P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 18:01:50 +02:00
Code Releases Activity

(v1.5.0.9016) only_rsi_columns update, documentation

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-02-08 14:18:42 +01:00
parent 8fda473e49
commit 4a84894f79
88 changed files with 654 additions and 375 deletions
Download Patch File Download Diff File Expand all files Collapse all files

23
docs/reference/mdro.html
View File

@ -82,7 +82,7 @@
</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">1.5.0.9014</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -243,33 +243,28 @@
</div>
<pre class="usage"><span class='fu'>mdro</span><span class='op'>(</span>
<span class='va'>x</span>,
x <span class='op'>=</span> <span class='cn'>NULL</span>,
guideline <span class='op'>=</span> <span class='st'>"CMI2012"</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
pct_required_classes <span class='op'>=</span> <span class='fl'>0.5</span>,
combine_SI <span class='op'>=</span> <span class='cn'>TRUE</span>,
verbose <span class='op'>=</span> <span class='cn'>FALSE</span>,
only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>custom_mdro_guideline</span><span class='op'>(</span><span class='va'>...</span>, as_factor <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>brmo</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"BRMO"</span>, only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>brmo</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mrgn</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"MRGN"</span>, only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mrgn</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mdr_tb</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"TB"</span>, only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mdr_tb</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mdr_cmi2012</span><span class='op'>(</span><span class='va'>x</span>, guideline <span class='op'>=</span> <span class='st'>"CMI2012"</span>, only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mdr_cmi2012</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span>
<span class='va'>x</span>,
guideline <span class='op'>=</span> <span class='st'>"EUCAST"</span>,
only_rsi_columns <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/any.html'>any</a></span><span class='op'>(</span><span class='fu'><a href='as.rsi.html'>is.rsi</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></pre>
<span class='fu'>eucast_exceptional_phenotypes</span><span class='op'>(</span>x <span class='op'>=</span> <span class='cn'>NULL</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -304,7 +299,7 @@
</tr>
<tr>
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only antibiotic columns must be detected that were <a href='[rsi]'>transformed to class <code>&lt;rsi&gt;</code></a> on beforehand. Defaults to <code>TRUE</code> if any column of <code>x</code> is of class <code>&lt;rsi&gt;</code>.</p></td>
<td><p>a logical to indicate whether only antibiotic columns must be detected that were <a href='[rsi]'>transformed to class <code>&lt;rsi&gt;</code></a> on beforehand (defaults to <code>FALSE</code>)</p></td>
</tr>
<tr>
<th>...</th>