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(v0.8.0.9037) complete documentation rewrite

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dr. M.S. (Matthijs) Berends
2019-11-28 23:00:37 +01:00
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docs/reference/first_isolate.html
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</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9036</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.8.0.9037</span>
</span>
</div>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><strong>WHY THIS IS SO IMPORTANT</strong> <br />
To conduct an analysis of antimicrobial resistance, you should only include the first isolate of every patient per episode [1](https://www.ncbi.nlm.nih.gov/pubmed/17304462). 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>
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'>(ref)</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>
<p>All isolates with a microbial ID of <code>NA</code> will be excluded as first isolate.</p>
<p>The functions <code>filter_first_isolate()</code> and <code>filter_first_weighted_isolate()</code> are helper functions to quickly filter on first isolates. The function <code>filter_first_isolate()</code> is essentially equal to:</p><pre> x %&gt;%
mutate(only_firsts = first_isolate(x, ...)) %&gt;%