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Get properties of an antibiotic
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<h1>Retrieve antimicrobial drugs from text</h1>
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<small class="dont-index">Source: <a href='https://gitlab.com/msberends/AMR/blob/master/R/ab_from_text.R'><code>R/ab_from_text.R</code></a></small>
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<div class="hidden name"><code>ab_from_text.Rd</code></div>
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<div class="ref-description">
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<p>Use this function on e.g. clinical texts from health care records. It returns a vector of antimicrobial drugs found in the texts.</p>
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<pre class="usage"><span class='fu'>ab_from_text</span>(<span class='no'>text</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>, <span class='no'>...</span>)</pre>
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<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
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<table class="ref-arguments">
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<colgroup><col class="name" /><col class="desc" /></colgroup>
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<tr>
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<th>text</th>
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<td><p>text to analyse</p></td>
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</tr>
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<tr>
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<th>collapse</th>
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<td><p>character to pass on to <code><a href='https://rdrr.io/r/base/paste.html'>paste(..., collapse = ...)</a></code> to only return one character per element of <code>text</code>, see Examples</p></td>
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</tr>
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<tr>
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<th>translate_ab</th>
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<td><p>a column name of the <a href='antibiotics.html'>antibiotics</a> data set to translate the antibiotic abbreviations to, using <code><a href='ab_property.html'>ab_property()</a></code>. Defaults to "name", which is equal to using <code>TRUE</code>. Use a value <code>FALSE</code>, <code>NULL</code> or <code>NA</code> to prevent translation of the <code><ab></code> code.</p></td>
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<tr>
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<th>...</th>
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<td><p>parameters passed on to <code><a href='as.ab.html'>as.ab()</a></code></p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>To use this for creating a new variable in a data set (e.g. with <code>mutate()</code>), it could be convenient to paste the outcome together with the <code>collapse</code> parameter so every value in your new variable will be a character of length 1:<br />
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<code>df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p>
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<p>This function is also internally used by <code><a href='as.ab.html'>as.ab()</a></code>, although it then only returns the first hit.</p>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><span class='co'># mind the bad spelling of amoxicillin in this line, </span>
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<span class='co'># straight from a true health care record:</span>
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<span class='fu'>ab_from_text</span>(<span class='st'>"28/03/2020 regular amoxicilliin 500mg po tds"</span>)
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<span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>)
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<span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>, <span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>", "</span>)
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<span class='co'># if you want to know which antibiotic groups were administered, check it:</span>
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<span class='no'>abx</span> <span class='kw'><-</span> <span class='fu'>ab_from_text</span>(<span class='st'>"administered amoxi/clav and cipro"</span>)
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<span class='fu'><a href='ab_property.html'>ab_group</a></span>(<span class='no'>abx</span>)</pre>
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<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <a href='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <a href='https://www.rug.nl/staff/a.w.friedrich/'>Alexander W. Friedrich</a>, <a href='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>, <a href='https://www.rug.nl/staff/c.j.albers/'>Casper J. Albers</a>, <a href='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>.</p>
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