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(v1.8.1.9006) added EUCAST 2022 and CLSI 2022

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dr. M.S. (Matthijs) Berends 2022-05-10 21:34:30 +02:00
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commit 859224e9d0
30 changed files with 3464 additions and 3392 deletions
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2
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR
Version: 1.8.1.9005
Version: 1.8.1.9006
Date: 2022-05-10
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)

5
NEWS.md
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@ -1,6 +1,9 @@
# `AMR` 1.8.1.9005
# `AMR` 1.8.1.9006
## <small>Last updated: 10 May 2022</small>
### New
* EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.
### Changed
* Fix for `as.rsi()` on certain EUCAST breakpoints for MIC values
* Removed `as.integer()` for MIC values, since MIC are not integer values and running `table()` on MIC values consequently failed for not being able to retrieve the level position (as that's how normally `as.integer()` on `factor`s work)

18
R/plot.R
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@ -79,7 +79,7 @@ plot.mic <- function(x,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -166,7 +166,7 @@ barplot.mic <- function(height,
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(height))),
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -299,7 +299,7 @@ fortify.mic <- function(object, ...) {
#' @importFrom graphics barplot axis mtext legend
#' @rdname plot
plot.disk <- function(x,
main = paste("Disk zones of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -386,7 +386,7 @@ plot.disk <- function(x,
#' @export
#' @noRd
barplot.disk <- function(height,
main = paste("Disk zones of", deparse(substitute(height))),
main = deparse(substitute(height)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -525,7 +525,7 @@ fortify.disk <- function(object, ...) {
plot.rsi <- function(x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = paste("Resistance Overview of", deparse(substitute(x))),
main = deparse(substitute(x)),
...) {
meet_criteria(ylab, allow_class = "character", has_length = 1)
meet_criteria(xlab, allow_class = "character", has_length = 1)
@ -576,7 +576,7 @@ plot.rsi <- function(x,
#' @export
#' @noRd
barplot.rsi <- function(height,
main = paste("Resistance Overview of", deparse(substitute(height))),
main = deparse(substitute(height)),
xlab = "Antimicrobial Interpretation",
ylab = "Frequency",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -738,7 +738,11 @@ plot_colours_subtitle_guideline <- function(x, mo, ab, guideline, colours_RSI, f
ab_name(ab, language = NULL, tolower = TRUE), " in ", moname)
guideline_txt <- ""
} else {
guideline_txt <- paste0("(", guideline, ")")
guideline_txt <- guideline
if (isTRUE(list(...)$uti)) {
guideline_txt <- paste("UTIs,", guideline_txt)
}
guideline_txt <- paste0("(", guideline_txt, ")")
}
sub <- bquote(.(abname)~"-"~italic(.(moname))~.(guideline_txt))
} else {

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data-raw/reproduction_of_rsi_translation.R
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@ -24,6 +24,7 @@
# ==================================================================== #
# This script runs in under a minute and renews all guidelines of CLSI and EUCAST!
# Run it with source("data-raw/reproduction_of_rsi_translation.R")
library(dplyr)
library(readr)
@ -32,9 +33,9 @@ library(AMR)
# Install the WHONET software on Windows (http://www.whonet.org/software.html),
# and copy the folder C:\WHONET\Codes to data-raw/WHONET/Codes
DRGLST <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"))
DRGLST1 <- readr::read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"))
ORGLIST <- readr::read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"))
DRGLST <- read_tsv("data-raw/WHONET/Codes/DRGLST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
DRGLST1 <- read_tsv("data-raw/WHONET/Codes/DRGLST1.txt", na = c("", "NA", "-"), show_col_types = FALSE)
ORGLIST <- read_tsv("data-raw/WHONET/Codes/ORGLIST.txt", na = c("", "NA", "-"), show_col_types = FALSE)
# create data set for generic rules (i.e., AB-specific but not MO-specific)
rsi_generic <- DRGLST %>%
@ -134,11 +135,17 @@ rsi_translation[which(rsi_translation$breakpoint_R == 1025), "breakpoint_R"] <-
# this will make an MIC of 12 I, which should be R, so:
eucast_mics <- which(rsi_translation$guideline %like% "EUCAST" &
rsi_translation$method == "MIC" &
log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0)
rsi_translation[eucast_mics, "breakpoint_R"] <- 2 ^ (log2(as.double(rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE])) - 1)
log2(as.double(rsi_translation$breakpoint_R)) - log2(as.double(rsi_translation$breakpoint_S)) != 0 &
!is.na(rsi_translation$breakpoint_R))
old_R <- rsi_translation[eucast_mics, "breakpoint_R", drop = TRUE]
old_S <- rsi_translation[eucast_mics, "breakpoint_S", drop = TRUE]
new_R <- 2 ^ (log2(old_R) - 1)
new_R[new_R < old_S | is.na(as.mic(new_R))] <- old_S[new_R < old_S | is.na(as.mic(new_R))]
rsi_translation[eucast_mics, "breakpoint_R"] <- new_R
eucast_disks <- which(rsi_translation$guideline %like% "EUCAST" &
rsi_translation$method == "DISK" &
rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0)
rsi_translation$method == "DISK" &
rsi_translation$breakpoint_S - rsi_translation$breakpoint_R != 0 &
!is.na(rsi_translation$breakpoint_R))
rsi_translation[eucast_disks, "breakpoint_R"] <- rsi_translation[eucast_disks, "breakpoint_R", drop = TRUE] + 1
# Greek symbols and EM dash symbols are not allowed by CRAN, so replace them with ASCII:

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3d85846458b19df96198695470e87ed6

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docs/404.html
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@ -43,7 +43,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>

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docs/LICENSE-text.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>

6
docs/articles/datasets.html
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@ -44,7 +44,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -1168,12 +1168,12 @@ column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>
<em>breakpoint_S</em>, <em>breakpoint_R</em> and <em>uti</em>.</p>
<p>This data set is in R available as <code>rsi_translation</code>,
after you load the <code>AMR</code> package.</p>
<p>It was last updated on 10 May 2022 13:51:53 UTC. Find more info about
<p>It was last updated on 10 May 2022 19:28:23 UTC. Find more info about
the structure of this data set <a href="https://msberends.github.io/AMR/reference/rsi_translation.html">here</a>.</p>
<p><strong>Direct download links:</strong></p>
<ul>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds" class="external-link">R
file</a> (39 kB)<br>
file</a> (40 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx" class="external-link">Excel
file</a> (0.7 MB)<br>

2
docs/authors.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>

5
docs/index.html
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@ -47,7 +47,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -195,7 +195,8 @@
<code>AMR</code> (for R) <img src="./logo.svg" align="right"><a class="anchor" aria-label="anchor" href="#amr-for-r-"></a>
</h1></div>
<blockquote>
<p>Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
<p>Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="reference/as.rsi.html">as.rsi()</a></code>!</p>
<p>Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.</p>
</blockquote>
<div class="section level3">
<h3 id="what-is-amr-for-r">What is <code>AMR</code> (for R)?<a class="anchor" aria-label="anchor" href="#what-is-amr-for-r"></a>

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docs/news/index.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -157,12 +157,16 @@
</div>
<div class="section level2">
<h2 class="page-header" data-toc-text="1.8.1.9005" id="amr-1819005">
<code>AMR</code> 1.8.1.9005<a class="anchor" aria-label="anchor" href="#amr-1819005"></a></h2>
<h2 class="page-header" data-toc-text="1.8.1.9006" id="amr-1819006">
<code>AMR</code> 1.8.1.9006<a class="anchor" aria-label="anchor" href="#amr-1819006"></a></h2>
<div class="section level3">
<h3 id="last-updated-may-1-8-1-9005"><small>Last updated: 10 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9005"></a></h3>
<h3 id="last-updated-may-1-8-1-9006"><small>Last updated: 10 May 2022</small><a class="anchor" aria-label="anchor" href="#last-updated-may-1-8-1-9006"></a></h3>
<div class="section level4">
<h4 id="changed-1-8-1-9005">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9005"></a></h4>
<h4 id="new-1-8-1-9006">New<a class="anchor" aria-label="anchor" href="#new-1-8-1-9006"></a></h4>
<ul><li>EUCAST 2022 and CLSI 2022 guidelines have been added for <code><a href="../reference/as.rsi.html">as.rsi()</a></code>. EUCAST 2022 is now the new default guideline for all MIC and disks diffusion interpretations.</li>
</ul></div>
<div class="section level4">
<h4 id="changed-1-8-1-9006">Changed<a class="anchor" aria-label="anchor" href="#changed-1-8-1-9006"></a></h4>
<ul><li>Fix for <code><a href="../reference/as.rsi.html">as.rsi()</a></code> on certain EUCAST breakpoints for MIC values</li>
<li>Removed <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> for MIC values, since MIC are not integer values and running <code><a href="https://rdrr.io/r/base/table.html" class="external-link">table()</a></code> on MIC values consequently failed for not being able to retrieve the level position (as that’s how normally <code><a href="https://rdrr.io/r/base/integer.html" class="external-link">as.integer()</a></code> on <code>factor</code>s work)</li>
<li>

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docs/reference/as.mic.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -194,7 +194,7 @@
</div>
<div id="details">
<h2>Details</h2>
<p>To interpret MIC values as RSI values, use <code><a href="as.rsi.html">as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021).</p>
<p>To interpret MIC values as RSI values, use <code><a href="as.rsi.html">as.rsi()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).</p>
<p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/r/base/factor.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p><div class="sourceCode"><pre><code><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/random.html">random_mic</a></span><span class="op">(</span><span class="fl">10</span><span class="op">)</span>
<span class="va">x</span>
<span class="co">#&gt; Class &lt;mic&gt;</span>

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -225,7 +225,7 @@
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antimicrobial code with <code><a href="as.ab.html">as.ab()</a></code></p></dd>
<dt>guideline</dt>
<dd><p>defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see <em>Details</em></p></dd>
<dd><p>defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see <em>Details</em></p></dd>
<dt>uti</dt>
<dd><p>(Urinary Tract Infection) A vector with <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s (<code>TRUE</code> or <code>FALSE</code>) to specify whether a UTI specific interpretation from the guideline should be chosen. For using <code>as.rsi()</code> on a <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a>, this can also be a column containing <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a>s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See <em>Examples</em>.</p></dd>
<dt>conserve_capped_values</dt>
@ -263,8 +263,8 @@
<h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2021"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2022"</code> or <code>"CLSI 2022"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
</div>
<div class="section">
@ -278,7 +278,7 @@
<h3 id="machine-readable-interpretation-guidelines">Machine-Readable Interpretation Guidelines<a class="anchor" aria-label="anchor" href="#machine-readable-interpretation-guidelines"></a></h3>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,318 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
<p>The repository of this package <a href="https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt" class="external-link">contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 20,369 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. <strong>This allows for easy implementation of these rules in laboratory information systems (LIS)</strong>. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.</p>
</div>
<div class="section">

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@ -17,7 +17,7 @@
</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="Released version">1.8.1.9004</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>

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docs/reference/plot.html
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@ -17,7 +17,7 @@
</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="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
<span class="fa fa-question-circle"></span>
How to
@ -168,7 +168,7 @@
mo <span class="op">=</span> <span class="cn">NULL</span>,
ab <span class="op">=</span> <span class="cn">NULL</span>,
guideline <span class="op">=</span> <span class="st">"EUCAST"</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"MIC values of"</span>, <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,
ylab <span class="op">=</span> <span class="st">"Frequency"</span>,
xlab <span class="op">=</span> <span class="st">"Minimum Inhibitory Concentration (mg/L)"</span>,
colours_RSI <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"#ED553B"</span>, <span class="st">"#3CAEA3"</span>, <span class="st">"#F6D55C"</span><span class="op">)</span>,
@ -178,7 +178,7 @@
<span class="op">)</span>
<span class="co"># S3 method for mic</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
ab <span class="op">=</span> <span class="cn">NULL</span>,
@ -193,12 +193,12 @@
<span class="op">)</span>
<span class="co"># S3 method for mic</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu">plot</span><span class="op">(</span>
<span class="va">x</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Disk zones of"</span>, <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,
ylab <span class="op">=</span> <span class="st">"Frequency"</span>,
xlab <span class="op">=</span> <span class="st">"Disk diffusion diameter (mm)"</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
@ -211,7 +211,7 @@
<span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
mo <span class="op">=</span> <span class="cn">NULL</span>,
ab <span class="op">=</span> <span class="cn">NULL</span>,
@ -226,19 +226,19 @@
<span class="op">)</span>
<span class="co"># S3 method for disk</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu">plot</span><span class="op">(</span>
<span class="va">x</span>,
ylab <span class="op">=</span> <span class="st">"Percentage"</span>,
xlab <span class="op">=</span> <span class="st">"Antimicrobial Interpretation"</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Overview of"</span>, <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
main <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,
<span class="va">...</span>
<span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/autoplot.html" class="external-link">autoplot</a></span><span class="op">(</span>
<span class="fu">autoplot</span><span class="op">(</span>
<span class="va">object</span>,
title <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span><span class="st">"Resistance Overview of"</span>, <span class="fu"><a href="https://rdrr.io/r/base/deparse.html" class="external-link">deparse</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/substitute.html" class="external-link">substitute</a></span><span class="op">(</span><span class="va">object</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>,
xlab <span class="op">=</span> <span class="st">"Antimicrobial Interpretation"</span>,
@ -249,7 +249,7 @@
<span class="op">)</span>
<span class="co"># S3 method for rsi</span>
<span class="fu"><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="external-link">fortify</a></span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
<span class="fu">fortify</span><span class="op">(</span><span class="va">object</span>, <span class="va">...</span><span class="op">)</span></code></pre></div>
</div>
<div id="arguments">
@ -283,7 +283,7 @@ The <code><a href="https://ggplot2.tidyverse.org/reference/fortify.html" class="
<div id="details">
<h2>Details</h2>
<p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".</p>
<p>For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the <code>guideline</code> argument are: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012" and "CLSI 2011".</p>
<p>Simply using <code>"CLSI"</code> or <code>"EUCAST"</code> as input will automatically select the latest version of that guideline.</p>
</div>
<div id="stable-lifecycle">
@ -336,7 +336,7 @@ The <a href="lifecycle.html">lifecycle</a> of this function is <strong>stable</s
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
</div>
</footer></div>

12
docs/reference/rsi_translation.html
View File

@ -1,5 +1,5 @@
<!DOCTYPE html>
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<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>Data Set for R/SI Interpretation — rsi_translation • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link href="https://cdnjs.cloudflare.com/ajax/libs/bootswatch/3.4.0/flatly/bootstrap.min.css" rel="stylesheet" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set for R/SI Interpretation — rsi_translation"><meta property="og:description" content="Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use as.rsi() to transform MICs or disks measurements to R/SI values."><meta property="og:image" content="https://msberends.github.io/AMR/logo.svg"><meta name="twitter:card" content="summary_large_image"><meta name="twitter:creator" content="@msberends"><meta name="twitter:site" content="@univgroningen"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
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@ -17,7 +17,7 @@
</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="Released version">1.8.1</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>
@ -30,7 +30,7 @@
</a>
</li>
<li class="dropdown">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" aria-expanded="false">
<a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
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How to
@ -158,7 +158,7 @@
</div>
<div class="ref-description">
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
<p>Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use <code><a href="as.rsi.html">as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<div id="ref-usage">
@ -167,7 +167,7 @@
<div id="format">
<h2>Format</h2>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 20,318 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> with 20,369 observations and 11 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
<li><p><code>method</code><br> Either "DISK" or "MIC"</p></li>
<li><p><code>site</code><br> Body site, e.g. "Oral" or "Respiratory"</p></li>
<li><p><code>mo</code><br> Microbial ID, see <code><a href="as.mo.html">as.mo()</a></code></p></li>
@ -212,7 +212,7 @@
</div>
<div class="pkgdown">
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.2.</p>
<p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.3.</p>
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2
docs/survey.html
View File

@ -17,7 +17,7 @@
</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="Released version">1.8.1.9005</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">1.8.1.9006</span>
</span>
</div>

4
index.md
View File

@ -1,6 +1,8 @@
# `AMR` (for R) <img src="./logo.svg" align="right"/>
> Update March 2022: All functions in this package are considered to be stable. Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
> Update May 2022: EUCAST 2022 and CLSI 2022 guidelines have been added for `as.rsi()`!
>
> Updates to the AMR interpretation rules (such as by EUCAST and CLSI), the microbial taxonomy, and the antibiotic dosages will all be updated every 6 to 12 months.
### What is `AMR` (for R)?

2
man/as.mic.Rd
View File

@ -38,7 +38,7 @@ Ordered \link{factor} with additional class \code{\link{mic}}, that in mathemati
This transforms vectors to a new class \code{\link{mic}}, which treats the input as decimal numbers, while maintaining operators (such as ">=") and only allowing valid MIC values known to the field of (medical) microbiology.
}
\details{
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2021) and CLSI (2010-2021).
To interpret MIC values as RSI values, use \code{\link[=as.rsi]{as.rsi()}} on MIC values. It supports guidelines from EUCAST (2011-2022) and CLSI (2011-2022).
This class for MIC values is a quite a special data type: formally it is an ordered \link{factor} with valid MIC values as \link{factor} levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:\preformatted{x <- random_mic(10)
x

8
man/as.rsi.Rd
View File

@ -68,7 +68,7 @@ is.rsi.eligible(x, threshold = 0.05)
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2021) and CLSI (2010-2021), see \emph{Details}}
\item{guideline}{defaults to the latest included EUCAST guideline, supports EUCAST (2011-2022) and CLSI (2011-2022), see \emph{Details}}
\item{uti}{(Urinary Tract Infection) A vector with \link{logical}s (\code{TRUE} or \code{FALSE}) to specify whether a UTI specific interpretation from the guideline should be chosen. For using \code{\link[=as.rsi]{as.rsi()}} on a \link{data.frame}, this can also be a column containing \link{logical}s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See \emph{Examples}.}
@ -111,9 +111,9 @@ your_data \%>\% mutate(across(where(is.disk), as.rsi)) # since dplyr 1.0.0
\subsection{Supported Guidelines}{
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021).
For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022).
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2021"} or \code{"CLSI 2021"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
Thus, the \code{guideline} argument must be set to e.g., \code{"EUCAST 2022"} or \code{"CLSI 2022"}. By simply using \code{"EUCAST"} (the default) or \code{"CLSI"} as input, the latest included version of that guideline will automatically be selected. You can set your own data set using the \code{reference_data} argument. The \code{guideline} argument will then be ignored.
}
\subsection{After Interpretation}{
@ -123,7 +123,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Interpretation Guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 20,318 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 20,369 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
}
\subsection{Other}{

8
man/plot.Rd
View File

@ -18,7 +18,7 @@
mo = NULL,
ab = NULL,
guideline = "EUCAST",
main = paste("MIC values of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Minimum Inhibitory Concentration (mg/L)",
colours_RSI = c("#ED553B", "#3CAEA3", "#F6D55C"),
@ -45,7 +45,7 @@
\method{plot}{disk}(
x,
main = paste("Disk zones of", deparse(substitute(x))),
main = deparse(substitute(x)),
ylab = "Frequency",
xlab = "Disk diffusion diameter (mm)",
mo = NULL,
@ -77,7 +77,7 @@
x,
ylab = "Percentage",
xlab = "Antimicrobial Interpretation",
main = paste("Resistance Overview of", deparse(substitute(x))),
main = deparse(substitute(x)),
...
)
@ -125,7 +125,7 @@ Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support f
\details{
The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012", "CLSI 2011" and "CLSI 2010".
For interpreting MIC values as well as disk diffusion diameters, supported guidelines to be used as input for the \code{guideline} argument are: "EUCAST 2022", "EUCAST 2021", "EUCAST 2020", "EUCAST 2019", "EUCAST 2018", "EUCAST 2017", "EUCAST 2016", "EUCAST 2015", "EUCAST 2014", "EUCAST 2013", "EUCAST 2012", "EUCAST 2011", "CLSI 2022", "CLSI 2021", "CLSI 2020", "CLSI 2019", "CLSI 2018", "CLSI 2017", "CLSI 2016", "CLSI 2015", "CLSI 2014", "CLSI 2013", "CLSI 2012" and "CLSI 2011".
Simply using \code{"CLSI"} or \code{"EUCAST"} as input will automatically select the latest version of that guideline.
}

4
man/rsi_translation.Rd
View File

@ -5,7 +5,7 @@
\alias{rsi_translation}
\title{Data Set for R/SI Interpretation}
\format{
A \link{data.frame} with 20,318 observations and 11 variables:
A \link{data.frame} with 20,369 observations and 11 variables:
\itemize{
\item \code{guideline}\cr Name of the guideline
\item \code{method}\cr Either "DISK" or "MIC"
@ -24,7 +24,7 @@ A \link{data.frame} with 20,318 observations and 11 variables:
rsi_translation
}
\description{
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2021). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
Data set containing reference data to interpret MIC and disk diffusion to R/SI values, according to international guidelines. Currently implemented guidelines are EUCAST (2011-2022) and CLSI (2011-2022). Use \code{\link[=as.rsi]{as.rsi()}} to transform MICs or disks measurements to R/SI values.
}
\details{
The repository of this \code{AMR} package contains a file comprising this exact data set: \url{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}. This file \strong{allows for machine reading EUCAST and CLSI guidelines}, which is almost impossible with the Excel and PDF files distributed by EUCAST and CLSI. The file is updated automatically and the \code{mo} and \code{ab} columns have been transformed to contain the full official names instead of codes.