P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-07-08 12:31:58 +02:00
Code Releases Activity

(v1.5.0.9039) handle first isolates for missing antibiograms

Browse Source
This commit is contained in:
dr. M.S. (Matthijs) Berends
2021-03-08 02:38:32 +01:00
parent 461793dc34
commit a7c9b4c295
21 changed files with 79 additions and 62 deletions
Download Patch File Download Diff File Expand all files Collapse all files

13
docs/reference/first_isolate.html
View File

@ -82,7 +82,7 @@
</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">1.5.0.9019</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.5.0.9039</span>
</span>
</div>
@ -260,6 +260,7 @@
points_threshold <span class='op'>=</span> <span class='fl'>2</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
include_unknown <span class='op'>=</span> <span class='cn'>FALSE</span>,
include_untested_rsi <span class='op'>=</span> <span class='cn'>TRUE</span>,
<span class='va'>...</span>
<span class='op'>)</span>
@ -325,7 +326,7 @@
</tr>
<tr>
<th>icu_exclude</th>
<td><p>logical whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>)</p></td>
<td><p>logical to indicate whether ICU isolates should be excluded (rows with value <code>TRUE</code> in the column set with <code>col_icu</code>)</p></td>
</tr>
<tr>
<th>specimen_group</th>
@ -337,7 +338,7 @@
</tr>
<tr>
<th>ignore_I</th>
<td><p>logical to determine whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see <em>Details</em></p></td>
<td><p>logical to indicate whether antibiotic interpretations with <code>"I"</code> will be ignored when <code>type = "keyantibiotics"</code>, see <em>Details</em></p></td>
</tr>
<tr>
<th>points_threshold</th>
@ -349,7 +350,11 @@
</tr>
<tr>
<th>include_unknown</th>
<td><p>logical to determine whether 'unknown' microorganisms should be included too, i.e. microbial code <code>"UNKNOWN"</code>, which defaults to <code>FALSE</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default. Isolates with a microbial ID of <code>NA</code> will always be excluded as first isolate.</p></td>
<td><p>logical to indicate whether 'unknown' microorganisms should be included too, i.e. microbial code <code>"UNKNOWN"</code>, which defaults to <code>FALSE</code>. For WHONET users, this means that all records with organism code <code>"con"</code> (<em>contamination</em>) will be excluded at default. Isolates with a microbial ID of <code>NA</code> will always be excluded as first isolate.</p></td>
</tr>
<tr>
<th>include_untested_rsi</th>
<td><p>logical to indicate whether also rows without antibiotic results are still eligible for becoming a first isolate. Use <code>include_untested_rsi = FALSE</code> to always return <code>FALSE</code> for such rows. This checks the data set for columns of class <code>&lt;rsi&gt;</code> and consequently requires transforming columns with antibiotic results using <code><a href='as.rsi.html'>as.rsi()</a></code> first.</p></td>
</tr>
<tr>
<th>...</th>