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(v1.5.0.9016) only_rsi_columns update, documentation

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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
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2
docs/reference/AMR-deprecated.html
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@ -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>

2
docs/reference/AMR.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>

2
docs/reference/WHOCC.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>

2
docs/reference/WHONET.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>

2
docs/reference/ab_from_text.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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>

4
docs/reference/ab_property.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>
@ -317,7 +317,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
<p>The function <code>ab_url()</code> will return the direct URL to the official WHO website. A warning will be returned if the required ATC code is not available.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

2
docs/reference/age.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>

2
docs/reference/age_groups.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>

34
docs/reference/antibiotic_class_selectors.html
View File

@ -83,7 +83,7 @@
</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">1.5.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -244,33 +244,35 @@
</strong></p>
</div>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>ab_class</span><span class='op'>(</span><span class='va'>ab_class</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>carbapenems</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins_1st</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_1st</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_2nd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_3rd</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins_4th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_4th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>cephalosporins_5th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>cephalosporins_5th</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>fluoroquinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>fluoroquinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>glycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>glycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>macrolides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>macrolides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span>
<span class='fu'>oxazolidinones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>NULL</span><span class='op'>)</span></pre>
<span class='fu'>penicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>tetracyclines</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -281,7 +283,7 @@
</tr>
<tr>
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only columns of class <a href='[rsi]'><code>&lt;rsi&gt;</code></a> must be selected. If set to <code>NULL</code> (default), it will be <code>TRUE</code> if any column of the data was <a href='[rsi]'>transformed to class <code>&lt;rsi&gt;</code></a> on beforehand, and <code>FALSE</code> otherwise.</p></td>
<td><p>a logical to indicate whether only columns of class <a href='[rsi]'><code>&lt;rsi&gt;</code></a> must be selected (defaults to <code>FALSE</code>)</p></td>
</tr>
</table>

2
docs/reference/antibiotics.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>

2
docs/reference/as.ab.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>

2
docs/reference/as.disk.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>

2
docs/reference/as.mic.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>

2
docs/reference/as.mo.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>

2
docs/reference/as.rsi.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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>

2
docs/reference/atc_online.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>

2
docs/reference/availability.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>

2
docs/reference/bug_drug_combinations.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>

2
docs/reference/catalogue_of_life.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>

2
docs/reference/catalogue_of_life_version.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>

2
docs/reference/count.html
View File

@ -83,7 +83,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
</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>

2
docs/reference/dosage.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>

6
docs/reference/eucast_rules.html
View File

@ -83,7 +83,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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>
@ -253,7 +253,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
version_breakpoints <span class='op'>=</span> <span class='fl'>11</span>,
version_expertrules <span class='op'>=</span> <span class='fl'>3.2</span>,
ampc_cephalosporin_resistance <span class='op'>=</span> <span class='cn'>NA</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>
@ -296,7 +296,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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>

2
docs/reference/example_isolates.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>

2
docs/reference/example_isolates_unclean.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>

118
docs/reference/filter_ab_class.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">1.5.0.9013</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -247,35 +247,121 @@
<span class='va'>ab_class</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</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'>filter_aminoglycosides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_aminoglycosides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_carbapenems</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_carbapenems</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_1st_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_1st_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_2nd_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_2nd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_3rd_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_3rd_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_4th_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_4th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_5th_cephalosporins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_5th_cephalosporins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_fluoroquinolones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_glycopeptides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_glycopeptides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_macrolides</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_macrolides</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_penicillins</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>filter_oxazolidinones</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_tetracyclines</span><span class='op'>(</span><span class='va'>x</span>, result <span class='op'>=</span> <span class='cn'>NULL</span>, scope <span class='op'>=</span> <span class='st'>"any"</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<span class='fu'>filter_penicillins</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</span>,
only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>filter_tetracyclines</span><span class='op'>(</span>
<span class='va'>x</span>,
result <span class='op'>=</span> <span class='cn'>NULL</span>,
scope <span class='op'>=</span> <span class='st'>"any"</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">
@ -298,7 +384,7 @@
</tr>
<tr>
<th>only_rsi_columns</th>
<td><p>a logical to indicate whether only columns must be included 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 columns must be included 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>

18
docs/reference/first_isolate.html
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@ -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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -243,7 +243,7 @@
</div>
<pre class="usage"><span class='fu'>first_isolate</span><span class='op'>(</span>
<span class='va'>x</span>,
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -264,7 +264,7 @@
<span class='op'>)</span>
<span class='fu'>filter_first_isolate</span><span class='op'>(</span>
<span class='va'>x</span>,
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -272,7 +272,7 @@
<span class='op'>)</span>
<span class='fu'>filter_first_weighted_isolate</span><span class='op'>(</span>
<span class='va'>x</span>,
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_date <span class='op'>=</span> <span class='cn'>NULL</span>,
col_patient_id <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -285,7 +285,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be left blank for automatic determination.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be left blank for automatic determination, see <em>Examples</em>.</p></td>
</tr>
<tr>
<th>col_date</th>
@ -399,7 +399,7 @@
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code><a href='key_antibiotics.html'>key_antibiotics()</a></code> function.</p></li>
<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
@ -422,10 +422,12 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<pre class="examples"><span class='co'># `example_isolates` is a data set available in the AMR package.</span>
<span class='co'># See ?example_isolates.</span>
<span class='co'># basic filtering on first isolates</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='co'># \donttest{</span>
<span class='co'># faster way, only works in R 3.2 and later:</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span>, <span class='op'>]</span>
<span class='co'># get all first Gram-negatives</span>
<span class='va'>example_isolates</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/which.html'>which</a></span><span class='op'>(</span><span class='fu'>first_isolate</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>&amp;</span> <span class='fu'><a href='mo_property.html'>mo_is_gram_negative</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='op'>]</span>

2
docs/reference/g.test.html
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@ -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>

2
docs/reference/get_episode.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>

2
docs/reference/ggplot_rsi.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>

6
docs/reference/guess_ab_col.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>
@ -246,7 +246,7 @@
x <span class='op'>=</span> <span class='cn'>NULL</span>,
search_string <span class='op'>=</span> <span class='cn'>NULL</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='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
@ -266,7 +266,7 @@
</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>
</table>

6
docs/reference/index.html
View File

@ -81,7 +81,7 @@
</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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -526,13 +526,13 @@
</tr><tr>
<td>
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
<p><code><a href="antibiotic_class_selectors.html">ab_class()</a></code> <code><a href="antibiotic_class_selectors.html">aminoglycosides()</a></code> <code><a href="antibiotic_class_selectors.html">carbapenems()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_1st()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_2nd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_3rd()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_4th()</a></code> <code><a href="antibiotic_class_selectors.html">cephalosporins_5th()</a></code> <code><a href="antibiotic_class_selectors.html">fluoroquinolones()</a></code> <code><a href="antibiotic_class_selectors.html">glycopeptides()</a></code> <code><a href="antibiotic_class_selectors.html">macrolides()</a></code> <code><a href="antibiotic_class_selectors.html">oxazolidinones()</a></code> <code><a href="antibiotic_class_selectors.html">penicillins()</a></code> <code><a href="antibiotic_class_selectors.html">tetracyclines()</a></code> </p>
</td>
<td><p>Antibiotic Class Selectors</p></td>
</tr><tr>
<td>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
<p><code><a href="filter_ab_class.html">filter_ab_class()</a></code> <code><a href="filter_ab_class.html">filter_aminoglycosides()</a></code> <code><a href="filter_ab_class.html">filter_carbapenems()</a></code> <code><a href="filter_ab_class.html">filter_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_1st_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_2nd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_3rd_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_4th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_5th_cephalosporins()</a></code> <code><a href="filter_ab_class.html">filter_fluoroquinolones()</a></code> <code><a href="filter_ab_class.html">filter_glycopeptides()</a></code> <code><a href="filter_ab_class.html">filter_macrolides()</a></code> <code><a href="filter_ab_class.html">filter_oxazolidinones()</a></code> <code><a href="filter_ab_class.html">filter_penicillins()</a></code> <code><a href="filter_ab_class.html">filter_tetracyclines()</a></code> </p>
</td>
<td><p>Filter Isolates on Result in Antimicrobial Class</p></td>
</tr><tr>

2
docs/reference/intrinsic_resistant.html
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@ -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>

2
docs/reference/isolate_identifier.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>

2
docs/reference/join.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>

6
docs/reference/key_antibiotics.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>
@ -243,7 +243,7 @@
</div>
<pre class="usage"><span class='fu'>key_antibiotics</span><span class='op'>(</span>
<span class='va'>x</span>,
x <span class='op'>=</span> <span class='cn'>NULL</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
universal_1 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin"</span><span class='op'>)</span>,
universal_2 <span class='op'>=</span> <span class='fu'><a href='guess_ab_col.html'>guess_ab_col</a></span><span class='op'>(</span><span class='va'>x</span>, <span class='st'>"amoxicillin/clavulanic acid"</span><span class='op'>)</span>,
@ -380,7 +380,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<li><p>Using <code>type = "keyantibiotics"</code> and argument <code>ignore_I</code></p>
<p>Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. Read more about this in the <code>key_antibiotics()</code> function.</p></li>
<li><p>Using <code>type = "points"</code> and argument <code>points_threshold</code></p>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which default to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
<p>A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, which defaults to <code>2</code>, an isolate will be (re)selected as a first weighted isolate.</p></li>
</ol>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>

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@ -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>

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@ -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>
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</span>
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@ -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>

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@ -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>

2
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@ -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>

2
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@ -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>

2
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@ -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>

8
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@ -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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>
@ -349,9 +349,9 @@
<p>The short name - <code>mo_shortname()</code> - almost always returns the first character of the genus and the full species, like <code>"E. coli"</code>. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href='as.mo.html'>as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will be considered <em>Escherichia coli</em>. In other words, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Since the top-level of the taxonomy is sometimes referred to as 'kingdom' and sometimes as 'domain', the functions <code>mo_kingdom()</code> and <code>mo_domain()</code> return the exact same results.</p>
<p>The Gram stain - <code>mo_gramstain()</code> - will be determined based on the taxonomic kingdom and phylum. According to Cavalier-Smith (2002, <a href='https://pubmed.ncbi.nlm.nih.gov/11837318'>PMID 11837318</a>), who defined subkingdoms Negibacteria and Posibacteria, only these phyla are Posibacteria: Actinobacteria, Chloroflexi, Firmicutes and Tenericutes. These bacteria are considered Gram-positive - all other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic phylum, class and order. Budding yeasts are true fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). The true yeasts are separated into one main order Saccharomycetales. For all microorganisms that are in one of those two groups, the function will return <code>TRUE</code>. It returns <code>FALSE</code> for all other taxonomic entries.</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output will be <a href='translate.html'>translate</a>d where possible.</p>
<p>Determination of yeasts - <code>mo_is_yeast()</code> - will be based on the taxonomic kingdom and class. <em>Budding yeasts</em> are fungi of the phylum Ascomycetes, class Saccharomycetes (also called Hemiascomycetes). <em>True yeasts</em> are aggregated into the underlying order Saccharomycetales. Thus, for all microorganisms that are fungi and member of the taxonomic class Saccharomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (except when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Intrinsic resistance - <code>mo_is_intrinsic_resistant()</code> - will be determined based on the <a href='intrinsic_resistant.html'>intrinsic_resistant</a> data set, which is based on <a href='https://www.eucast.org/expert_rules_and_intrinsic_resistance/'>'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes' v3.2</a> (2020). The <code>mo_is_intrinsic_resistant()</code> functions can be vectorised over arguments <code>x</code> (input for microorganisms) and over <code>ab</code> (input for antibiotics).</p>
<p>All output <a href='translate.html'>will be translated</a> where possible.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species.</p>
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>

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@ -83,7 +83,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
</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>
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2
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@ -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>
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2
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@ -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>
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</span>
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2
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@ -83,7 +83,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
</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>
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2
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@ -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>

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@ -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>
@ -287,7 +287,7 @@
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x</th>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be left blank for automatic determination.</p></td>
<td><p>a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> containing isolates. Can be left blank for automatic determination, see <em>Examples</em>.</p></td>
</tr>
<tr>
<th>col_ab</th>

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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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</span>
</div>

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@ -83,7 +83,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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<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>
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</span>
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2
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@ -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">1.5.0.9015</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9016</span>
</span>
</div>