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fix for antibiograms on R < 3.5

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dr. M.S. (Matthijs) Berends
2023-02-24 09:43:10 +01:00
parent e70f2cd32c
commit 049baf0a71
13 changed files with 108 additions and 101 deletions
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2
data-raw/antibiograms.Rmd
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@ -2,7 +2,7 @@
title: "Generating antibiograms with the AMR package"
author: "AMR package developers"
date: "`r Sys.Date()`"
output: html_document
output: pdf_document
---
```{r setup, include=FALSE}

123
data-raw/antibiograms.html
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@ -11,7 +11,7 @@
<meta name="author" content="AMR package developers" />
<meta name="date" content="2023-02-23" />
<meta name="date" content="2023-02-24" />
<title>Generating antibiograms with the AMR package</title>
@ -299,23 +299,17 @@ overflow-y: auto;
border: 1px solid #ddd;
border-radius: 4px;
}
.tabset-dropdown > .nav-tabs > li.active:before {
content: "";
.tabset-dropdown > .nav-tabs > li.active:before, .tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "\e259";
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: "";
border: none;
}
.tabset-dropdown > .nav-tabs.nav-tabs-open:before {
content: "";
content: "\e258";
font-family: 'Glyphicons Halflings';
display: inline-block;
padding: 10px;
border-right: 1px solid #ddd;
border: none;
}
.tabset-dropdown > .nav-tabs > li.active {
display: block;
@ -359,7 +353,7 @@ display: none;
<h1 class="title toc-ignore">Generating antibiograms with the AMR
package</h1>
<h4 class="author">AMR package developers</h4>
<h4 class="date">2023-02-23</h4>
<h4 class="date">2023-02-24</h4>
</div>
@ -370,26 +364,25 @@ 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
## &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>
## 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>antibiogram(example_isolates,
@ -397,7 +390,7 @@ looks like:</p>
<table>
<thead>
<tr class="header">
<th align="left">Pathogeen (N min-max)</th>
<th align="left">Pathogen (N min-max)</th>
<th align="right">AMK</th>
<th align="right">GEN</th>
<th align="right">IPM</th>
@ -408,7 +401,7 @@ looks like:</p>
</thead>
<tbody>
<tr class="odd">
<td align="left">CNS (43-309)</td>
<td align="left">CoNS (43-309)</td>
<td align="right">0</td>
<td align="right">86</td>
<td align="right">52</td>
@ -507,7 +500,7 @@ looks like:</p>
<table>
<thead>
<tr class="header">
<th align="left">Pathogeen (N min-max)</th>
<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>
@ -515,7 +508,7 @@ looks like:</p>
</thead>
<tbody>
<tr class="odd">
<td align="left">CNS (29-274)</td>
<td align="left">CoNS (29-274)</td>
<td align="right">30</td>
<td align="right">97</td>
<td align="right"></td>
@ -577,10 +570,20 @@ looks like:</p>
antibiotics = c(aminoglycosides(), carbapenems()),
syndromic_group = &quot;ward&quot;)</code></pre>
<table>
<colgroup>
<col width="25%" />
<col width="37%" />
<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">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
<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>
@ -592,7 +595,7 @@ looks like:</p>
<tbody>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">CNS (23-205)</td>
<td align="left">CoNS (23-205)</td>
<td align="right"></td>
<td align="right">89</td>
<td align="right">57</td>
@ -602,7 +605,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">CNS (10-73)</td>
<td align="left">CoNS (10-73)</td>
<td align="right"></td>
<td align="right">79</td>
<td align="right"></td>
@ -612,7 +615,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Outpatient</td>
<td align="left">CNS (3-31)</td>
<td align="left">CoNS (3-31)</td>
<td align="right"></td>
<td align="right">84</td>
<td align="right"></td>
@ -622,7 +625,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">E. <em>coli</em> (0-299)</td>
<td align="left"><em>E. coli</em> (0-299)</td>
<td align="right">100</td>
<td align="right">98</td>
<td align="right">100</td>
@ -632,7 +635,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">E. <em>coli</em> (0-137)</td>
<td align="left"><em>E. coli</em> (0-137)</td>
<td align="right">100</td>
<td align="right">99</td>
<td align="right">100</td>
@ -642,7 +645,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">K. <em>pneumoniae</em> (0-51)</td>
<td align="left"><em>K. pneumoniae</em> (0-51)</td>
<td align="right"></td>
<td align="right">92</td>
<td align="right">100</td>
@ -652,7 +655,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">P. <em>mirabilis</em> (0-30)</td>
<td align="left"><em>P. mirabilis</em> (0-30)</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right"></td>
@ -662,7 +665,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>aureus</em> (2-150)</td>
<td align="left"><em>S. aureus</em> (2-150)</td>
<td align="right"></td>
<td align="right">99</td>
<td align="right"></td>
@ -672,7 +675,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. <em>aureus</em> (0-66)</td>
<td align="left"><em>S. aureus</em> (0-66)</td>
<td align="right"></td>
<td align="right">100</td>
<td align="right"></td>
@ -682,7 +685,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>epidermidis</em> (4-79)</td>
<td align="left"><em>S. epidermidis</em> (4-79)</td>
<td align="right"></td>
<td align="right">82</td>
<td align="right"></td>
@ -692,7 +695,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">ICU</td>
<td align="left">S. <em>epidermidis</em> (4-75)</td>
<td align="left"><em>S. epidermidis</em> (4-75)</td>
<td align="right"></td>
<td align="right">72</td>
<td align="right"></td>
@ -702,7 +705,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">Clinical</td>
<td align="left">S. <em>hominis</em> (1-45)</td>
<td align="left"><em>S. hominis</em> (1-45)</td>
<td align="right"></td>
<td align="right">96</td>
<td align="right"></td>
@ -712,7 +715,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">Clinical</td>
<td align="left">S. <em>pneumoniae</em> (5-78)</td>
<td align="left"><em>S. pneumoniae</em> (5-78)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right"></td>
@ -722,7 +725,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">ICU</td>
<td align="left">S. <em>pneumoniae</em> (5-30)</td>
<td align="left"><em>S. pneumoniae</em> (5-30)</td>
<td align="right">0</td>
<td align="right">0</td>
<td align="right"></td>
@ -742,9 +745,9 @@ looks like:</p>
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%;">
<table>
<colgroup>
<col width="22%" />
<col width="23%" />
<col width="35%" />
<col width="5%" />
<col width="14%" />
@ -753,8 +756,8 @@ looks like:</p>
</colgroup>
<thead>
<tr class="header">
<th align="left">Syndroomgroep</th>
<th align="left">Pathogeen (N min-max)</th>
<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>
@ -764,7 +767,7 @@ looks like:</p>
<tbody>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-negatief (261-285)</td>
<td align="left">Gram-negative (261-285)</td>
<td align="right">76</td>
<td align="right">95</td>
<td align="right">89</td>
@ -772,7 +775,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-negatief (380-442)</td>
<td align="left">Gram-negative (380-442)</td>
<td align="right">76</td>
<td align="right">98</td>
<td align="right">88</td>
@ -780,7 +783,7 @@ looks like:</p>
</tr>
<tr class="odd">
<td align="left">WISCA Group 1</td>
<td align="left">Gram-positief (123-406)</td>
<td align="left">Gram-positive (123-406)</td>
<td align="right">76</td>
<td align="right">89</td>
<td align="right">81</td>
@ -788,7 +791,7 @@ looks like:</p>
</tr>
<tr class="even">
<td align="left">WISCA Group 2</td>
<td align="left">Gram-positief (222-732)</td>
<td align="left">Gram-positive (222-732)</td>
<td align="right">76</td>
<td align="right">89</td>
<td align="right">88</td>

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data-raw/reproduction_of_poorman.R
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@ -107,3 +107,4 @@ contents <- c(
writeLines(contents, "R/aa_helper_pm_functions.R")
# note: pm_left_join() will be overwritten by aaa_helper_functions.R, which contains a faster implementation
# replace `res <- as.data.frame(res)` with `res <- as.data.frame(res, stringsAsFactors = FALSE)`