P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-12 17:01:57 +02:00
Code Releases Activity

(v0.7.1.9004) atc class removal

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2019-06-27 11:57:45 +02:00
parent 6013fbefae
commit 65c6702b21
49 changed files with 393 additions and 706 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
docs/reference/portion.html
View File

@ -81,7 +81,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</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">0.7.1.9003</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">0.7.1.9004</span>
</span>
</div>
@ -283,7 +283,7 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
</tr>
<tr>
<th>also_single_tested</th>
<td><p>a logical to indicate whether (in combination therapies) also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This would lead to selection bias in almost all cases.</strong></p></td>
<td><p>a logical to indicate whether for combination therapies also observations should be included where not all antibiotics were tested, but at least one of the tested antibiotics contains a target interpretation (e.g. S in case of <code>portion_S</code> and R in case of <code>portion_R</code>). <strong>This could lead to selection bias.</strong></p></td>
</tr>
<tr>
<th>data</th>
@ -403,6 +403,15 @@ portion_R and portion_IR can be used to calculate resistance, portion_S and port
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'>portion_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># S = 92.3%</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span> <span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>) <span class='co'># n = 1798</span>
<span class='co'># Using `also_single_tested` can be useful ...</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'>portion_S</span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># S = 92.6%</span>
<span class='co'># ... but can also lead to selection bias - the data only has 2,000 rows:</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<span class='fu'><a href='count.html'>count_all</a></span>(<span class='no'>AMC</span>, <span class='no'>GEN</span>,
<span class='kw'>also_single_tested</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) <span class='co'># n = 2555</span>
<span class='no'>septic_patients</span> <span class='kw'>%&gt;%</span>
<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'>%&gt;%</span>