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<img src="../logo.svg" class="logo" alt=""><h1>Retrieve Antimicrobial Drug Names and Doses from Clinical Text</h1>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/HEAD/R/ab_from_text.R" class="external-link"><code>R/ab_from_text.R</code></a></small>
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<div class="d-none name"><code>ab_from_text.Rd</code></div>
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<div class="ref-description section level2">
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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" class="external-link">list</a> with all antimicrobial drugs, doses and forms of administration found in the texts.</p>
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<div class="section level2">
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<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">ab_from_text</span><span class="op">(</span></span>
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<span> <span class="va">text</span>,</span>
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<span> type <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"drug"</span>, <span class="st">"dose"</span>, <span class="st">"administration"</span><span class="op">)</span>,</span>
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<span> collapse <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> translate_ab <span class="op">=</span> <span class="cn">FALSE</span>,</span>
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<span> thorough_search <span class="op">=</span> <span class="cn">NULL</span>,</span>
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<span> info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
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<span> <span class="va">...</span></span>
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<span><span class="op">)</span></span></code></pre></div>
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</div>
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<div class="section level2">
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<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
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<dl><dt>text</dt>
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<dd><p>text to analyse</p></dd>
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<dt>type</dt>
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<dd><p>type of property to search for, either <code>"drug"</code>, <code>"dose"</code> or <code>"administration"</code>, see <em>Examples</em></p></dd>
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<dt>collapse</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to pass on to <code>paste(, collapse = ...)</code> to only return one <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> per element of <code>text</code>, see <em>Examples</em></p></dd>
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<dt>translate_ab</dt>
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<dd><p>if <code>type = "drug"</code>: 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>. The default is <code>FALSE</code>. Using <code>TRUE</code> is equal to using "name".</p></dd>
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<dt>thorough_search</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to <code>TRUE</code> will take considerably more time than when using <code>FALSE</code>. At default, it will turn <code>TRUE</code> when all input elements contain a maximum of three words.</p></dd>
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<dt>info</dt>
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<dd><p>a <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether a progress bar should be printed - the default is <code>TRUE</code> only in interactive mode</p></dd>
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<dt>...</dt>
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<dd><p>arguments passed on to <code><a href="as.ab.html">as.ab()</a></code></p></dd>
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</dl></div>
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<div class="section level2">
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<h2 id="value">Value<a class="anchor" aria-label="anchor" href="#value"></a></h2>
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<p>A <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>, or a <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> if <code>collapse</code> is not <code>NULL</code></p>
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<div class="section level2">
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<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
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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 searches for the first drug name and will throw a note if more drug names could have been returned. Note: the <code><a href="as.ab.html">as.ab()</a></code> function may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.</p><div class="section">
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<h3 id="argument-type">Argument <code>type</code><a class="anchor" aria-label="anchor" href="#argument-type"></a></h3>
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<p>At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses <code><a href="as.ab.html">as.ab()</a></code> internally, it will correct for misspelling.</p>
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<p>With <code>type = "dose"</code> (or similar, like "dosing", "doses"), all text elements will be searched for <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a> values that are higher than 100 and do not resemble years. The output will be <a href="https://rdrr.io/r/base/numeric.html" class="external-link">numeric</a>. It supports any unit (g, mg, IE, etc.) and multiple values in one clinical text, see <em>Examples</em>.</p>
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<p>With <code>type = "administration"</code> (or abbreviations, like "admin", "adm"), all text elements will be searched for a form of drug administration. It supports the following forms (including common abbreviations): buccal, implant, inhalation, instillation, intravenous, nasal, oral, parenteral, rectal, sublingual, transdermal and vaginal. Abbreviations for oral (such as 'po', 'per os') will become "oral", all values for intravenous (such as 'iv', 'intraven') will become "iv". It supports multiple values in one clinical text, see <em>Examples</em>.</p>
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</div>
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<div class="section">
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<h3 id="argument-collapse">Argument <code>collapse</code><a class="anchor" aria-label="anchor" href="#argument-collapse"></a></h3>
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<p>Without using <code>collapse</code>, this function will return a <a href="https://rdrr.io/r/base/list.html" class="external-link">list</a>. This can be convenient to use e.g. inside a <code><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate()</a></code>):<br><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_*</a></code> functions such as <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> argument.</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" class="external-link">character</a>:<br><code>df %>% mutate(abx = ab_from_text(clinical_text, collapse = "|"))</code></p>
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</div>
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</div>
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<div class="section level2">
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># mind the bad spelling of amoxicillin in this line,</span></span></span>
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<span class="r-in"><span><span class="co"># straight from a true health care record:</span></span></span>
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<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"28/03/2020 regular amoxicilliin 500mg po tid"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] AMX</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] AMX CIP</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span>, type <span class="op">=</span> <span class="st">"dose"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] 500 400</span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
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<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "oral" "iv" </span>
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<span class="r-out co"><span class="r-pr">#></span> </span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span>, collapse <span class="op">=</span> <span class="st">", "</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "AMX, CIP"</span>
|
||
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
|
||
<span class="r-in"><span><span class="co"># if you want to know which antibiotic groups were administered, do e.g.:</span></span></span>
|
||
<span class="r-in"><span><span class="va">abx</span> <span class="op"><-</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="st">"500 mg amoxi po and 400mg cipro iv"</span><span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_group</a></span><span class="op">(</span><span class="va">abx</span><span class="op">[[</span><span class="fl">1</span><span class="op">]</span><span class="op">]</span><span class="op">)</span></span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> [1] "Beta-lactams/penicillins" "Quinolones" </span>
|
||
<span class="r-in"><span></span></span>
|
||
<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a></span><span class="op">(</span>clinical_text <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> <span class="st">"given 400mg cipro and 500 mg amox"</span>,</span></span>
|
||
<span class="r-in"><span> <span class="st">"started on doxy iv today"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
|
||
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/mutate.html" class="external-link">mutate</a></span><span class="op">(</span></span></span>
|
||
<span class="r-in"><span> abx_codes <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"doses"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, type <span class="op">=</span> <span class="st">"admin"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_coll <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>, collapse <span class="op">=</span> <span class="st">"|"</span><span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_coll_names <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span>,</span></span>
|
||
<span class="r-in"><span> translate_ab <span class="op">=</span> <span class="st">"name"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_coll_doses <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"doses"</span>,</span></span>
|
||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span>,</span></span>
|
||
<span class="r-in"><span> abx_coll_admin <span class="op">=</span> <span class="fu">ab_from_text</span><span class="op">(</span><span class="va">clinical_text</span>,</span></span>
|
||
<span class="r-in"><span> type <span class="op">=</span> <span class="st">"admin"</span>,</span></span>
|
||
<span class="r-in"><span> collapse <span class="op">=</span> <span class="st">"|"</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span> <span class="op">)</span></span></span>
|
||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Loading required package: dplyr</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> Attaching package: ‘dplyr’</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:stats’:</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> filter, lag</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:base’:</span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||
<span class="r-msg co"><span class="r-pr">#></span> intersect, setdiff, setequal, union</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 8</span></span>
|
||
<span class="r-out co"><span class="r-pr">#></span> clinical_text abx_codes abx_doses abx_admin abx_coll abx_coll_names</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><list></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> given 400mg cipro and 5… <span style="color: #949494;"><ab [2]></span> <span style="color: #949494;"><dbl [2]></span> <span style="color: #949494;"><chr [1]></span> CIP|AMX Ciprofloxacin…</span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> started on doxy iv today <span style="color: #949494;"><ab [1]></span> <span style="color: #949494;"><dbl [1]></span> <span style="color: #949494;"><chr [1]></span> DOX Doxycycline </span>
|
||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 2 more variables: abx_coll_doses <chr>, abx_coll_admin <chr></span></span>
|
||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||
</code></pre></div>
|
||
</div>
|
||
</main><aside class="col-md-3"><nav id="toc"><h2>On this page</h2>
|
||
</nav></aside></div>
|
||
|
||
|
||
<footer><div class="pkgdown-footer-left">
|
||
<p></p><p><code>AMR</code> (for R). Free and open-source, licenced under the <a target="_blank" href="https://github.com/msberends/AMR/blob/main/LICENSE" class="external-link">GNU General Public License version 2.0 (GPL-2)</a>.<br>Developed at the <a target="_blank" href="https://www.rug.nl" class="external-link">University of Groningen</a> and <a target="_blank" href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a> in The Netherlands.</p>
|
||
</div>
|
||
|
||
<div class="pkgdown-footer-right">
|
||
<p></p><p><a target="_blank" href="https://www.rug.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_rug.svg" style="max-width: 150px;"></a><a target="_blank" href="https://www.umcg.nl" class="external-link"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/logos/logo_umcg.svg" style="max-width: 150px;"></a></p>
|
||
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|
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|
||
</footer></div>
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|
||
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|
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