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<h1>Retrieve antimicrobial drugs from clinical 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 <a href='https://rdrr.io/r/base/list.html'>list</a> with all 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='fl'>FALSE</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 <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></td>
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</tr>
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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="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>A <a href='https://rdrr.io/r/base/list.html'>list</a>, or a <a href='https://rdrr.io/r/base/character.html'>character</a> if <code>collapse</code> is not <code>NULL</code></p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p>Without using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/list.html'>list</a>. This can be convenient to use e.g. inside a <code><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate()</a></code>):<br />
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<code>df %>% mutate(abx = ab_from_text(clinical_text))</code></p>
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<p>The returned AB codes can be transformed to official names, groups, etc. with all <code><a href='ab_property.html'>ab_property()</a></code> functions like <code><a href='ab_property.html'>ab_name()</a></code> and <code><a href='ab_property.html'>ab_group()</a></code>, or by using the <code>translate_ab</code> parameter.</p>
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<p>With using <code>collapse</code>, this function will return a <a href='https://rdrr.io/r/base/character.html'>character</a>:<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 and will throw a note if more results could have been returned.</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><span class='kw'>[[</span><span class='fl'>1</span>]])
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<span class='kw'>if</span> (<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>dplyr</span>)) {
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/reexports.html'>tibble</a></span>(<span class='kw'>clinical_text</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"given cipro and mero"</span>,
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<span class='st'>"started on doxy today"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>abx</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>),
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<span class='kw'>abx2</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
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<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>),
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<span class='kw'>abx3</span> <span class='kw'>=</span> <span class='fu'>ab_from_text</span>(<span class='no'>clinical_text</span>,
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<span class='kw'>collapse</span> <span class='kw'>=</span> <span class='st'>"|"</span>,
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<span class='kw'>translate_ab</span> <span class='kw'>=</span> <span class='st'>"name"</span>))
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}</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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