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AMR/data-raw/antibiograms.html

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pm update, unit test fix?
2023-02-08 13:48:06 +01:00
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<meta http-equiv="X-UA-Compatible" content="IE=EDGE" />
<meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-08" />
<title>Generating antibiograms with the AMR package</title>
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<div id="header">
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-08</h4>
</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
## date patient age gender ward mo PEN OXA FLC AMX
## &lt;date&gt; &lt;chr&gt; &lt;dbl&gt; &lt;chr&gt; &lt;chr&gt; &lt;mo&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt; &lt;sir&gt;
## 1 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
## 2 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA
## 3 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
## 4 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA
## 5 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
## 6 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA
## 7 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
## 8 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R
## 9 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA
## 10 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA
## # … with 1,990 more rows, and 36 more variables: 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;, CLI &lt;sir&gt;, AZM &lt;sir&gt;, IPM &lt;sir&gt;, MEM &lt;sir&gt;, MTR &lt;sir&gt;,
## # CHL &lt;sir&gt;, COL &lt;sir&gt;, MUP &lt;sir&gt;, RIF &lt;sir&gt;</code></pre>
<div id="traditional-antibiogram" class="section level3">
<h3>Traditional Antibiogram</h3>
<pre class="r"><code>print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
)</code></pre>
<table>
<thead>
<tr class="header">
<th align="left">Pathogen (N min-max)</th>
<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">CoNS (43-309)</td>
<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">
<td align="left">E. coli (0-462)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">E. faecalis (0-39)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">100</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">K. pneumoniae (0-58)</td>
<td align="right">NA</td>
<td align="right">90</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">90</td>
</tr>
<tr class="odd">
<td align="left">P. aeruginosa (17-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">P. mirabilis (0-34)</td>
<td align="right">NA</td>
<td align="right">94</td>
<td align="right">94</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">S. aureus (2-233)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left">S. epidermidis (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right">NA</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">51</td>
</tr>
<tr class="odd">
<td align="left">S. hominis (3-80)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">85</td>
</tr>
<tr class="even">
<td align="left">S. pneumoniae (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
</tr>
</tbody>
</table>
</div>
<div id="combined-antibiogram" class="section level3">
<h3>Combined Antibiogram</h3>
<pre class="r"><code>print(
antibiogram(example_isolates,
antibiotics = c(&quot;TZP&quot;, &quot;TZP+TOB&quot;, &quot;TZP+GEN&quot;))
)</code></pre>
<table>
<thead>
<tr class="header">
<th align="left">Pathogen (N min-max)</th>
<th align="right">TZP</th>
<th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th>
</tr>
</thead>
<tbody>
<tr class="odd">
<td align="left">CoNS (29-274)</td>
<td align="right">30</td>
<td align="right">97</td>
<td align="right">NA</td>
</tr>
<tr class="even">
<td align="left">E. coli (416-461)</td>
<td align="right">94</td>
<td align="right">100</td>
<td align="right">99</td>
</tr>
<tr class="odd">
<td align="left">K. pneumoniae (53-58)</td>
<td align="right">89</td>
<td align="right">93</td>
<td align="right">93</td>
</tr>
<tr class="even">
<td align="left">P. aeruginosa (27-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">P. mirabilis (27-34)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. aureus (7-231)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. epidermidis (5-128)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">S. hominis (0-74)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left">S. pneumoniae (112-112)</td>
<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>
<pre class="r"><code>print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = &quot;ward&quot;)
)</code></pre>
<table>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
<th align="left">Pathogen (N min-max)</th>
<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>
<td align="left">CoNS (23-205)</td>
<td align="right">NA</td>
<td align="right">89</td>
<td align="right">57</td>
<td align="right">NA</td>
<td align="right">57</td>
<td align="right">26</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">CoNS (10-73)</td>
<td align="right">NA</td>
<td align="right">79</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="left">CoNS (3-31)</td>
<td align="right">NA</td>
<td align="right">84</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">E. coli (0-299)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">98</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">E. coli (0-137)</td>
<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">96</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. pneumoniae (0-51)</td>
<td align="right">NA</td>
<td align="right">92</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">92</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. mirabilis (0-30)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. aureus (2-150)</td>
<td align="right">NA</td>
<td align="right">99</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. aureus (0-66)</td>
<td align="right">NA</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. epidermidis (4-79)</td>
<td align="right">NA</td>
<td align="right">82</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">55</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. epidermidis (4-75)</td>
<td align="right">NA</td>
<td align="right">72</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">41</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. hominis (1-45)</td>
<td align="right">NA</td>
<td align="right">96</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">S. pneumoniae (5-78)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">S. pneumoniae (5-30)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right">0</td>
<td align="right">NA</td>
<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>
<pre class="r"><code>print(
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>
<colgroup>
<col width="23%" />
<col width="35%" />
<col width="5%" />
<col width="14%" />
<col width="5%" />
<col width="14%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
<th align="left">Pathogen (N min-max)</th>
<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>
<td align="left">Gram-negative (261-285)</td>
<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>
<td align="left">Gram-negative (380-442)</td>
<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>
<td align="left">Gram-positive (123-406)</td>
<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>
<td align="left">Gram-positive (222-732)</td>
<td align="right">76</td>
<td align="right">89</td>
<td align="right">88</td>
<td align="right">95</td>
</tr>
</tbody>
</table>
</div>
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