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AMR
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pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<!DOCTYPE html>
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<head>
<meta charset="utf-8" />
<meta name="generator" content="pandoc" />
<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="AMR package developers" />
knitr format
2023-02-23 16:27:40 +01:00
<meta name="date" content="2023-02-23" />
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<title>Generating antibiograms with the AMR package</title>
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knitr format
2023-02-23 16:27:40 +01:00
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
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font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
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content: "";
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border: none;
}
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.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
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.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
.tabset-dropdown > .nav-tabs > li > a,
.tabset-dropdown > .nav-tabs > li > a:focus,
.tabset-dropdown > .nav-tabs > li > a:hover {
border: none;
display: inline-block;
border-radius: 4px;
background-color: transparent;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li {
display: block;
float: none;
}
.tabset-dropdown > .nav-tabs > li {
display: none;
}
</style>
<!-- code folding -->
</head>
<body>
<div class="container-fluid main-container">
<div id="header">
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
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<h4 class="date">2023-02-23</h4>
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</div>
<p>This is an example R Markdown file to show the use of
<code>antibiogram()</code> of the AMR package.</p>
<p>For starters, this is what our <code>example_isolates</code> data set
looks like:</p>
<pre class="r"><code>example_isolates</code></pre>
<pre><code>## # A tibble: 2,000 × 46
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## date patient age gender ward mo PEN
## &lt;date&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;mo&gt; &lt;sir&gt;
## 1 2002-01-02 A77334 65 F Clini… B_ESCHR_COLI R
## 2 2002-01-03 A77334 65 F Clini… B_ESCHR_COLI R
## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R
## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R
## 7 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
## 8 2002-01-14 462729 78 M Clini… B_STPHY_AURS R
## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R
## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R
## # … with 1,990 more rows, and 39 more variables: OXA &lt;sir&gt;,
## # FLC &lt;sir&gt;, AMX &lt;sir&gt;, AMC &lt;sir&gt;, AMP &lt;sir&gt;, TZP &lt;sir&gt;,
## # CZO &lt;sir&gt;, FEP &lt;sir&gt;, CXM &lt;sir&gt;, FOX &lt;sir&gt;, CTX &lt;sir&gt;,
## # CAZ &lt;sir&gt;, CRO &lt;sir&gt;, GEN &lt;sir&gt;, TOB &lt;sir&gt;, AMK &lt;sir&gt;,
## # KAN &lt;sir&gt;, TMP &lt;sir&gt;, SXT &lt;sir&gt;, NIT &lt;sir&gt;, FOS &lt;sir&gt;,
## # LNZ &lt;sir&gt;, CIP &lt;sir&gt;, MFX &lt;sir&gt;, VAN &lt;sir&gt;, TEC &lt;sir&gt;,
## # TCY &lt;sir&gt;, TGC &lt;sir&gt;, DOX &lt;sir&gt;, ERY &lt;sir&gt;, …
## # ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</code></pre>
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<div id="traditional-antibiogram" class="section level3">
<h3>Traditional Antibiogram</h3>
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<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))</code></pre>
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<table>
<thead>
<tr class="header">
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<th align="left">Pathogeen (N min-max)</th>
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<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
<th align="right">KAN</th>
<th align="right">MEM</th>
<th align="right">TOB</th>
</tr>
</thead>
<tbody>
<tr class="odd">
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<td align="left">CNS (43-309)</td>
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<td align="right">0</td>
<td align="right">86</td>
<td align="right">52</td>
<td align="right">0</td>
<td align="right">52</td>
<td align="right">22</td>
</tr>
<tr class="even">
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<td align="left"><em>E. coli</em> (0-462)</td>
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<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">97</td>
</tr>
<tr class="odd">
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<td align="left"><em>E. faecalis</em> (0-39)</td>
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<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
<td align="right">0</td>
knitr format
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<td align="right"></td>
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<td align="right">0</td>
</tr>
<tr class="even">
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<td align="left"><em>K. pneumoniae</em> (0-58)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">90</td>
<td align="right">100</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">90</td>
</tr>
<tr class="odd">
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<td align="left"><em>P. aeruginosa</em> (17-30)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">0</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
</tr>
<tr class="even">
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<td align="left"><em>P. mirabilis</em> (0-34)</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">94</td>
<td align="right">94</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
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<td align="right">94</td>
</tr>
<tr class="odd">
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<td align="left"><em>S. aureus</em> (2-233)</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">99</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">98</td>
</tr>
<tr class="even">
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<td align="left"><em>S. epidermidis</em> (8-163)</td>
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<td align="right">0</td>
<td align="right">79</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">0</td>
knitr format
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<td align="right"></td>
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<td align="right">51</td>
</tr>
<tr class="odd">
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<td align="left"><em>S. hominis</em> (3-80)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">92</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
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<td align="right">85</td>
</tr>
<tr class="even">
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<td align="left"><em>S. pneumoniae</em> (11-117)</td>
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<td align="right">0</td>
<td align="right">0</td>
knitr format
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<td align="right"></td>
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<td align="right">0</td>
knitr format
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<td align="right"></td>
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<td align="right">0</td>
</tr>
</tbody>
</table>
</div>
<div id="combined-antibiogram" class="section level3">
<h3>Combined Antibiogram</h3>
knitr format
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<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(&quot;TZP&quot;, &quot;TZP+TOB&quot;, &quot;TZP+GEN&quot;))</code></pre>
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<table>
<thead>
<tr class="header">
knitr format
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<th align="left">Pathogeen (N min-max)</th>
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<th align="right">TZP</th>
<th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th>
</tr>
</thead>
<tbody>
<tr class="odd">
knitr format
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<td align="left">CNS (29-274)</td>
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<td align="right">30</td>
<td align="right">97</td>
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<td align="right"></td>
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</tr>
<tr class="even">
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<td align="left"><em>E. coli</em> (416-461)</td>
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<td align="right">94</td>
<td align="right">100</td>
<td align="right">99</td>
</tr>
<tr class="odd">
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<td align="left"><em>K. pneumoniae</em> (53-58)</td>
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<td align="right">89</td>
<td align="right">93</td>
<td align="right">93</td>
</tr>
<tr class="even">
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<td align="left"><em>P. aeruginosa</em> (27-30)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
make `rsi` work in more cases, documentation update
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<td align="left"><em>P. mirabilis</em> (27-34)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
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<td align="left"><em>S. aureus</em> (7-231)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
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<td align="left"><em>S. epidermidis</em> (5-128)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
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<td align="left"><em>S. hominis</em> (0-74)</td>
knitr format
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<td align="right"></td>
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<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
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<td align="left"><em>S. pneumoniae</em> (112-112)</td>
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<td align="right">100</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
</tbody>
</table>
</div>
<div id="syndromic-antibiogram" class="section level3">
<h3>Syndromic Antibiogram</h3>
knitr format
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<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = &quot;ward&quot;)</code></pre>
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<table>
<thead>
<tr class="header">
knitr format
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<th align="left">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
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<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
<th align="right">KAN</th>
<th align="right">MEM</th>
<th align="right">TOB</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
knitr format
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<td align="left">CNS (23-205)</td>
<td align="right"></td>
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<td align="right">89</td>
<td align="right">57</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">57</td>
<td align="right">26</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
knitr format
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<td align="left">CNS (10-73)</td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">79</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
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</tr>
<tr class="odd">
<td align="left">Outpatient</td>
knitr format
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<td align="left">CNS (3-31)</td>
<td align="right"></td>
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<td align="right">84</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
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</tr>
<tr class="even">
<td align="left">Clinical</td>
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<td align="left">E. <em>coli</em> (0-299)</td>
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<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">100</td>
<td align="right">98</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
make `rsi` work in more cases, documentation update
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<td align="left">E. <em>coli</em> (0-137)</td>
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<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">100</td>
<td align="right">96</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
make `rsi` work in more cases, documentation update
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<td align="left">K. <em>pneumoniae</em> (0-51)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">92</td>
<td align="right">100</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">100</td>
<td align="right">92</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
make `rsi` work in more cases, documentation update
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<td align="left">P. <em>mirabilis</em> (0-30)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">100</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
make `rsi` work in more cases, documentation update
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<td align="left">S. <em>aureus</em> (2-150)</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">99</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
make `rsi` work in more cases, documentation update
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<td align="left">S. <em>aureus</em> (0-66)</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">100</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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</tr>
<tr class="even">
<td align="left">Clinical</td>
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<td align="left">S. <em>epidermidis</em> (4-79)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">82</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">55</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
make `rsi` work in more cases, documentation update
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<td align="left">S. <em>epidermidis</em> (4-75)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">72</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
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<td align="right">41</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
make `rsi` work in more cases, documentation update
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<td align="left">S. <em>hominis</em> (1-45)</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
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<td align="right">96</td>
knitr format
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<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
make `rsi` work in more cases, documentation update
2023-02-22 14:38:57 +01:00
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
pm update, unit test fix?
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<td align="right">0</td>
<td align="right">0</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
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<td align="right">0</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
make `rsi` work in more cases, documentation update
2023-02-22 14:38:57 +01:00
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">0</td>
<td align="right">0</td>
knitr format
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<td align="right"></td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">0</td>
knitr format
2023-02-23 16:27:40 +01:00
<td align="right"></td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">0</td>
</tr>
</tbody>
</table>
</div>
<div id="weighted-incidence-syndromic-combination-antibiogram-wisca" class="section level3">
<h3>Weighted-Incidence Syndromic Combination Antibiogram (WISCA)</h3>
knitr format
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<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(&quot;AMC&quot;, &quot;AMC+CIP&quot;, &quot;TZP&quot;, &quot;TZP+TOB&quot;),
mo_transform = &quot;gramstain&quot;,
minimum = 10, # this should be &gt;= 30, but now just as example
syndromic_group = ifelse(example_isolates$age &gt;= 65 &amp;
example_isolates$gender == &quot;M&quot;,
&quot;WISCA Group 1&quot;, &quot;WISCA Group 2&quot;))</code></pre>
<table style="width:100%;">
pm update, unit test fix?
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<colgroup>
knitr format
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<col width="22%" />
<col width="35%" />
pm update, unit test fix?
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<col width="5%" />
<col width="14%" />
<col width="5%" />
<col width="14%" />
</colgroup>
<thead>
<tr class="header">
knitr format
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<th align="left">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
pm update, unit test fix?
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<th align="right">AMC</th>
<th align="right">AMC + CIP</th>
<th align="right">TZP</th>
<th align="right">TZP + TOB</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">WISCA Group 1</td>
knitr format
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<td align="left">Gram-negatief (261-285)</td>
pm update, unit test fix?
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<td align="right">76</td>
<td align="right">95</td>
<td align="right">89</td>
<td align="right">99</td>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
knitr format
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<td align="left">Gram-negatief (380-442)</td>
pm update, unit test fix?
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<td align="right">76</td>
<td align="right">98</td>
<td align="right">88</td>
<td align="right">98</td>
</tr>
<tr class="odd">
<td align="left">WISCA Group 1</td>
knitr format
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<td align="left">Gram-positief (123-406)</td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">76</td>
<td align="right">89</td>
<td align="right">81</td>
<td align="right">95</td>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
knitr format
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<td align="left">Gram-positief (222-732)</td>
pm update, unit test fix?
2023-02-08 13:48:06 +01:00
<td align="right">76</td>
<td align="right">89</td>
<td align="right">88</td>
<td align="right">95</td>
</tr>
</tbody>
</table>
</div>
</div>
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