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<meta property="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." />
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<h1>Data set with 2000 blood culture isolates of septic patients</h1>
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<div class="hidden name"><code>septic_patients.Rd</code></div>
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</div>
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<div class="ref-description">
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<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>
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<pre class="usage"><span class='no'>septic_patients</span></pre>
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<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
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<p>A <code><a href='https://www.rdocumentation.org/packages/base/topics/data.frame'>data.frame</a></code> with 2,000 observations and 49 variables:</p><dl class='dl-horizontal'>
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<dt><code>date</code></dt><dd><p>date of receipt at the laboratory</p></dd>
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<dt><code>hospital_id</code></dt><dd><p>ID of the hospital, from A to D</p></dd>
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<dt><code>ward_icu</code></dt><dd><p>logical to determine if ward is an intensive care unit</p></dd>
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<dt><code>ward_clinical</code></dt><dd><p>logical to determine if ward is a regular clinical ward</p></dd>
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<dt><code>ward_outpatient</code></dt><dd><p>logical to determine if ward is an outpatient clinic</p></dd>
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<dt><code>age</code></dt><dd><p>age of the patient</p></dd>
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<dt><code>gender</code></dt><dd><p>gender of the patient</p></dd>
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<dt><code>patient_id</code></dt><dd><p>ID of the patient, first 10 characters of an SHA hash containing irretrievable information</p></dd>
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<dt><code>mo</code></dt><dd><p>ID of microorganism created with <code><a href='as.mo.html'>as.mo</a></code>, see also <code><a href='microorganisms.html'>microorganisms</a></code></p></dd>
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<dt><code>peni:rifa</code></dt><dd><p>40 different antibiotics with class <code>rsi</code> (see <code><a href='as.rsi.html'>as.rsi</a></code>); these column names occur in <code><a href='antibiotics.html'>antibiotics</a></code> data set and can be translated with <code><a href='abname.html'>abname</a></code></p></dd>
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</dl>
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<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
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<pre class="examples"><div class='input'><span class='co'># ----------- #</span>
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<span class='co'># PREPARATION #</span>
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<span class='co'># ----------- #</span>
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<span class='co'># Save this example data set to an object, so we can edit it:</span>
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<span class='no'>my_data</span> <span class='kw'><-</span> <span class='no'>septic_patients</span>
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<span class='co'># load the dplyr package to make data science A LOT easier</span>
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<span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/library'>library</a></span>(<span class='no'>dplyr</span>)
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<span class='co'># Add first isolates to our data set:</span>
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<span class='no'>my_data</span> <span class='kw'><-</span> <span class='no'>my_data</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span>(<span class='kw'>first_isolates</span> <span class='kw'>=</span> <span class='fu'><a href='first_isolate.html'>first_isolate</a></span>(<span class='no'>my_data</span>, <span class='st'>"date"</span>, <span class='st'>"patient_id"</span>, <span class='st'>"mo"</span>))</div><div class='output co'>#> <span class='message'>=> Found <span style='font-weight: bold;'>1,315 first isolates</span><span> (65.8% of total)</span></div><div class='input'>
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<span class='co'># -------- #</span>
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<span class='co'># ANALYSIS #</span>
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<span class='co'># -------- #</span>
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<span class='co'># 1. Get the amoxicillin resistance percentages (p)</span>
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<span class='co'># and numbers (n) of E. coli, divided by hospital:</span>
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<span class='no'>my_data</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>guess_mo</a></span>(<span class='st'>"E. coli"</span>),
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<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='no'>hospital_id</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amox</span>),
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amox</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 19 results available (minimum set to 30).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 4 x 3</span><span>
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#> hospital_id n p
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#> </span><span style='color: #949494;font-style: italic;'><fct></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
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#> </span><span style='color: #BCBCBC;'>1</span><span> A 19 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>2</span><span> B 65 0.477
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#> </span><span style='color: #BCBCBC;'>3</span><span> C 35 0.543
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#> </span><span style='color: #BCBCBC;'>4</span><span> D 93 0.495</div><div class='input'>
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<span class='co'># 2. Get the amoxicillin/clavulanic acid resistance</span>
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<span class='co'># percentages of E. coli, trend over the years:</span>
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<span class='no'>my_data</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>mo</span> <span class='kw'>==</span> <span class='fu'><a href='as.mo.html'>guess_mo</a></span>(<span class='st'>"E. coli"</span>),
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<span class='no'>first_isolates</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/group_by.html'>group_by</a></span>(<span class='kw'>year</span> <span class='kw'>=</span> <span class='fu'><a href='https://www.rdocumentation.org/packages/base/topics/format'>format</a></span>(<span class='no'>date</span>, <span class='st'>"%Y"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='http://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>n</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>amcl</span>),
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<span class='kw'>p</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>amcl</span>, <span class='kw'>minimum</span> <span class='kw'>=</span> <span class='fl'>20</span>))</div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 14 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 15 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 16 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 17 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 18 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 10 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> <span class='warning'>Warning: Introducing NA: only 13 results available (minimum set to 20).</span></div><div class='output co'>#> </span><span style='color: #949494;'># A tibble: 16 x 3</span><span>
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#> year n p
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#> </span><span style='color: #949494;font-style: italic;'><chr></span><span> </span><span style='color: #949494;font-style: italic;'><int></span><span> </span><span style='color: #949494;font-style: italic;'><dbl></span><span>
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#> </span><span style='color: #BCBCBC;'> 1</span><span> 2002 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 2</span><span> 2003 14 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 3</span><span> 2004 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 4</span><span> 2005 15 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 5</span><span> 2006 16 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 6</span><span> 2007 17 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 7</span><span> 2008 17 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 8</span><span> 2009 18 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'> 9</span><span> 2010 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>10</span><span> 2011 21 0.095</span><span style='text-decoration: underline;'>2</span><span>
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#> </span><span style='color: #BCBCBC;'>11</span><span> 2012 10 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>12</span><span> 2013 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>13</span><span> 2014 20 0.2
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#> </span><span style='color: #BCBCBC;'>14</span><span> 2015 13 </span><span style='color: #BB0000;'>NA</span><span>
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#> </span><span style='color: #BCBCBC;'>15</span><span> 2016 21 0.190
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#> </span><span style='color: #BCBCBC;'>16</span><span> 2017 20 0.4 </div></span></pre>
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