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(v1.7.1.9024) unit tests

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dr. M.S. (Matthijs) Berends committed 2021-08-17 14:34:11 +02:00
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docs/reference/AMR-deprecated.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/AMR.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/WHOCC.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/WHONET.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/ab_from_text.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/ab_property.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
@@ -262,8 +262,6 @@
snake_case <span class='op'>=</span> <span class='va'>property</span> <span class='op'>==</span> <span class='st'>"name"</span>
<span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_synonyms</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -272,6 +270,8 @@
<span class='fu'>ab_group</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='va'>x</span>, only_first <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_atc_group1</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_atc_group2</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
@@ -319,6 +319,10 @@
<th>snake_case</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether the names should be in so-called <a href='https://en.wikipedia.org/wiki/Snake_case'>snake case</a>: in lower case and all spaces/slashes replaced with an underscore (<code>_</code>)</p></td>
</tr>
<tr>
<th>only_first</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether only the first ATC code must be returned, with giving preference to J0-codes (i.e., the antimicrobial drug group)</p></td>
</tr>
<tr>
<th>administration</th>
<td><p>way of administration, either <code>"oral"</code> or <code>"iv"</code></p></td>
@@ -376,7 +380,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># all properties:</span>
<span class='fu'>ab_name</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "Amoxicillin"</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># J01CA04 (ATC code from the WHO)</span>
<span class='fu'>ab_atc</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># "J01CA04" (ATC code from the WHO)</span>
<span class='fu'>ab_cid</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># 33613 (Compound ID from PubChem)</span>
<span class='fu'>ab_synonyms</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># a list with brand names of amoxicillin</span>
<span class='fu'>ab_tradenames</span><span class='op'>(</span><span class='st'>"AMX"</span><span class='op'>)</span> <span class='co'># same</span>
docs/reference/age.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/age_groups.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/antibiotic_class_selectors.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
@@ -253,63 +253,63 @@
<p>These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by <code>cephalosporins()</code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><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>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><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>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>ab_selector</span><span class='op'>(</span><span class='va'>filter</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>ab_selector</span><span class='op'>(</span><span class='va'>filter</span>, only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>administrable_per_os</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>administrable_per_os</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'>administrable_iv</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>administrable_iv</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'>aminoglycosides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</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>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>aminopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>aminopenicillins</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'>antifungals</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>antifungals</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'>antimycobacterials</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>antimycobacterials</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'>betalactams</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>betalactams</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</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>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</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>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</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</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'>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_1st</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'>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_2nd</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'>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_3rd</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'>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_4th</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'>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'>cephalosporins_5th</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'>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'>fluoroquinolones</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'>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'>glycopeptides</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'>lincosamides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>lincosamides</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'>lipoglycopeptides</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>lipoglycopeptides</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'>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'>macrolides</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'>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'>oxazolidinones</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'>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'>penicillins</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'>polymyxins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span>
<span class='fu'>polymyxins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span>, only_treatable <span class='op'>=</span> <span class='cn'>TRUE</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>streptogramins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>streptogramins</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'>quinolones</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>quinolones</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'>tetracyclines</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='va'>...</span><span class='op'>)</span>
<span class='fu'>trimethoprims</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
<span class='fu'>trimethoprims</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'>ureidopenicillins</span><span class='op'>(</span>only_rsi_columns <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span></code></pre></div>
<span class='fu'>ureidopenicillins</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></code></pre></div>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@@ -326,6 +326,10 @@
<th>only_treatable</th>
<td><p>a <a href='https://rdrr.io/r/base/logical.html'>logical</a> to indicate whether agents that are only for laboratory tests should be excluded (defaults to <code>TRUE</code>), such as gentamicin-high (<code>GEH</code>) and imipenem/EDTA (<code>IPE</code>)</p></td>
</tr>
<tr>
<th>...</th>
<td><p>ignored, only in place to allow future extensions</p></td>
</tr>
<tr>
<th>filter</th>
<td><p>an <a href='https://rdrr.io/r/base/expression.html'>expression</a> to be evaluated in the <a href='antibiotics.html'>antibiotics</a> data set, such as <code>name %like% "trim"</code></p></td>
docs/reference/antibiotics.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/as.ab.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/as.disk.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/as.mic.html
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@@ -93,7 +93,7 @@
</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
docs/reference/as.mo.html
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</button>
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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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
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</button>
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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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
@@ -375,7 +375,7 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><a href='mdro.html'>mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://rdrr.io/r/base/NULL.html'>NULL</a>(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&amp;showdescription=no)), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>c("J01MA12", "S01AE05")</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>c("J01CA01", "S01AA19")</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",'>J01CA04</a>&amp;showdescription=no)), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CA12</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",'>J01CR05</a>&amp;showdescription=no)), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA13</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>c("A01AB22", "J01AA02")</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>c("J01FA10", "S01AA26")</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",'>J01FA09</a>&amp;showdescription=no)), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CR02</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>c("J01MA02", "S01AE03", "S02AA15", "S03AA07")</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>c("J01MA14", "S01AE07")</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>c("J01MA01", "S01AE01", "S02AA16")</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>c("A01AB23", "D10AF07", "J01AA08")</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01FA06</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01CF04</a>), ceftazidime (<code>CAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02&amp;showdescription=no'>J01CF05</a>), ceftriaxone (<code>CRO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04&amp;showdescription=no'>c("J01CE01", "S01AA14")</a>), cefuroxime (<code>CXM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",'>c("D06AX01", "D09AA02", "J01XC01", "S01AA13")</a>&amp;showdescription=no)), cephalexin (<code>LEX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB01&amp;showdescription=no'>J01FF02</a>), cephalothin (<code>CEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB03&amp;showdescription=no'>J04AB02</a>), chloramphenicol (<code>CHL</code>, J01XX09(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&amp;showdescription=no)), ciprofloxacin (<code>CIP</code>, J01XX08(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&amp;showdescription=no)), clarithromycin (<code>CLR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09&amp;showdescription=no'>J01DB04</a>), clindamycin (<code>CLI</code>, J01DC01(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&amp;showdescription=no)), colistin (<code>COL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",'>c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")</a>&amp;showdescription=no)), daptomycin (<code>DAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09&amp;showdescription=no'>J01XE01</a>), doxycycline (<code>DOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",'>J01AA12</a>&amp;showdescription=no)), epicillin (<code>EPC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA07&amp;showdescription=no'>c("J01DC02", "S01AA27")</a>), ertapenem (<code>ETP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03&amp;showdescription=no'>c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")</a>), flucloxacillin (<code>FLC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05&amp;showdescription=no'>c("A07AA10", "J01XB01")</a>), fosfomycin (<code>FOS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01&amp;showdescription=no'>J01DD01</a>), fusidic acid (<code>FUS</code>, J01DD04(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&amp;showdescription=no)), gentamicin (<code>GEN</code>, J01DF01(https://www.whocc.no/atc_ddd_indexLine truncated
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>S01AE08</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01MA02</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01MA23</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01MA04</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01MA08</a>), arbekacin (<code>ARB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB12&amp;showdescription=no'>J01MA19</a>), aspoxicillin (<code>APX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA19&amp;showdescription=no'>J01MA16</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01MA15</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01MA11</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01MA12</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01MA24</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01MA07</a>), bekanamycin (<code>BEK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB13&amp;showdescription=no'>J01MA14</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&amp;showdescription=no'>D10AF05</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&amp;showdescription=no'>J01MA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01MA01</a>), besifloxacin (<code>BES</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=S01AE08&amp;showdescription=no'>J01MA18</a>), biapenem (<code>BIA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH05&amp;showdescription=no'>J01MA03</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01MA17</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01MA10</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01MA21</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01MA09</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01MA05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>P01AA05</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01MA22</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01MA13</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01CA01</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01CA04</a>), cefcapene (<code>CCP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD17&amp;showdescription=no'>J01CA12</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01CR05</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01CA13</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01AA02</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01FA10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01FA09</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01CR02</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01AA08</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01FA06</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01CF04</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01CF05</a>),Line truncated
<h2 class="hasAnchor" id="stable-lifecycle"><a class="anchor" href="#stable-lifecycle"></a>Stable Lifecycle</h2>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</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">1.7.1.9023</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
</span>
</div>
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</tr><tr>
<td>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
<p><code><a href="ab_property.html">ab_name()</a></code> <code><a href="ab_property.html">set_ab_names()</a></code> <code><a href="ab_property.html">ab_cid()</a></code> <code><a href="ab_property.html">ab_synonyms()</a></code> <code><a href="ab_property.html">ab_tradenames()</a></code> <code><a href="ab_property.html">ab_group()</a></code> <code><a href="ab_property.html">ab_atc()</a></code> <code><a href="ab_property.html">ab_atc_group1()</a></code> <code><a href="ab_property.html">ab_atc_group2()</a></code> <code><a href="ab_property.html">ab_loinc()</a></code> <code><a href="ab_property.html">ab_ddd()</a></code> <code><a href="ab_property.html">ab_ddd_units()</a></code> <code><a href="ab_property.html">ab_info()</a></code> <code><a href="ab_property.html">ab_url()</a></code> <code><a href="ab_property.html">ab_property()</a></code> </p>
</td>
<td><p>Get Properties of an Antibiotic</p></td>
</tr><tr>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9023</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9024</span>
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<p>To define antibiotics column names, leave as it is to determine it automatically with <code><a href='guess_ab_col.html'>guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are eligible for the functions <code><a href='eucast_rules.html'>eucast_rules()</a></code> and <code>mdro()</code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <a href='https://www.whocc.no/atc/structure_and_principles/'>ATC code</a>)', sorted alphabetically:</p>
<p>Amikacin (<code>AMK</code>, <a href='https://rdrr.io/r/base/NULL.html'>NULL</a>(https://www.whocc.no/atc_ddd_index/?code=c("D06AX12", "J01GB06", "S01AA21")&amp;showdescription=no)), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>c("J01MA12", "S01AE05")</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>c("J01CA01", "S01AA19")</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CA01",'>J01CA04</a>&amp;showdescription=no)), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01CA12</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01FA10",'>J01CR05</a>&amp;showdescription=no)), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01CA13</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>c("A01AB22", "J01AA02")</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>c("J01FA10", "S01AA26")</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01CE01",'>J01FA09</a>&amp;showdescription=no)), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01CR02</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>c("J01MA02", "S01AE03", "S02AA15", "S03AA07")</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>c("J01MA14", "S01AE07")</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>c("J01MA01", "S01AE01", "S02AA16")</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>c("A01AB23", "D10AF07", "J01AA08")</a>), cefotaxime (<code>CTX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD01&amp;showdescription=no'>J01FA06</a>), cefoxitin (<code>FOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC01&amp;showdescription=no'>J01CF04</a>), ceftazidime (<code>CAZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD02&amp;showdescription=no'>J01CF05</a>), ceftriaxone (<code>CRO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD04&amp;showdescription=no'>c("J01CE01", "S01AA14")</a>), cefuroxime (<code>CXM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("J01DC02",'>c("D06AX01", "D09AA02", "J01XC01", "S01AA13")</a>&amp;showdescription=no)), cephalexin (<code>LEX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB01&amp;showdescription=no'>J01FF02</a>), cephalothin (<code>CEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB03&amp;showdescription=no'>J04AB02</a>), chloramphenicol (<code>CHL</code>, J01XX09(https://www.whocc.no/atc_ddd_index/?code=c("D06AX02", "D10AF03", "G01AA05", "J01BA01", "S01AA01", "S02AA01", "S03AA08")&amp;showdescription=no)), ciprofloxacin (<code>CIP</code>, J01XX08(https://www.whocc.no/atc_ddd_index/?code=c("J01MA02", "S01AE03", "S02AA15", "S03AA07")&amp;showdescription=no)), clarithromycin (<code>CLR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA09&amp;showdescription=no'>J01DB04</a>), clindamycin (<code>CLI</code>, J01DC01(https://www.whocc.no/atc_ddd_index/?code=c("D10AF01", "G01AA10", "J01FF01")&amp;showdescription=no)), colistin (<code>COL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A07AA10",'>c("A01AB13", "D06AA04", "J01AA07", "S01AA09", "S02AA08", "S03AA02")</a>&amp;showdescription=no)), daptomycin (<code>DAP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX09&amp;showdescription=no'>J01XE01</a>), doxycycline (<code>DOX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=c("A01AB22",'>J01AA12</a>&amp;showdescription=no)), epicillin (<code>EPC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA07&amp;showdescription=no'>c("J01DC02", "S01AA27")</a>), ertapenem (<code>ETP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH03&amp;showdescription=no'>c("A07AA05", "J01XB02", "S01AA18", "S02AA11", "S03AA03")</a>), flucloxacillin (<code>FLC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CF05&amp;showdescription=no'>c("A07AA10", "J01XB01")</a>), fosfomycin (<code>FOS</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01XX01&amp;showdescription=no'>J01DD01</a>), fusidic acid (<code>FUS</code>, J01DD04(https://www.whocc.no/atc_ddd_index/?code=c("D06AX01", "D09AA02", "J01XC01", "S01AA13")&amp;showdescription=no)), gentamicin (<code>GEN</code>, J01DF01(https://www.whocc.no/atc_ddd_indexLine truncated
<p>Amikacin (<code>AMK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB06&amp;showdescription=no'>S01AE08</a>), amoxicillin (<code>AMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA04&amp;showdescription=no'>J01MA02</a>), amoxicillin/clavulanic acid (<code>AMC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR02&amp;showdescription=no'>J01MA23</a>), ampicillin (<code>AMP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA01&amp;showdescription=no'>J01MA04</a>), ampicillin/sulbactam (<code>SAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CR01&amp;showdescription=no'>J01MA08</a>), arbekacin (<code>ARB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB12&amp;showdescription=no'>J01MA19</a>), aspoxicillin (<code>APX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA19&amp;showdescription=no'>J01MA16</a>), azidocillin (<code>AZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE04&amp;showdescription=no'>J01MA15</a>), azithromycin (<code>AZM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01FA10&amp;showdescription=no'>J01MA11</a>), azlocillin (<code>AZL</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA09&amp;showdescription=no'>J01MA12</a>), aztreonam (<code>ATM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DF01&amp;showdescription=no'>J01MA24</a>), bacampicillin (<code>BAM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA06&amp;showdescription=no'>J01MA07</a>), bekanamycin (<code>BEK</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01GB13&amp;showdescription=no'>J01MA14</a>), benzathine benzylpenicillin (<code>BNB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE08&amp;showdescription=no'>D10AF05</a>), benzathine phenoxymethylpenicillin (<code>BNP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE10&amp;showdescription=no'>J01MA06</a>), benzylpenicillin (<code>PEN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CE01&amp;showdescription=no'>J01MA01</a>), besifloxacin (<code>BES</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=S01AE08&amp;showdescription=no'>J01MA18</a>), biapenem (<code>BIA</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DH05&amp;showdescription=no'>J01MA03</a>), carbenicillin (<code>CRB</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA03&amp;showdescription=no'>J01MA17</a>), carindacillin (<code>CRN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01CA05&amp;showdescription=no'>J01MA10</a>), cefacetrile (<code>CAC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB10&amp;showdescription=no'>J01MA21</a>), cefaclor (<code>CEC</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC04&amp;showdescription=no'>J01MA09</a>), cefadroxil (<code>CFR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB05&amp;showdescription=no'>J01MA05</a>), cefaloridine (<code>RID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB02&amp;showdescription=no'>P01AA05</a>), cefamandole (<code>MAN</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC03&amp;showdescription=no'>J01MA22</a>), cefatrizine (<code>CTZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB07&amp;showdescription=no'>J01MA13</a>), cefazedone (<code>CZD</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB06&amp;showdescription=no'>J01CA01</a>), cefazolin (<code>CZO</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DB04&amp;showdescription=no'>J01CA04</a>), cefcapene (<code>CCP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD17&amp;showdescription=no'>J01CA12</a>), cefdinir (<code>CDR</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD15&amp;showdescription=no'>J01CR05</a>), cefditoren (<code>DIT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD16&amp;showdescription=no'>J01CA13</a>), cefepime (<code>FEP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DE01&amp;showdescription=no'>J01AA02</a>), cefetamet (<code>CAT</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD10&amp;showdescription=no'>J01FA10</a>), cefixime (<code>CFM</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD08&amp;showdescription=no'>J01FA09</a>), cefmenoxime (<code>CMX</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD05&amp;showdescription=no'>J01CR02</a>), cefmetazole (<code>CMZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC09&amp;showdescription=no'>J01AA08</a>), cefodizime (<code>DIZ</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD09&amp;showdescription=no'>J01FA06</a>), cefonicid (<code>CID</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DC06&amp;showdescription=no'>J01CF04</a>), cefoperazone (<code>CFP</code>, <a href='https://www.whocc.no/atc_ddd_index/?code=J01DD12&amp;showdescription=no'>J01CF05</a>),Line truncated
<h2 class="hasAnchor" id="interpretation-of-r-and-s-i"><a class="anchor" href="#interpretation-of-r-and-s-i"></a>Interpretation of R and S/I</h2>
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<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
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docs/reference/random.html
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docs/reference/resistance_predict.html
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docs/reference/rsi_translation.html
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docs/reference/skewness.html
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docs/reference/translate.html
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@@ -93,7 +93,7 @@
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