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dr. M.S. (Matthijs) Berends
2023-02-23 16:27:40 +01:00
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36
data-raw/antibiograms.Rmd
View File

@ -22,41 +22,33 @@ example_isolates
### Traditional Antibiogram
```{r trad}
print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
)
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))
```
### Combined Antibiogram
```{r comb}
print(
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
)
antibiogram(example_isolates,
antibiotics = c("TZP", "TZP+TOB", "TZP+GEN"))
```
### Syndromic Antibiogram
```{r synd}
print(
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
)
antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = "ward")
```
### Weighted-Incidence Syndromic Combination Antibiogram (WISCA)
```{r wisca}
print(
antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
)
antibiogram(example_isolates,
antibiotics = c("AMC", "AMC+CIP", "TZP", "TZP+TOB"),
mo_transform = "gramstain",
minimum = 10, # this should be >= 30, but now just as example
syndromic_group = ifelse(example_isolates$age >= 65 &
example_isolates$gender == "M",
"WISCA Group 1", "WISCA Group 2"))
```

285
data-raw/antibiograms.html
View File

@ -11,7 +11,7 @@
<meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-18" />
<meta name="date" content="2023-02-23" />
<title>Generating antibiograms with the AMR package</title>
@ -299,18 +299,24 @@ overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open > li.active:before {
content: "\e258";
font-family: 'Glyphicons Halflings';
content: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
}
@ -353,7 +359,7 @@ display: none;
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-18</h4>
<h4 class="date">2023-02-23</h4>
</div>
@ -364,35 +370,34 @@ package</h1>
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>
## 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>
<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>
<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()))</code></pre>
<table>
<thead>
<tr class="header">
<th align="left">Pathogen (N min-max)</th>
<th align="left">Pathogeen (N min-max)</th>
<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
@ -403,7 +408,7 @@ looks like:</p>
</thead>
<tbody>
<tr class="odd">
<td align="left">CoNS (43-309)</td>
<td align="left">CNS (43-309)</td>
<td align="right">0</td>
<td align="right">86</td>
<td align="right">52</td>
@ -416,7 +421,7 @@ looks like:</p>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">97</td>
</tr>
@ -426,70 +431,70 @@ looks like:</p>
<td align="right">0</td>
<td align="right">100</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
<tr class="even">
<td align="left"><em>K. pneumoniae</em> (0-58)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">90</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">90</td>
</tr>
<tr class="odd">
<td align="left"><em>P. aeruginosa</em> (17-30)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left"><em>P. mirabilis</em> (0-34)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">94</td>
<td align="right">94</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right">94</td>
</tr>
<tr class="odd">
<td align="left"><em>S. aureus</em> (2-233)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">99</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">98</td>
</tr>
<tr class="even">
<td align="left"><em>S. epidermidis</em> (8-163)</td>
<td align="right">0</td>
<td align="right">79</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">51</td>
</tr>
<tr class="odd">
<td align="left"><em>S. hominis</em> (3-80)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">92</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">85</td>
</tr>
<tr class="even">
<td align="left"><em>S. pneumoniae</em> (11-117)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
</tbody>
@ -497,14 +502,12 @@ looks like:</p>
</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>
<pre class="r"><code>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="left">Pathogeen (N min-max)</th>
<th align="right">TZP</th>
<th align="right">TZP + GEN</th>
<th align="right">TZP + TOB</th>
@ -512,10 +515,10 @@ looks like:</p>
</thead>
<tbody>
<tr class="odd">
<td align="left">CoNS (29-274)</td>
<td align="left">CNS (29-274)</td>
<td align="right">30</td>
<td align="right">97</td>
<td align="right">NA</td>
<td align="right"></td>
</tr>
<tr class="even">
<td align="left"><em>E. coli</em> (416-461)</td>
@ -531,31 +534,31 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left"><em>P. aeruginosa</em> (27-30)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left"><em>P. mirabilis</em> (27-34)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left"><em>S. aureus</em> (7-231)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="odd">
<td align="left"><em>S. epidermidis</em> (5-128)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left"><em>S. hominis</em> (0-74)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">100</td>
</tr>
@ -570,26 +573,14 @@ looks like:</p>
</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>
<pre class="r"><code>antibiogram(example_isolates,
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = &quot;ward&quot;)</code></pre>
<table>
<colgroup>
<col width="29%" />
<col width="33%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
<col width="6%" />
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
<th align="left">Pathogen (N min-max)</th>
<th align="left">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
@ -601,33 +592,33 @@ looks like:</p>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">CoNS (23-205)</td>
<td align="right">NA</td>
<td align="left">CNS (23-205)</td>
<td align="right"></td>
<td align="right">89</td>
<td align="right">57</td>
<td align="right">NA</td>
<td align="right"></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="left">CNS (10-73)</td>
<td align="right"></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>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="left">CoNS (3-31)</td>
<td align="right">NA</td>
<td align="left">CNS (3-31)</td>
<td align="right"></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>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
@ -635,7 +626,7 @@ looks like:</p>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">98</td>
</tr>
@ -645,78 +636,78 @@ looks like:</p>
<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">96</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. <em>pneumoniae</em> (0-51)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">92</td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">92</td>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. <em>mirabilis</em> (0-30)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">100</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>aureus</em> (2-150)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">99</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">97</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. <em>aureus</em> (0-66)</td>
<td align="right">NA</td>
<td align="right"></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>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>epidermidis</em> (4-79)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">82</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">55</td>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. <em>epidermidis</em> (4-75)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">72</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">41</td>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>hominis</em> (1-45)</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">96</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right"></td>
<td align="right"></td>
<td align="right">94</td>
</tr>
<tr class="odd">
@ -724,9 +715,9 @@ looks like:</p>
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
<tr class="even">
@ -734,9 +725,9 @@ looks like:</p>
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
<td align="right">NA</td>
<td align="right"></td>
<td align="right">0</td>
</tr>
</tbody>
@ -744,19 +735,17 @@ looks like:</p>
</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>
<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%;">
<colgroup>
<col width="24%" />
<col width="34%" />
<col width="22%" />
<col width="35%" />
<col width="5%" />
<col width="14%" />
<col width="5%" />
@ -764,8 +753,8 @@ looks like:</p>
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndromic Group</th>
<th align="left">Pathogen (N min-max)</th>
<th align="left">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
<th align="right">AMC</th>
<th align="right">AMC + CIP</th>
<th align="right">TZP</th>
@ -775,7 +764,7 @@ looks like:</p>
<tbody>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-negative (261-285)</td>
<td align="left">Gram-negatief (261-285)</td>
<td align="right">76</td>
<td align="right">95</td>
<td align="right">89</td>
@ -783,7 +772,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-negative (380-442)</td>
<td align="left">Gram-negatief (380-442)</td>
<td align="right">76</td>
<td align="right">98</td>
<td align="right">88</td>
@ -791,7 +780,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-positive (123-406)</td>
<td align="left">Gram-positief (123-406)</td>
<td align="right">76</td>
<td align="right">89</td>
<td align="right">81</td>
@ -799,7 +788,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-positive (222-732)</td>
<td align="left">Gram-positief (222-732)</td>
<td align="right">76</td>
<td align="right">89</td>
<td align="right">88</td>