">
<h1 class="page-header">
<a href="#amr-0-8-0-9032" class="anchor"></a>AMR 0.8.0.9032<small> Unreleased </small>
<a href="#amr-0-8-0-9033" class="anchor"></a>AMR 0.8.0.9033<small> Unreleased </small>
</h1>
<p><small>Last updated: 15-Nov-2019</small></p>
<div id="last-updated-18-nov-2019" class="section level2">
<h2 class="hasAnchor">
<a href="#last-updated-18-nov-2019" class="anchor"></a><small>Last updated: 18-Nov-2019</small>
</h2>
<div id="breaking" class="section level3">
<h3 class="hasAnchor">
<a href="#breaking" class="anchor"></a>Breaking</h3>
@ -271,6 +274,7 @@
<li>The new Verbose mode (<code><a href="../reference/mdro.html">mdro(...., verbose = TRUE)</a></code>) returns an informative data set where the reason for MDRO determination is given for every isolate, and an list of the resistant antimicrobial agents</li>
</ul>
</li>
<li><p>Data set <code>antivirals</code>, containing all entries from the ATC J05 group with their DDDs for oral and parenteral treatment</p></li>
</ul>
</div>
<div id="changes" class="section level3">
@ -303,7 +307,7 @@
<li>Improvements for <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>:
<ul>
<li>Fix where <em>Stenotrophomonas maltophilia</em> would always become ceftazidime R (following EUCAST v3.1)</li>
<li>Fix where <em>Leuconostoc</em> and <em>Pediococcus</em> would not always become glyopeptides R</li>
<li>Fix where <em>Leuconostoc</em> and <em>Pediococcus</em> would not always become glycopeptides R</li>
<li>non-EUCAST rules in <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code> are now applied first and not as last anymore. This is to improve the dependency on certain antibiotics for the official EUCAST rules. Please see <code><a href="../reference/eucast_rules.html">?eucast_rules</a></code>.</li>
</ul>
</li>
@ -314,6 +318,7 @@
</li>
<li>Added ATC codes for ceftaroline, ceftobiprole and faropenem and fixed two typos in the <code>antibiotics</code> data set</li>
<li>More robust way of determining valid MIC values</li>
<li>Small changed to the <code>example_isolates</code> data set to better reflect reality</li>
</ul>
</div>
<div id="other" class="section level3">
@ -324,6 +329,7 @@
<li>Added Dr. Sofia Ny as contributor</li>
</ul>
</div>
</div>
</div>
<div id="amr-0-8-0" class="section level1">
<h1 class="page-header">
@ -1385,7 +1391,7 @@ 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-0-8-0-9032">0.8.0.9032</a></li>
<li><a href="#amr-0-8-0-9033">0.8.0.9033</a></li>
<li><a href="#amr-0-8-0">0.8.0</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>