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added mdr_tb()

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dr. M.S. (Matthijs) Berends
2019-05-23 16:58:59 +02:00
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docs/reference/mdro.html
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@ -80,7 +80,7 @@
</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">0.6.1.9033</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.6.1.9035</span>
</span>
</div>
@ -116,6 +116,13 @@
Predict antimicrobial resistance
</a>
</li>
<li>
<a href="../articles/MDR.html">
<span class="fa fa-skull-crossbones"></span>
Determine multi-drug resistance (MDR)
</a>
</li>
<li>
<a href="../articles/WHONET.html">
<span class="fa fa-globe-americas"></span>
@ -241,14 +248,16 @@
</div>
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='no'>...</span>)
<span class='fu'>brmo</span>(<span class='no'>...</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"nl"</span>)
<span class='fu'>mrgn</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"de"</span>, <span class='no'>...</span>)
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>country</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
<span class='fu'>mdr_tb</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"TB"</span>, <span class='no'>...</span>)
<span class='fu'>eucast_exceptional_phenotypes</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"EUCAST"</span>, <span class='no'>...</span>)</pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -259,7 +268,11 @@
</tr>
<tr>
<th>country</th>
<td><p>country code to determine guidelines. EUCAST rules will be used when left empty, see Details. Should be or a code from the <a href='https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements'>list of ISO 3166-1 alpha-2 country codes</a>. Case-insensitive. Currently supported are <code>de</code> (Germany) and <code>nl</code> (the Netherlands).</p></td>
<td><p>country code to determine guidelines. Should be or a code from the <a href='https://en.wikipedia.org/wiki/ISO_3166-1_alpha-2#Officially_assigned_code_elements'>list of ISO 3166-1 alpha-2 country codes</a>. Case-insensitive.</p></td>
</tr>
<tr>
<th>guideline</th>
<td><p>a specific guideline to mention. For some countries this will be determined automatically, see Details. EUCAST guidelines will be used when left empty, see Details.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -285,7 +298,15 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>When <code>country</code> will be left blank, guidelines will be taken from EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>).</p>
<p>When <code>country</code> is set, the parameter guideline will be ignored as these guidelines will be used:</p>
<ul>
<li><p><code>country = "nl"</code>: Rijksinstituut voor Volksgezondheid en Milieu "WIP-richtlijn BRMO (Bijzonder Resistente Micro-Organismen) [ZKH]" (<a href='https://www.rivm.nl/Documenten_en_publicaties/Professioneel_Praktisch/Richtlijnen/Infectieziekten/WIP_Richtlijnen/WIP_Richtlijnen/Ziekenhuizen/WIP_richtlijn_BRMO_Bijzonder_Resistente_Micro_Organismen_ZKH'>link</a>)</p></li>
</ul>
<p>Please suggest your own country's specific guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<p>Other currently supported guidelines are:</p><ul>
<li><p><code>guideline = "eucast"</code>: EUCAST Expert Rules Version 3.1 "Intrinsic Resistance and Exceptional Phenotypes Tables" (<a href='http://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf'>link</a>)</p></li>
<li><p><code>guideline = "tb"</code>: World Health Organization "Companion handbook to the WHO guidelines for the programmatic management of drug-resistant tuberculosis" (<a href='https://www.who.int/tb/publications/pmdt_companionhandbook/en/'>link</a>)</p></li>
</ul>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>