<metaproperty="og:title"content="Data set with 2000 blood culture isolates of septic patients — septic_patients"/>
<metaproperty="og:description"content="An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This data.frame can be used to practice AMR analysis. For examples, press F1."/>
<p>An anonymised data set containing 2,000 microbial blood culture isolates with their full antibiograms found in septic patients in 4 different hospitals in the Netherlands, between 2001 and 2017. It is true, genuine data. This <code>data.frame</code> can be used to practice AMR analysis. For examples, press F1.</p>
<p>A <code><ahref='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,000 observations and 49 variables:</p><dlclass='dl-horizontal'>
<dt><code>date</code></dt><dd><p>date of receipt at the laboratory</p></dd>
<dt><code>hospital_id</code></dt><dd><p>ID of the hospital, from A to D</p></dd>
<dt><code>ward_icu</code></dt><dd><p>logical to determine if ward is an intensive care unit</p></dd>
<dt><code>ward_clinical</code></dt><dd><p>logical to determine if ward is a regular clinical ward</p></dd>
<dt><code>ward_outpatient</code></dt><dd><p>logical to determine if ward is an outpatient clinic</p></dd>
<dt><code>age</code></dt><dd><p>age of the patient</p></dd>
<dt><code>gender</code></dt><dd><p>gender of the patient</p></dd>
<dt><code>patient_id</code></dt><dd><p>ID of the patient, first 10 characters of an SHA hash containing irretrievable information</p></dd>
<dt><code>mo</code></dt><dd><p>ID of microorganism created with <code><ahref='as.mo.html'>as.mo</a></code>, see also <code><ahref='microorganisms.html'>microorganisms</a></code></p></dd>
<dt><code>peni:rifa</code></dt><dd><p>40 different antibiotics with class <code>rsi</code> (see <code><ahref='as.rsi.html'>as.rsi</a></code>); these column names occur in <code><ahref='antibiotics.html'>antibiotics</a></code> data set and can be translated with <code><ahref='abname.html'>abname</a></code></p></dd>
<spanclass='fu'><ahref='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<spanclass='kw'>first_isolates</span><spanclass='kw'>=</span><spanclass='fu'><ahref='first_isolate.html'>first_isolate</a></span>(<spanclass='no'>my_data</span>, <spanclass='st'>"date"</span>, <spanclass='st'>"patient_id"</span>, <spanclass='st'>"mo"</span>))</div><divclass='output co'>#><spanclass='message'>=> Found <spanstyle='font-weight: bold;'>1,317 first isolates</span><span> (65.9% of total)</span></div><divclass='input'>
<spanclass='kw'>p</span><spanclass='kw'>=</span><spanclass='fu'><ahref='portion.html'>portion_IR</a></span>(<spanclass='no'>amox</span>))</div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 19 results available (minimum set to 30).</span></div><divclass='output co'>#></span><spanstyle='color: #949494;'># A tibble: 4 x 3</span><span>
<spanclass='kw'>p</span><spanclass='kw'>=</span><spanclass='fu'><ahref='portion.html'>portion_IR</a></span>(<spanclass='no'>amcl</span>, <spanclass='kw'>minimum</span><spanclass='kw'>=</span><spanclass='fl'>20</span>))</div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 15 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 16 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 18 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 10 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><divclass='output co'>#><spanclass='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><divclass='output co'>#></span><spanstyle='color: #949494;'># A tibble: 16 x 3</span><span>
<p>Developed by <ahref='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, <ahref='https://www.rug.nl/staff/c.f.luz/'>Christian F. Luz</a>, <ahref='https://www.rug.nl/staff/c.glasner/'>Corinna Glasner</a>, <ahref='https://www.rug.nl/staff/a.w.friedrich/'>Alex W. Friedrich</a>, <ahref='https://www.rug.nl/staff/b.sinha/'>Bhanu N. M. Sinha</a>.</p>
