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(v0.7.1.9007) mdro update

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dr. M.S. (Matthijs) Berends
2019-07-04 15:26:07 +02:00
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commit c57ad26c5b
26 changed files with 146 additions and 117 deletions
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2
docs/reference/AMR-deprecated.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

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docs/reference/WHONET.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

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docs/reference/as.mo.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="Latest development version">0.7.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

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docs/reference/as.rsi.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

2
docs/reference/count.html
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@ -81,7 +81,7 @@ count_R and count_IR can be used to count resistant isolates, count_S and count_
</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">0.7.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

8
docs/reference/freq.html
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@ -81,7 +81,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</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">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>
@ -245,14 +245,14 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
<pre class="usage"><span class='fu'>freq</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>),
<span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(),
<span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>,
<span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>), <span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span>
<span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
<span class='fu'>frequency_tbl</span>(<span class='no'>x</span>, <span class='no'>...</span>, <span class='kw'>sort.count</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>nmax</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"max.print.freq"</span>), <span class='kw'>na.rm</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>row.names</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
<span class='kw'>markdown</span> <span class='kw'>=</span> !<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/interactive'>interactive</a></span>(), <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>quote</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
<span class='kw'>header</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>title</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>na</span> <span class='kw'>=</span> <span class='st'>"&lt;NA&gt;"</span>, <span class='kw'>droplevels</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
<span class='kw'>sep</span> <span class='kw'>=</span> <span class='st'>" "</span>, <span class='kw'>decimal.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/options'>getOption</a></span>(<span class='st'>"OutDec"</span>),
<span class='kw'>big.mark</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/ifelse'>ifelse</a></span>(<span class='no'>decimal.mark</span> <span class='kw'>!=</span> <span class='st'>","</span>, <span class='st'>","</span>, <span class='st'>"."</span>))
@ -304,7 +304,7 @@ top_freq can be used to get the top/bottom n items of a frequency table, with co
</tr>
<tr>
<th>quote</th>
<td><p>a logical value indicating whether or not strings should be printed with surrounding quotes</p></td>
<td><p>a logical value indicating whether or not strings should be printed with surrounding quotes. Default is to print them only around characters that are actually numeric values.</p></td>
</tr>
<tr>
<th>header</th>

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docs/reference/ggplot_rsi.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

2
docs/reference/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">0.7.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

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docs/reference/mdro.html
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@ -47,7 +47,7 @@
<script src="../extra.js"></script>
<meta property="og:title" content="Determine multidrug-resistant organisms (MDRO) — mdro" />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines." />
<meta property="og:description" content="Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines." />
<meta property="og:image" content="https://msberends.gitlab.io/AMR/logo.png" />
<meta name="twitter:card" content="summary" />
@ -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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>
@ -237,16 +237,16 @@
<div class="ref-description">
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to country-specific guidelines.</p>
<p>Determine which isolates are multidrug-resistant organisms (MDRO) according to (country-specific) guidelines.</p>
</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'>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>)
<pre class="usage"><span class='fu'>mdro</span>(<span class='no'>x</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'>brmo</span>(<span class='no'>...</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"BRMO"</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'>mrgn</span>(<span class='no'>x</span>, <span class='kw'>guideline</span> <span class='kw'>=</span> <span class='st'>"MRGN"</span>, <span class='no'>...</span>)
<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>)
@ -259,13 +259,9 @@
<th>x</th>
<td><p>table with antibiotic columns, like e.g. <code>AMX</code> and <code>AMC</code></p></td>
</tr>
<tr>
<th>country</th>
<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>
<td><p>a specific guideline to mention, see Details. EUCAST guidelines will be used when left empty, see Details.</p></td>
</tr>
<tr>
<th>col_mo</th>
@ -285,21 +281,26 @@
</tr>
</table>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
<p>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>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>
<p>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>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; Positive</code>.</p>
<p>For TB (<code>mdr_tb()</code>): Ordered factor with levels <code>Negative &lt; Mono-resistance &lt; Poly-resistance &lt; Multidrug resistance &lt; Extensive drug resistance</code>.</p>
<p>For everything else: Ordered factor with levels <code>Negative &lt; Positive, unconfirmed &lt; Positive</code>. The value <code>"Positive, unconfirmed"</code> means that, according to the guideline, it is not entirely sure if the isolate is multi-drug resistant and this should be confirmed with additional (e.g. molecular) tests.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<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>
<p>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>
<li><p><code>guideline = "MRGN"</code>: (work in progress)</p></li>
<li><p><code>guideline = "BRMO"</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-specific) guidelines by letting us know: <a href='https://gitlab.com/msberends/AMR/issues/new'>https://gitlab.com/msberends/AMR/issues/new</a>.</p>
<h2 class="hasAnchor" id="antibiotics"><a class="anchor" href="#antibiotics"></a>Antibiotics</h2>
@ -399,6 +400,8 @@
<ul class="nav nav-pills nav-stacked">
<li><a href="#arguments">Arguments</a></li>
<li><a href="#source">Source</a></li>
<li><a href="#value">Value</a></li>
<li><a href="#details">Details</a></li>

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docs/reference/mo_property.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

2
docs/reference/portion.html
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@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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">0.7.1.9006</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>

2
docs/reference/septic_patients.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="Latest development version">0.7.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9007</span>
</span>
</div>