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<h1>Determine first (weighted) isolates</h1>
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<div class="hidden name"><code>first_isolate.Rd</code></div>
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<div class="ref-description">
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<p>Determine first (weighted) isolates of all microorganisms of every patient per episode and (if needed) per specimen type.</p>
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</div>
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<pre class="usage"><span class='fu'>first_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_testcode</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_specimen</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>col_icu</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>episode_days</span> <span class='kw'>=</span> <span class='fl'>365</span>,
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<span class='kw'>testcodes_exclude</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>icu_exclude</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
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<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"keyantibiotics"</span>, <span class='kw'>ignore_I</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>,
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<span class='kw'>points_threshold</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>info</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='no'>...</span>)
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<span class='fu'>filter_first_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
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<span class='fu'>filter_first_weighted_isolate</span>(<span class='no'>tbl</span>, <span class='kw'>col_date</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
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<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>tbl</th>
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<td><p>a <code>data.frame</code> containing isolates.</p></td>
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</tr>
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<tr>
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<th>col_date</th>
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<td><p>column name of the result date (or date that is was received on the lab), defaults to the first column of with a date class</p></td>
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</tr>
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<tr>
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<th>col_patient_id</th>
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<td><p>column name of the unique IDs of the patients, defaults to the first column that starts with 'patient' or 'patid' (case insensitive)</p></td>
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</tr>
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<tr>
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<th>col_mo</th>
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<td><p>column name of the unique IDs of the microorganisms (see <code><a href='as.mo.html'>mo</a></code>), defaults to the first column of class <code>mo</code>. Values will be coerced using <code><a href='as.mo.html'>as.mo</a></code>.</p></td>
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</tr>
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<tr>
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<th>col_testcode</th>
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<td><p>column name of the test codes. Use <code>col_testcode = NULL</code> to <strong>not</strong> exclude certain test codes (like test codes for screening). In that case <code>testcodes_exclude</code> will be ignored.</p></td>
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</tr>
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<tr>
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<th>col_specimen</th>
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<td><p>column name of the specimen type or group</p></td>
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</tr>
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<tr>
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<th>col_icu</th>
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<td><p>column name of the logicals (<code>TRUE</code>/<code>FALSE</code>) whether a ward or department is an Intensive Care Unit (ICU)</p></td>
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</tr>
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<tr>
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<th>col_keyantibiotics</th>
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<td><p>column name of the key antibiotics to determine first <em>weighted</em> isolates, see <code><a href='key_antibiotics.html'>key_antibiotics</a></code>. Defaults to the first column that starts with 'key' followed by 'ab' or 'antibiotics' (case insensitive). Use <code>col_keyantibiotics = FALSE</code> to prevent this.</p></td>
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</tr>
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<tr>
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<th>episode_days</th>
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<td><p>episode in days after which a genus/species combination will be determined as 'first isolate' again</p></td>
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</tr>
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<tr>
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<th>testcodes_exclude</th>
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<td><p>character vector with test codes that should be excluded (case-insensitive)</p></td>
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</tr>
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<tr>
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<th>icu_exclude</th>
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<td><p>logical whether ICU isolates should be excluded (rows with value <code>TRUE</code> in column <code>col_icu</code>)</p></td>
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</tr>
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<tr>
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<th>specimen_group</th>
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<td><p>value in column <code>col_specimen</code> to filter on</p></td>
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</tr>
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<tr>
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<th>type</th>
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<td><p>type to determine weighed isolates; can be <code>"keyantibiotics"</code> or <code>"points"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>ignore_I</th>
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<td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>points_threshold</th>
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<td><p>points until the comparison of key antibiotics will lead to inclusion of an isolate when <code>type = "points"</code>, see Details</p></td>
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</tr>
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<tr>
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<th>info</th>
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<td><p>print progress</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 the <code>first_isolate</code> function</p></td>
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</tr>
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</table>
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<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
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<p>Methodology of this function is based on: <strong>M39 Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data, 4th Edition</strong>, 2014, <em>Clinical and Laboratory Standards Institute (CLSI)</em>. <a href='https://clsi.org/standards/products/microbiology/documents/m39/'>https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p>
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<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
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<p>Logical vector</p>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
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<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
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To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode <a href='https://www.ncbi.nlm.nih.gov/pubmed/17304462'>[1]</a>. If you would not do this, you could easily get an overestimate or underestimate of the resistance of an antibiotic. Imagine that a patient was admitted with an MRSA and that it was found in 5 different blood cultures the following week. The resistance percentage of oxacillin of all <em>S. aureus</em> isolates would be overestimated, because you included this MRSA more than once. It would be <a href='https://en.wikipedia.org/wiki/Selection_bias'>selection bias</a>.</p>
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<p>The function <code>filter_first_isolate</code> is essentially equal to:</p><pre>
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tbl %>%
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mutate(only_firsts = first_isolate(tbl, ...)) %>%
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filter(only_firsts == TRUE) %>%
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select(-only_firsts)
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</pre><p>The function <code>filter_first_weighted_isolate</code> is essentially equal to:</p><pre>
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tbl %>%
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mutate(keyab = key_antibiotics(.)) %>%
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mutate(only_weighted_firsts = first_isolate(tbl,
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col_keyantibiotics = "keyab", ...)) %>%
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filter(only_weighted_firsts == TRUE) %>%
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select(-only_weighted_firsts)
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</pre>
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<h2 class="hasAnchor" id="key-antibiotics"><a class="anchor" href="#key-antibiotics"></a>Key antibiotics</h2>
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<p>There are two ways to determine whether isolates can be included as first <em>weighted</em> isolates which will give generally the same results: <br /></p>
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<p><strong>1. Using</strong> <code>type = "keyantibiotics"</code> <strong>and parameter</strong> <code>ignore_I</code> <br />
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Any difference from S to R (or vice versa) will (re)select an isolate as a first weighted isolate. With <code>ignore_I = FALSE</code>, also differences from I to S|R (or vice versa) will lead to this. This is a reliable method and 30-35 times faster than method 2. <br /></p>
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<p><strong>2. Using</strong> <code>type = "points"</code> <strong>and parameter</strong> <code>points_threshold</code> <br />
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A difference from I to S|R (or vice versa) means 0.5 points, a difference from S to R (or vice versa) means 1 point. When the sum of points exceeds <code>points_threshold</code>, an isolate will be (re)selected as a first weighted isolate.</p>
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<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on our website!</h2>
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<p><img src='figures/logo.png' height=40px style=margin-bottom:5px /> <br />
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On our website <a href='https://msberends.gitlab.io/AMR'>https://msberends.gitlab.io/AMR</a> you can find <a href='https://msberends.gitlab.io/AMR/articles/AMR.html'>a omprehensive tutorial</a> about how to conduct AMR analysis and find <a href='https://msberends.gitlab.io/AMR/reference'>the complete documentation of all functions</a>, which reads a lot easier than in R.</p>
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<h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
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<div class='dont-index'><p><code><a href='key_antibiotics.html'>key_antibiotics</a></code></p></div>
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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'># NOT RUN {</span>
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<span class='co'># septic_patients is a dataset available in the AMR package. It is true, genuine data.</span>
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?<span class='no'>septic_patients</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'># Filter on first isolates:</span>
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<span class='no'>septic_patients</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'>first_isolate</span> <span class='kw'>=</span> <span class='fu'>first_isolate</span>(<span class='no'>.</span>,
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<span class='kw'>col_date</span> <span class='kw'>=</span> <span class='st'>"date"</span>,
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<span class='kw'>col_patient_id</span> <span class='kw'>=</span> <span class='st'>"patient_id"</span>,
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<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='st'>"mo"</span>)) <span class='kw'>%>%</span>
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<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span>(<span class='no'>first_isolate</span> <span class='kw'>==</span> <span class='fl'>TRUE</span>)
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<span class='co'># Which can be shortened to:</span>
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<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_isolate</span>()
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<span class='co'># or for first weighted isolates:</span>
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|
<span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_weighted_isolate</span>()
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<span class='co'># Now let's see if first isolates matter:</span>
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|
<span class='no'>A</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'><a href='https://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='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
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<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
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<span class='no'>B</span> <span class='kw'><-</span> <span class='no'>septic_patients</span> <span class='kw'>%>%</span>
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<span class='fu'>filter_first_weighted_isolate</span>() <span class='kw'>%>%</span> <span class='co'># the 1st isolate filter</span>
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<span class='fu'><a href='https://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='https://dplyr.tidyverse.org/reference/summarise.html'>summarise</a></span>(<span class='kw'>count</span> <span class='kw'>=</span> <span class='fu'><a href='count.html'>n_rsi</a></span>(<span class='no'>gent</span>), <span class='co'># gentamicin availability</span>
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<span class='kw'>resistance</span> <span class='kw'>=</span> <span class='fu'><a href='portion.html'>portion_IR</a></span>(<span class='no'>gent</span>)) <span class='co'># gentamicin resistance</span>
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<span class='co'># Have a look at A and B.</span>
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|
<span class='co'># B is more reliable because every isolate is only counted once.</span>
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<span class='co'># Gentamicin resitance in hospital D appears to be 5.4% higher than</span>
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<span class='co'># when you (erroneously) would have used all isolates!</span>
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<span class='co'>## OTHER EXAMPLES:</span>
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<span class='co'># }</span><span class='co'># NOT RUN {</span>
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<span class='co'># set key antibiotics to a new variable</span>
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<span class='no'>tbl</span>$<span class='no'>keyab</span> <span class='kw'><-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>tbl</span>)
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<span class='no'>tbl</span>$<span class='no'>first_isolate</span> <span class='kw'><-</span>
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<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>)
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<span class='no'>tbl</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'><-</span>
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<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
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<span class='no'>tbl</span>$<span class='no'>first_blood_isolate</span> <span class='kw'><-</span>
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<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>)
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<span class='no'>tbl</span>$<span class='no'>first_blood_isolate_weighed</span> <span class='kw'><-</span>
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<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>,
|
|
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
|
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|
|
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate</span> <span class='kw'><-</span>
|
|
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>)
|
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|
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate_weighed</span> <span class='kw'><-</span>
|
|
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>,
|
|
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
|
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|
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate</span> <span class='kw'><-</span>
|
|
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>)
|
|
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|
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate_weighed</span> <span class='kw'><-</span>
|
|
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
|
|
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>,
|
|
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
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|
<span class='co'># }</span></pre>
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</div>
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<div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
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<h2>Contents</h2>
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<ul class="nav nav-pills nav-stacked">
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<li><a href="#arguments">Arguments</a></li>
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<li><a href="#source">Source</a></li>
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<li><a href="#value">Value</a></li>
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<li><a href="#details">Details</a></li>
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<li><a href="#key-antibiotics">Key antibiotics</a></li>
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<li><a href="#read-more-on-our-website-">Read more on our website!</a></li>
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<li><a href="#see-also">See also</a></li>
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<li><a href="#examples">Examples</a></li>
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