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first isolate missing dates fix

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dr. M.S. (Matthijs) Berends
2019-05-13 14:56:23 +02:00
parent c4aa92b4a7
commit cc403169c6
15 changed files with 200 additions and 146 deletions
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docs/reference/first_isolate.html
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@ -241,17 +241,17 @@
</div>
<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>,
<pre class="usage"><span class='fu'>first_isolate</span>(<span class='no'>x</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>,
<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>,
<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>,
<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>,
<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>,
<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>)
<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>,
<span class='fu'>filter_first_isolate</span>(<span class='no'>x</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>,
<span class='kw'>col_mo</span> <span class='kw'>=</span> <span class='kw'>NULL</span>, <span class='no'>...</span>)
<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>,
<span class='fu'>filter_first_weighted_isolate</span>(<span class='no'>x</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>, <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>,
<span class='no'>...</span>)</pre>
@ -259,7 +259,7 @@
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>tbl</th>
<th>x</th>
<td><p>a <code>data.frame</code> containing isolates.</p></td>
</tr>
<tr>
@ -341,14 +341,14 @@
<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 <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>
<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>
tbl %&gt;%
mutate(only_firsts = first_isolate(tbl, ...)) %&gt;%
x %&gt;%
mutate(only_firsts = first_isolate(x, ...)) %&gt;%
filter(only_firsts == TRUE) %&gt;%
select(-only_firsts)
</pre><p>The function <code>filter_first_weighted_isolate</code> is essentially equal to:</p><pre>
tbl %&gt;%
x %&gt;%
mutate(keyab = key_antibiotics(.)) %&gt;%
mutate(only_weighted_firsts = first_isolate(tbl,
mutate(only_weighted_firsts = first_isolate(x,
col_keyantibiotics = "keyab", ...)) %&gt;%
filter(only_weighted_firsts == TRUE) %&gt;%
select(-only_weighted_firsts)
@ -416,39 +416,39 @@ To conduct an analysis of antimicrobial resistance, you should only include the
<span class='co'># }</span><span class='co'># NOT RUN {</span>
<span class='co'># set key antibiotics to a new variable</span>
<span class='no'>tbl</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>tbl</span>)
<span class='no'>x</span>$<span class='no'>keyab</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='key_antibiotics.html'>key_antibiotics</a></span>(<span class='no'>x</span>)
<span class='no'>tbl</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>)
<span class='no'>x</span>$<span class='no'>first_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>)
<span class='no'>tbl</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>col_keyantibiotics</span> <span class='kw'>=</span> <span class='st'>'keyab'</span>)
<span class='no'>tbl</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_blood_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Blood'</span>)
<span class='no'>tbl</span>$<span class='no'>first_blood_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_blood_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</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>)
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_urine_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Urine'</span>)
<span class='no'>tbl</span>$<span class='no'>first_urine_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_urine_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</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>)
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_resp_isolate</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</span>,
<span class='kw'>specimen_group</span> <span class='kw'>=</span> <span class='st'>'Respiratory'</span>)
<span class='no'>tbl</span>$<span class='no'>first_resp_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>tbl</span>,
<span class='no'>x</span>$<span class='no'>first_resp_isolate_weighed</span> <span class='kw'>&lt;-</span>
<span class='fu'>first_isolate</span>(<span class='no'>x</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>)
<span class='co'># }</span></pre>