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(v1.7.1.9053) fortify() methods

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dr. M.S. (Matthijs) Berends 2021-11-01 13:51:13 +01:00
parent 91149d6d35
commit 9a2c431e16
25 changed files with 1046 additions and 965 deletions
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42
DESCRIPTION
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@ -1,6 +1,6 @@
Package: AMR
Version: 1.7.1.9052
Date: 2021-10-06
Version: 1.7.1.9053
Date: 2021-11-01
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
@ -12,32 +12,32 @@ Authors@R: c(
email = "m.s.berends@umcg.nl",
role = c("aut", "cre"),
comment = c(ORCID = "0000-0001-7620-1800")),
person(given = "Dennis",
family = "Souverein",
role = c("aut", "ctb"),
comment = c(ORCID = "0000-0003-0455-0336")),
person(given = c("Erwin", "E.", "A."),
family = "Hassing",
role = c("aut", "ctb")),
person(given = c("Christian", "F."),
family = "Luz",
role = c("aut", "ctb"),
comment = c(ORCID = "0000-0001-5809-5995")),
person(given = c("Alexander", "W."),
family = "Friedrich",
role = "ths",
comment = c(ORCID = "0000-0003-4881-038X")),
person(given = c("Bhanu", "N.", "M."),
family = "Sinha",
role = "ths",
comment = c(ORCID = "0000-0003-1634-0010")),
person(given = c("Casper", "J."),
family = "Albers",
role = "ths",
comment = c(ORCID = "0000-0002-9213-6743")),
person(given = c("Judith", "M."),
family = "Fonville",
role = "ctb"),
person(given = c("Alexander", "W."),
family = "Friedrich",
role = "ths",
comment = c(ORCID = "0000-0003-4881-038X")),
person(given = "Corinna",
family = "Glasner",
role = "ths",
comment = c(ORCID = "0000-0003-1241-1328")),
person(given = c("Judith", "M."),
family = "Fonville",
role = "ctb"),
person(given = c("Erwin", "E.", "A."),
family = "Hassing",
role = "ctb"),
person(given = c("Eric", "H.", "L.", "C.", "M."),
family = "Hazenberg",
role = "ctb"),
@ -59,10 +59,10 @@ Authors@R: c(
person(given = c("Rogier", "P."),
family = "Schade",
role = "ctb"),
person(given = "Dennis",
family = "Souverein",
role = "ctb",
comment = c(ORCID = "0000-0003-0455-0336")),
person(given = c("Bhanu", "N.", "M."),
family = "Sinha",
role = "ths",
comment = c(ORCID = "0000-0003-1634-0010")),
person(given = "Anthony",
family = "Underwood",
role = "ctb",
@ -83,7 +83,7 @@ Suggests:
tinytest,
xml2
VignetteBuilder: knitr,rmarkdown
URL: https://github.com/msberends/AMR, https://msberends.github.io/AMR
URL: https://msberends.github.io/AMR, https://github.com/msberends/AMR
BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE
Encoding: UTF-8

10
NEWS.md
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@ -1,5 +1,5 @@
# `AMR` 1.7.1.9052
## <small>Last updated: 6 October 2021</small>
# `AMR` 1.7.1.9053
## <small>Last updated: 1 November 2021</small>
### Breaking changes
* Removed `p_symbol()` and all `filter_*()` functions (except for `filter_first_isolate()`), which were all deprecated in a previous package version
@ -39,7 +39,7 @@
* When printing a tibble with any old MO code, a warning will be thrown that old codes should be updated using `as.mo()`
* Improved automatic column selector when `col_*` arguments are left blank, e.g. in `first_isolate()`
* The right input types for `random_mic()`, `random_disk()` and `random_rsi()` are now enforced
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Dutch, English, French, German, Italian, Portuguese and Spanish
* `as.rsi()` can now correct for textual input (such as "Susceptible", "Resistant") in Danish, Dutch, English, French, German, Italian, Portuguese and Spanish
* When warnings are thrown because of too few isolates in any `count_*()`, `proportion_*()` function (or `resistant()` or `susceptible()`), the `dplyr` group will be shown, if available
* Fix for legends created with `scale_rsi_colours()` when using `ggplot2` v3.3.4 or higher (this is ggplot2 bug 4511, soon to be fixed)
* Fix for minor translation errors
@ -47,6 +47,10 @@
* Improved algorithm for generating random MICs with `random_mic()`
* Improved plot legends for MICs and disk diffusion values
* Improved speed of `as.ab()` and all `ab_*()` functions
* Added `fortify()` extensions for plotting methods
### Other
* This package is now being maintained by two epidemiologists and a data scientist from two different non-profit healthcare organisations. All functions in this package are now all 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 yearly from now on.
# AMR 1.7.1

67
R/aa_helper_functions.R
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@ -53,15 +53,68 @@ pm_left_join <- function(x, y, by = NULL, suffix = c(".x", ".y")) {
merged
}
quick_case_when <- function(...) {
vectors <- list(...)
split <- lapply(vectors, function(x) unlist(strsplit(paste(deparse(x), collapse = ""), "~", fixed = TRUE)))
for (i in seq_len(length(vectors))) {
if (eval(parse(text = split[[i]][1]), envir = parent.frame())) {
return(eval(parse(text = split[[i]][2]), envir = parent.frame()))
# copied and slightly rewritten from poorman under same license (2021-10-15)
quick_case_when <- function (...) {
fs <- list(...)
lapply(fs, function(x) if (class(x) != "formula")
stop("`case_when()` requires formula inputs."))
n <- length(fs)
if (n == 0L)
stop("No cases provided.")
validate_case_when_length <- function (query, value, fs) {
lhs_lengths <- lengths(query)
rhs_lengths <- lengths(value)
all_lengths <- unique(c(lhs_lengths, rhs_lengths))
if (length(all_lengths) <= 1L)
return(all_lengths[[1L]])
non_atomic_lengths <- all_lengths[all_lengths != 1L]
len <- non_atomic_lengths[[1L]]
if (length(non_atomic_lengths) == 1L)
return(len)
inconsistent_lengths <- non_atomic_lengths[-1L]
lhs_problems <- lhs_lengths %in% inconsistent_lengths
rhs_problems <- rhs_lengths %in% inconsistent_lengths
problems <- lhs_problems | rhs_problems
if (any(problems)) {
stop("The following formulas must be length ", len, " or 1, not ",
paste(inconsistent_lengths, collapse = ", "), ".\n ",
paste(fs[problems], collapse = "\n "),
call. = FALSE)
}
}
return(NA)
replace_with <- function (x, i, val, arg_name) {
if (is.null(val))
return(x)
i[is.na(i)] <- FALSE
if (length(val) == 1L) {
x[i] <- val
}
else {
x[i] <- val[i]
}
x
}
query <- vector("list", n)
value <- vector("list", n)
default_env <- parent.frame()
for (i in seq_len(n)) {
query[[i]] <- eval(fs[[i]][[2]], envir = default_env)
value[[i]] <- eval(fs[[i]][[3]], envir = default_env)
if (!is.logical(query[[i]]))
stop(fs[[i]][[2]], " does not return a `logical` vector.")
}
m <- validate_case_when_length(query, value, fs)
out <- value[[1]][rep(NA_integer_, m)]
replaced <- rep(FALSE, m)
for (i in seq_len(n)) {
out <- replace_with(out, query[[i]] & !replaced, value[[i]],
NULL)
replaced <- replaced | (query[[i]] & !is.na(query[[i]]))
}
out
}
# No export, no Rd

29
R/plot.R
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@ -28,7 +28,7 @@
#' Functions to plot classes `rsi`, `mic` and `disk`, with support for base \R and `ggplot2`.
#' @inheritSection lifecycle Maturing Lifecycle
#' @inheritSection AMR Read more on Our Website!
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()]
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()])
#' @param mo any (vector of) text that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
@ -46,7 +46,9 @@
#' @name plot
#' @rdname plot
#' @return The `autoplot()` functions return a [`ggplot`][ggplot2::ggplot()] model that is extendible with any `ggplot2` function.
#' @param ... arguments passed on to [as.rsi()]
#'
#' The `fortify()` functions return a [data.frame] as an extension for usage in the [ggplot2::ggplot()] function.
#' @param ... arguments passed on to methods
#' @examples
#' some_mic_values <- random_mic(size = 100)
#' some_disk_values <- random_disk(size = 100, mo = "Escherichia coli", ab = "cipro")
@ -283,6 +285,13 @@ autoplot.mic <- function(object,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method fortify mic
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.mic <- function(object, ...) {
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
c("x", "y"))
}
#' @method plot disk
#' @export
@ -500,6 +509,14 @@ autoplot.disk <- function(object,
ggplot2::labs(title = title, x = xlab, y = ylab, subtitle = cols_sub$sub)
}
#' @method fortify disk
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.disk <- function(object, ...) {
stats::setNames(as.data.frame(plot_prepare_table(object, expand = FALSE)),
c("x", "y"))
}
#' @method plot rsi
#' @export
#' @importFrom graphics plot text axis
@ -646,6 +663,14 @@ autoplot.rsi <- function(object,
ggplot2::theme(legend.position = "none")
}
#' @method fortify rsi
#' @rdname plot
# will be exported using s3_register() in R/zzz.R
fortify.rsi <- function(object, ...) {
stats::setNames(as.data.frame(table(object)),
c("x", "y"))
}
plot_prepare_table <- function(x, expand) {
x <- x[!is.na(x)]
stop_if(length(x) == 0, "no observations to plot", call = FALSE)

4
R/zzz.R
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@ -66,6 +66,10 @@ if (utf8_supported && !is_latex) {
s3_register("ggplot2::autoplot", "mic")
s3_register("ggplot2::autoplot", "disk")
s3_register("ggplot2::autoplot", "resistance_predict")
# Support for fortify from the ggplot2 package
s3_register("ggplot2::fortify", "rsi")
s3_register("ggplot2::fortify", "mic")
s3_register("ggplot2::fortify", "disk")
# Support vctrs package for use in e.g. dplyr verbs
s3_register("vctrs::vec_ptype2", "ab.character")
s3_register("vctrs::vec_ptype2", "character.ab")

BIN
data-raw/AMR_latest.tar.gz
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178
docs/articles/datasets.html
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@ -30,8 +30,6 @@
<![endif]-->
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-article">
<header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
<div class="container">
@ -44,7 +42,7 @@
</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="Latest development version">1.7.1.9052</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -169,7 +167,7 @@
</ul>
<ul class="nav navbar-nav navbar-right">
<li>
<a href="https://github.com/msberends/AMR" class="external-link">
<a href="https://github.com/msberends/AMR">
<span class="fab fa-github"></span>
Source Code
@ -190,9 +188,9 @@
<div class="page-header toc-ignore">
<h1 data-toc-skip>Data sets for download / own use</h1>
<h4 data-toc-skip class="date">06 October 2021</h4>
<h4 class="date">01 November 2021</h4>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/master/vignettes/datasets.Rmd"><code>vignettes/datasets.Rmd</code></a></small>
<div class="hidden name"><code>datasets.Rmd</code></div>
</div>
@ -206,40 +204,40 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</p>
<div id="microorganisms-currently-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-currently-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (currently accepted names)</h2>
<a href="#microorganisms-currently-accepted-names" class="anchor"></a>Microorganisms (currently accepted names)</h2>
<p>A data set with 70,760 rows and 16 columns, containing the following column names:<br><em>mo</em>, <em>fullname</em>, <em>kingdom</em>, <em>phylum</em>, <em>class</em>, <em>order</em>, <em>family</em>, <em>genus</em>, <em>species</em>, <em>subspecies</em>, <em>rank</em>, <em>ref</em>, <em>species_id</em>, <em>source</em>, <em>prevalence</em> and <em>snomed</em>.</p>
<p>This data set is in R available as <code>microorganisms</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 09:31:11 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.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/microorganisms.rds" class="external-link">R file</a> (2.2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.rds">R file</a> (2.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx" class="external-link">Excel file</a> (6.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.xlsx">Excel file</a> (6.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt" class="external-link">plain text file</a> (14.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.txt">plain text file</a> (14.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas" class="external-link">SAS file</a> (30.7 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sas">SAS file</a> (30.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav" class="external-link">SPSS file</a> (18 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.sav">SPSS file</a> (18 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta" class="external-link">Stata file</a> (29.2 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.dta">Stata file</a> (29.2 MB)</li>
</ul>
<p><strong>NOTE: The exported files for SAS, SPSS and Stata do not contain SNOMED codes, as their file size would exceed 100 MB; the file size limit of GitHub.</strong> Advice? Use R instead.</p>
<div id="source" class="section level3">
<h3 class="hasAnchor">
<a href="#source" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source" class="anchor"></a>Source</h3>
<p>Our full taxonomy of microorganisms is based on the authoritative and comprehensive:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009" class="external-link">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<li>US Edition of SNOMED CT from 1 September 2020, retrieved from the <a href="https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009">Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)</a>, OID 2.16.840.1.114222.4.11.1009, version 12</li>
</ul>
</div>
<div id="example-content" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content" class="anchor"></a>Example content</h3>
<p>Included (sub)species per taxonomic kingdom:</p>
<table class="table">
<thead><tr class="header">
@ -426,39 +424,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="microorganisms-previously-accepted-names" class="section level2">
<h2 class="hasAnchor">
<a href="#microorganisms-previously-accepted-names" class="anchor" aria-hidden="true"></a>Microorganisms (previously accepted names)</h2>
<a href="#microorganisms-previously-accepted-names" class="anchor"></a>Microorganisms (previously accepted names)</h2>
<p>A data set with 14,338 rows and 4 columns, containing the following column names:<br><em>fullname</em>, <em>fullname_new</em>, <em>ref</em> and <em>prevalence</em>.</p>
<p><strong>Note:</strong> remember that the ‘ref’ columns contains the scientific reference to the old taxonomic entries, i.e. of column <em>‘fullname’</em>. For the scientific reference of the new names, i.e. of column <em>‘fullname_new’</em>, see the <code>microorganisms</code> data set.</p>
<p>This data set is in R available as <code>microorganisms.old</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 5 October 2021 13:12:28 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.old.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/microorganisms.old.rds" class="external-link">R file</a> (0.2 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.rds">R file</a> (0.2 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx" class="external-link">Excel file</a> (0.5 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.xlsx">Excel file</a> (0.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt" class="external-link">plain text file</a> (1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.txt">plain text file</a> (1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas" class="external-link">SAS file</a> (2.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sas">SAS file</a> (2.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav" class="external-link">SPSS file</a> (1.3 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.sav">SPSS file</a> (1.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta" class="external-link">Stata file</a> (2 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/microorganisms.old.dta">Stata file</a> (2 MB)</li>
</ul>
<div id="source-1" class="section level3">
<h3 class="hasAnchor">
<a href="#source-1" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source-1" class="anchor"></a>Source</h3>
<p>This data set contains old, previously accepted taxonomic names. The data sources are the same as the <code>microorganisms</code> data set:</p>
<ul>
<li>
<a href="http://www.catalogueoflife.org" class="external-link">Catalogue of Life</a> (included version: 2019)</li>
<a href="http://www.catalogueoflife.org">Catalogue of Life</a> (included version: 2019)</li>
<li>
<a href="https://lpsn.dsmz.de" class="external-link">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
<a href="https://lpsn.dsmz.de">List of Prokaryotic names with Standing in Nomenclature</a> (LPSN, last updated: 5 October 2021)</li>
</ul>
</div>
<div id="example-content-1" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-1" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content-1" class="anchor"></a>Example content</h3>
<p>Example rows when filtering on <em>Escherichia</em>:</p>
<table class="table">
<thead><tr class="header">
@ -492,39 +490,39 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="antibiotic-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antibiotic-agents" class="anchor" aria-hidden="true"></a>Antibiotic agents</h2>
<a href="#antibiotic-agents" class="anchor"></a>Antibiotic agents</h2>
<p>A data set with 456 rows and 14 columns, containing the following column names:<br><em>ab</em>, <em>cid</em>, <em>name</em>, <em>group</em>, <em>atc</em>, <em>atc_group1</em>, <em>atc_group2</em>, <em>abbreviations</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em>, <em>iv_units</em> and <em>loinc</em>.</p>
<p>This data set is in R available as <code>antibiotics</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 2 September 2021 11:50:06 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.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/antibiotics.rds" class="external-link">R file</a> (32 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.rds">R file</a> (32 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx" class="external-link">Excel file</a> (65 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.xlsx">Excel file</a> (65 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt" class="external-link">plain text file</a> (0.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.txt">plain text file</a> (0.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas" class="external-link">SAS file</a> (1.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sas">SAS file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav" class="external-link">SPSS file</a> (0.3 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.sav">SPSS file</a> (0.3 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta" class="external-link">Stata file</a> (0.3 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antibiotics.dta">Stata file</a> (0.3 MB)</li>
</ul>
<div id="source-2" class="section level3">
<h3 class="hasAnchor">
<a href="#source-2" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source-2" class="anchor"></a>Source</h3>
<p>This data set contains all EARS-Net and ATC codes gathered from WHO and WHONET, and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
<li><a href="https://whonet.org" class="external-link">WHONET software 2019</a></li>
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
<li><a href="https://whonet.org">WHONET software 2019</a></li>
</ul>
</div>
<div id="example-content-2" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-2" class="anchor" aria-hidden="true"></a>Example content</h3>
<table style="width:100%;" class="table">
<a href="#example-content-2" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="1%">
<col width="2%">
@ -660,37 +658,37 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="antiviral-agents" class="section level2">
<h2 class="hasAnchor">
<a href="#antiviral-agents" class="anchor" aria-hidden="true"></a>Antiviral agents</h2>
<a href="#antiviral-agents" class="anchor"></a>Antiviral agents</h2>
<p>A data set with 102 rows and 9 columns, containing the following column names:<br><em>atc</em>, <em>cid</em>, <em>name</em>, <em>atc_group</em>, <em>synonyms</em>, <em>oral_ddd</em>, <em>oral_units</em>, <em>iv_ddd</em> and <em>iv_units</em>.</p>
<p>This data set is in R available as <code>antivirals</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 29 August 2020 19:53:07 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/antibiotics.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/antivirals.rds" class="external-link">R file</a> (5 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.rds">R file</a> (5 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx" class="external-link">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.xlsx">Excel file</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt" class="external-link">plain text file</a> (16 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.txt">plain text file</a> (16 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas" class="external-link">SAS file</a> (80 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sas">SAS file</a> (80 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav" class="external-link">SPSS file</a> (68 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.sav">SPSS file</a> (68 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta" class="external-link">Stata file</a> (67 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/antivirals.dta">Stata file</a> (67 kB)</li>
</ul>
<div id="source-3" class="section level3">
<h3 class="hasAnchor">
<a href="#source-3" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source-3" class="anchor"></a>Source</h3>
<p>This data set contains all ATC codes gathered from WHO and all compound IDs from PubChem. It also contains all brand names (synonyms) as found on PubChem and Defined Daily Doses (DDDs) for oral and parenteral administration.</p>
<ul>
<li>
<a href="https://www.whocc.no/atc_ddd_index/" class="external-link">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov" class="external-link">PubChem by the US National Library of Medicine</a></li>
<a href="https://www.whocc.no/atc_ddd_index/">ATC/DDD index from WHO Collaborating Centre for Drug Statistics Methodology</a> (note: this may not be used for commercial purposes, but is freely available from the WHO CC website for personal use)</li>
<li><a href="https://pubchem.ncbi.nlm.nih.gov">PubChem by the US National Library of Medicine</a></li>
</ul>
</div>
<div id="example-content-3" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-3" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content-3" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="4%">
@ -787,32 +785,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="intrinsic-bacterial-resistance" class="section level2">
<h2 class="hasAnchor">
<a href="#intrinsic-bacterial-resistance" class="anchor" aria-hidden="true"></a>Intrinsic bacterial resistance</h2>
<a href="#intrinsic-bacterial-resistance" class="anchor"></a>Intrinsic bacterial resistance</h2>
<p>A data set with 93,892 rows and 2 columns, containing the following column names:<br><em>microorganism</em> and <em>antibiotic</em>.</p>
<p>This data set is in R available as <code>intrinsic_resistant</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 6 October 2021 08:29:50 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.html">here</a>.</p>
<p>It was last updated on 6 October 2021 14:38:29 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/intrinsic_resistant.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/intrinsic_resistant.rds" class="external-link">R file</a> (69 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.rds">R file</a> (69 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx" class="external-link">Excel file</a> (0.9 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.xlsx">Excel file</a> (0.9 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt" class="external-link">plain text file</a> (3.5 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.txt">plain text file</a> (3.5 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas" class="external-link">SAS file</a> (7.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sas">SAS file</a> (7.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav" class="external-link">SPSS file</a> (5.1 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.sav">SPSS file</a> (5.1 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta" class="external-link">Stata file</a> (7 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/intrinsic_resistant.dta">Stata file</a> (7 MB)</li>
</ul>
<div id="source-4" class="section level3">
<h3 class="hasAnchor">
<a href="#source-4" class="anchor" aria-hidden="true"></a>Source</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
<a href="#source-4" class="anchor"></a>Source</h3>
<p>This data set contains all defined intrinsic resistance by EUCAST of all bug-drug combinations, and is based on <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">‘EUCAST Expert Rules’ and ‘EUCAST Intrinsic Resistance and Unusual Phenotypes’ v3.2</a> (2020).</p>
</div>
<div id="example-content-4" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-4" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content-4" class="anchor"></a>Example content</h3>
<p>Example rows when filtering on <em>Enterobacter cloacae</em>:</p>
<table class="table">
<thead><tr class="header">
@ -1002,32 +1000,32 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="interpretation-from-mic-values-disk-diameters-to-rsi" class="section level2">
<h2 class="hasAnchor">
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor" aria-hidden="true"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<a href="#interpretation-from-mic-values-disk-diameters-to-rsi" class="anchor"></a>Interpretation from MIC values / disk diameters to R/SI</h2>
<p>A data set with 22,000 rows and 10 columns, containing the following column names:<br><em>guideline</em>, <em>method</em>, <em>site</em>, <em>mo</em>, <em>ab</em>, <em>ref_tbl</em>, <em>disk_dose</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 5 October 2021 13:13:41 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>It was last updated on 6 October 2021 14:38:29 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> (37 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.rds">R file</a> (37 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>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.xlsx">Excel file</a> (0.7 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt" class="external-link">plain text file</a> (1.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.txt">plain text file</a> (1.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas" class="external-link">SAS file</a> (3.8 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sas">SAS file</a> (3.8 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav" class="external-link">SPSS file</a> (2.4 MB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.sav">SPSS file</a> (2.4 MB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta" class="external-link">Stata file</a> (3.5 MB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/rsi_translation.dta">Stata file</a> (3.5 MB)</li>
</ul>
<div id="source-5" class="section level3">
<h3 class="hasAnchor">
<a href="#source-5" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source-5" class="anchor"></a>Source</h3>
<p>This data set contains interpretation rules for MIC values and disk diffusion diameters. Included guidelines are CLSI (2010-2020) and EUCAST (2011-2021).</p>
</div>
<div id="example-content-5" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-5" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content-5" class="anchor"></a>Example content</h3>
<table class="table">
<colgroup>
<col width="8%">
@ -1132,33 +1130,33 @@ If you are reading this page from within R, please <a href="https://msberends.gi
</div>
<div id="dosage-guidelines-from-eucast" class="section level2">
<h2 class="hasAnchor">
<a href="#dosage-guidelines-from-eucast" class="anchor" aria-hidden="true"></a>Dosage guidelines from EUCAST</h2>
<a href="#dosage-guidelines-from-eucast" class="anchor"></a>Dosage guidelines from EUCAST</h2>
<p>A data set with 169 rows and 9 columns, containing the following column names:<br><em>ab</em>, <em>name</em>, <em>type</em>, <em>dose</em>, <em>dose_times</em>, <em>administration</em>, <em>notes</em>, <em>original_txt</em> and <em>eucast_version</em>.</p>
<p>This data set is in R available as <code>dosage</code>, after you load the <code>AMR</code> package.</p>
<p>It was last updated on 25 January 2021 20:58:20 UTC. Find more info about the structure of this data set <a href="https://msberends.github.io/AMR/reference/dosage.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/dosage.rds" class="external-link">R file</a> (3 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.rds">R file</a> (3 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx" class="external-link">Excel file</a> (14 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.xlsx">Excel file</a> (14 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt" class="external-link">plain text file</a> (15 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.txt">plain text file</a> (15 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas" class="external-link">SAS file</a> (52 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sas">SAS file</a> (52 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav" class="external-link">SPSS file</a> (45 kB)<br>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.sav">SPSS file</a> (45 kB)<br>
</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta" class="external-link">Stata file</a> (44 kB)</li>
<li>Download as <a href="https://github.com/msberends/AMR/raw/main/data-raw/../data-raw/dosage.dta">Stata file</a> (44 kB)</li>
</ul>
<div id="source-6" class="section level3">
<h3 class="hasAnchor">
<a href="#source-6" class="anchor" aria-hidden="true"></a>Source</h3>
<a href="#source-6" class="anchor"></a>Source</h3>
<p>EUCAST breakpoints used in this package are based on the dosages in this data set.</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/" class="external-link">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
<p>Currently included dosages in the data set are meant for: <a href="https://www.eucast.org/clinical_breakpoints/">‘EUCAST Clinical Breakpoint Tables’ v11.0</a> (2021).</p>
</div>
<div id="example-content-6" class="section level3">
<h3 class="hasAnchor">
<a href="#example-content-6" class="anchor" aria-hidden="true"></a>Example content</h3>
<a href="#example-content-6" class="anchor"></a>Example content</h3>
<table class="table">
<thead><tr class="header">
<th align="center">ab</th>
@ -1255,13 +1253,11 @@ If you are reading this page from within R, please <a href="https://msberends.gi
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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<h1>The <code>AMR</code> Package</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/amr.R'><code>R/amr.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/amr.R'><code>R/amr.R</code></a></small>
<div class="hidden name"><code>AMR.Rd</code></div>
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<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p><code>AMR</code> is a free, open-source and independent <span style="R">R</span> package to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible antimicrobial resistance data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.</p>
<p>After installing this package, <span style="R">R</span> knows ~70,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>After installing this package, <span style="R">R</span> knows ~71,000 distinct microbial species and all ~560 antibiotic, antimycotic and antiviral drugs by name and code (including ATC, EARS-NET, LOINC and SNOMED CT), and knows all about valid R/SI and MIC values. It supports any data format, including WHONET/EARS-Net data.</p>
<p>This package is fully independent of any other <span style="R">R</span> package and works on Windows, macOS and Linux with all versions of <span style="R">R</span> since R-3.0.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen, in collaboration with non-profit organisations Certe Medical Diagnostics and Advice and University Medical Center Groningen. This <span style="R">R</span> package is actively maintained and free software; you can freely use and distribute it for both personal and commercial (but not patent) purposes under the terms of the GNU General Public License version 2.0 (GPL-2), as published by the Free Software Foundation.</p>
<p>This package can be used for:</p><ul>
<li><p>Reference for the taxonomy of microorganisms, since the package contains all microbial (sub)species from the Catalogue of Life and List of Prokaryotic names with Standing in Nomenclature</p></li>
@ -310,11 +302,11 @@ The Netherlands
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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<div class="col-md-9 contents">
<div class="page-header">
<h1>Data Sets with 558 Antimicrobial Drugs</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>antibiotics.Rd</code></div>
</div>
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<p>Two data sets containing all antibiotics/antimycotics and antivirals. Use <code><a href='as.ab.html'>as.ab()</a></code> or one of the <code><a href='ab_property.html'>ab_*</a></code> functions to retrieve values from the antibiotics data set. Three identifiers are included in this data set: an antibiotic ID (<code>ab</code>, primarily used in this package) as defined by WHONET/EARS-Net, an ATC code (<code>atc</code>) as defined by the WHO, and a Compound ID (<code>cid</code>) as found in PubChem. Other properties in this data set are derived from one or more of these codes. Note that some drugs have multiple ATC codes.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>antibiotics</span>
<pre class="usage"><span class='va'>antibiotics</span>
<span class='va'>antivirals</span></code></pre></div>
<span class='va'>antivirals</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-antibiotics-'><a class='anchor' aria-hidden='true' href='#list-antibiotics-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>group</code><br /> A short and concise group name, based on WHONET and WHOCC definitions</p></li>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC, like <code>J01CR02</code></p></li>
<li><p><code>atc_group1</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC, like <code>"Macrolides, lincosamides and streptogramins"</code></p></li>
<li><p><code>atc_group2</code><br /> Official chemical subgroup (4th level ATC code) as defined by the WHOCC, like <code>"Macrolides"</code></p></li>
<li><p><code>abbr</code><br /> List of abbreviations as used in many countries, also for antibiotic susceptibility testing (AST)</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment, currently available for 170 drugs</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 145 drugs</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
<li><p><code>loinc</code><br /> All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use <code><a href='ab_property.html'>ab_loinc()</a></code> to retrieve them quickly, see <code><a href='ab_property.html'>ab_property()</a></code>.</p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antibiotics data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 456 observations and 14 variables:</h3>
<ul>
<li><p><code>ab</code><br /> Antibiotic ID as used in this package (such as <code>AMC</code>), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available</p></li>
@ -346,59 +266,7 @@
</ul>
<h3 class='hasAnchor' id='for-the-'><a class='anchor' aria-hidden='true' href='#for-the-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-antivirals-'><a class='anchor' aria-hidden='true' href='#list-antivirals-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-data-set-a-'><a class='anchor' aria-hidden='true' href='#-data-set-a-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='list-data-frame-'><a class='anchor' aria-hidden='true' href='#list-data-frame-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
<li><p><code>cid</code><br /> Compound ID as found in PubChem</p></li>
<li><p><code>name</code><br /> Official name as used by WHONET/EARS-Net or the WHO</p></li>
<li><p><code>atc_group</code><br /> Official pharmacological subgroup (3rd level ATC code) as defined by the WHOCC</p></li>
<li><p><code>synonyms</code><br /> Synonyms (often trade names) of a drug, as found in PubChem based on their compound ID</p></li>
<li><p><code>oral_ddd</code><br /> Defined Daily Dose (DDD), oral treatment</p></li>
<li><p><code>oral_units</code><br /> Units of <code>oral_ddd</code></p></li>
<li><p><code>iv_ddd</code><br /> Defined Daily Dose (DDD), parenteral treatment</p></li>
<li><p><code>iv_units</code><br /> Units of <code>iv_ddd</code></p></li>
</ul>
<h3 class='hasAnchor' id='-with-observations-and-variables-'><a class='anchor' aria-hidden='true' href='#-with-observations-and-variables-'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>For the antivirals data set: a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 102 observations and 9 variables:</h3>
<ul>
<li><p><code>atc</code><br /> ATC codes (Anatomical Therapeutic Chemical) as defined by the WHOCC</p></li>
@ -422,7 +290,7 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Properties that are based on an ATC code are only available when an ATC is available. These properties are: <code>atc_group1</code>, <code>atc_group2</code>, <code>oral_ddd</code>, <code>oral_units</code>, <code>iv_ddd</code> and <code>iv_units</code>.</p>
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
<p>Synonyms (i.e. trade names) were derived from the Compound ID (<code>cid</code>) and consequently only available where a CID is available.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>These data sets are available as 'flat files' for use even without <span style="R">R</span> - you can find the files here:</p><ul>
@ -470,11 +338,11 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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@ -483,8 +351,6 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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docs/reference/as.mo.html
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@ -58,8 +58,6 @@
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@ -71,15 +69,9 @@
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@ -93,7 +85,7 @@
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<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="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Transform Input to a Microorganism Code</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo.R'><code>R/mo.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo.R'><code>R/mo.R</code></a></small>
<div class="hidden name"><code>as.mo.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>Use this function to determine a valid microorganism code (<code>mo</code>). Determination is done using intelligent rules and the complete taxonomic kingdoms Bacteria, Chromista, Protozoa, Archaea and most microbial species from the kingdom Fungi (see <em>Source</em>). The input can be almost anything: a full name (like <code>"Staphylococcus aureus"</code>), an abbreviated name (such as <code>"S. aureus"</code>), an abbreviation known in the field (such as <code>"MRSA"</code>), or just a genus. See <em>Examples</em>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.mo</span><span class='op'>(</span>
<pre class="usage"><span class='fu'>as.mo</span><span class='op'>(</span>
<span class='va'>x</span>,
Becker <span class='op'>=</span> <span class='cn'>FALSE</span>,
Lancefield <span class='op'>=</span> <span class='cn'>FALSE</span>,
@ -264,7 +256,7 @@
<span class='fu'>mo_uncertainties</span><span class='op'>(</span><span class='op'>)</span>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<span class='fu'>mo_renamed</span><span class='op'>(</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -315,10 +307,10 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='general-info'><a class='anchor' aria-hidden='true' href='#general-info'></a>General Info</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>General Info</h3>
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre><code> Code Full name
<p>A microorganism (MO) code from this package (class: <code>mo</code>) is human readable and typically looks like these examples:</p><pre> Code Full name
--------------- --------------------------------------
B_KLBSL Klebsiella
B_KLBSL_PNMN Klebsiella pneumoniae
@ -330,7 +322,7 @@
| \----&gt; genus, a 5-7 letter acronym
\----&gt; taxonomic kingdom: A (Archaea), AN (Animalia), B (Bacteria),
C (Chromista), F (Fungi), P (Protozoa)
</code></pre>
</pre>
<p>Values that cannot be coerced will be considered 'unknown' and will get the MO code <code>UNKNOWN</code>.</p>
<p>Use the <code><a href='mo_property.html'>mo_*</a></code> functions to get properties based on the returned code, see <em>Examples</em>.</p>
@ -343,7 +335,7 @@
<p>This will lead to the effect that e.g. <code>"E. coli"</code> (a microorganism highly prevalent in humans) will return the microbial ID of <em>Escherichia coli</em> and not <em>Entamoeba coli</em> (a microorganism less prevalent in humans), although the latter would alphabetically come first.</p>
<h3 class='hasAnchor' id='coping-with-uncertain-results'><a class='anchor' aria-hidden='true' href='#coping-with-uncertain-results'></a>Coping with Uncertain Results</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Coping with Uncertain Results</h3>
<p>In addition, the <code>as.mo()</code> function can differentiate four levels of uncertainty to guess valid results:</p><ul>
@ -367,7 +359,7 @@
</ul>
<h3 class='hasAnchor' id='microbial-prevalence-of-pathogens-in-humans'><a class='anchor' aria-hidden='true' href='#microbial-prevalence-of-pathogens-in-humans'></a>Microbial Prevalence of Pathogens in Humans</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Microbial Prevalence of Pathogens in Humans</h3>
<p>The intelligent rules consider the prevalence of microorganisms in humans grouped into three groups, which is available as the <code>prevalence</code> columns in the <a href='microorganisms.html'>microorganisms</a> and <a href='microorganisms.old.html'>microorganisms.old</a> data sets. The grouping into human pathogenic prevalence is explained in the section <em>Matching Score for Microorganisms</em> below.</p>
@ -382,7 +374,7 @@
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (March 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
</ol>
@ -416,7 +408,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
@ -434,7 +426,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<p>The <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_genus()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>) to get properties based on the returned code.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='co'># These examples all return "B_STPHY_AURS", the ID of S. aureus:</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"sau"</span><span class='op'>)</span> <span class='co'># WHONET code</span>
<span class='fu'>as.mo</span><span class='op'>(</span><span class='st'>"stau"</span><span class='op'>)</span>
@ -471,7 +463,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'><a href='mo_property.html'>mo_gramstain</a></span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># returns "Gram negative"</span>
<span class='fu'><a href='mo_property.html'>mo_is_intrinsic_resistant</a></span><span class='op'>(</span><span class='st'>"E. coli"</span>, <span class='st'>"vanco"</span><span class='op'>)</span> <span class='co'># returns TRUE</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -483,11 +475,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@ -496,8 +488,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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42
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@ -58,8 +58,6 @@
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<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@ -71,15 +69,9 @@
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@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -246,7 +238,7 @@
<p>Interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI, or clean up existing R/SI values. This transforms the input to a new class <code>rsi</code>, which is an ordered <a href='https://rdrr.io/r/base/factor.html'>factor</a> with levels <code>S &lt; I &lt; R</code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>as.rsi</span><span class='op'>(</span><span class='va'>x</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>is.rsi</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span>
@ -287,7 +279,7 @@
conserve_capped_values <span class='op'>=</span> <span class='cn'>FALSE</span>,
add_intrinsic_resistance <span class='op'>=</span> <span class='cn'>FALSE</span>,
reference_data <span class='op'>=</span> <span class='fu'>AMR</span><span class='fu'>::</span><span class='va'><a href='rsi_translation.html'>rsi_translation</a></span>
<span class='op'>)</span></code></pre></div>
<span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -344,43 +336,43 @@
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<h3 class='hasAnchor' id='how-it-works'><a class='anchor' aria-hidden='true' href='#how-it-works'></a>How it Works</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>How it Works</h3>
<p>The <code>as.rsi()</code> function works in four ways:</p><ol>
<li><p>For <strong>cleaning raw / untransformed data</strong>. The data will be cleaned to only contain values S, I and R and will try its best to determine this with some intelligence. For example, mixed values with R/SI interpretations and MIC values such as <code>"&lt;0.25; S"</code> will be coerced to <code>"S"</code>. Combined interpretations for multiple test methods (as seen in laboratory records) such as <code>"S; S"</code> will be coerced to <code>"S"</code>, but a value like <code>"S; I"</code> will return <code>NA</code> with a warning that the input is unclear.</p></li>
<li><p>For <strong>interpreting minimum inhibitory concentration (MIC) values</strong> according to EUCAST or CLSI. You must clean your MIC values first using <code><a href='as.mic.html'>as.mic()</a></code>, that also gives your columns the new data class <code><a href='as.mic.html'>mic</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.mic</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.mic</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</code></pre></li>
</pre></li>
<li><p>Operators like "&lt;=" will be stripped before interpretation. When using <code>conserve_capped_values = TRUE</code>, an MIC value of e.g. "&gt;2" will always return "R", even if the breakpoint according to the chosen guideline is "&gt;=4". This is to prevent that capped values from raw laboratory data would not be treated conservatively. The default behaviour (<code>conserve_capped_values = FALSE</code>) considers "&gt;2" to be lower than "&gt;=4" and might in this case return "S" or "I".</p></li>
</ul></li>
<li><p>For <strong>interpreting disk diffusion diameters</strong> according to EUCAST or CLSI. You must clean your disk zones first using <code><a href='as.disk.html'>as.disk()</a></code>, that also gives your columns the new data class <code><a href='as.disk.html'>disk</a></code>. Also, be sure to have a column with microorganism names or codes. It will be found automatically, but can be set manually using the <code>mo</code> argument.</p><ul>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre class='sourceCode r'><code><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<li><p>Using <code>dplyr</code>, R/SI interpretation can be done very easily with either:</p><pre><span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate_all.html'>mutate_if</a></span><span class='op'>(</span><span class='va'>is.disk</span>, <span class='va'>as.rsi</span><span class='op'>)</span> <span class='co'># until dplyr 1.0.0</span>
<span class='va'>your_data</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://dplyr.tidyverse.org/reference/mutate.html'>mutate</a></span><span class='op'>(</span><span class='fu'><a href='https://dplyr.tidyverse.org/reference/across.html'>across</a></span><span class='op'>(</span><span class='fu'>where</span><span class='op'>(</span><span class='va'>is.disk</span><span class='op'>)</span>, <span class='va'>as.rsi</span><span class='op'>)</span><span class='op'>)</span> <span class='co'># since dplyr 1.0.0</span>
</code></pre></li>
</pre></li>
</ul></li>
<li><p>For <strong>interpreting a complete data set</strong>, with automatic determination of MIC values, disk diffusion diameters, microorganism names or codes, and antimicrobial test results. This is done very simply by running <code>as.rsi(data)</code>.</p></li>
</ol>
<h3 class='hasAnchor' id='supported-guidelines'><a class='anchor' aria-hidden='true' href='#supported-guidelines'></a>Supported Guidelines</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Supported Guidelines</h3>
<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are EUCAST (2011-2021) and CLSI (2010-2020).</p>
<p>Thus, the <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2021"</code> or <code>"CLSI 2020"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest 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>
<h3 class='hasAnchor' id='after-interpretation'><a class='anchor' aria-hidden='true' href='#after-interpretation'></a>After Interpretation</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>After Interpretation</h3>
<p>After using <code>as.rsi()</code>, you can use the <code><a href='eucast_rules.html'>eucast_rules()</a></code> defined by EUCAST to (1) apply inferred susceptibility and resistance based on results of other antimicrobials and (2) apply intrinsic resistance based on taxonomic properties of a microorganism.</p>
<h3 class='hasAnchor' id='machine-readable-interpretation-guidelines'><a class='anchor' aria-hidden='true' href='#machine-readable-interpretation-guidelines'></a>Machine-Readable Interpretation Guidelines</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Machine-Readable Interpretation Guidelines</h3>
<p>The repository of this package <a href='https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt'>contains a machine-readable version</a> of all guidelines. This is a CSV file consisting of 22,000 rows and 10 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>
<h3 class='hasAnchor' id='other'><a class='anchor' aria-hidden='true' href='#other'></a>Other</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Other</h3>
<p>The function <code>is.rsi()</code> detects if the input contains class <code>&lt;rsi&gt;</code>. If the input is a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a>, it iterates over all columns and returns a <a href='https://rdrr.io/r/base/logical.html'>logical</a> vector.</p>
@ -422,7 +414,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<div class='dont-index'><p><code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code>, <code><a href='as.mo.html'>as.mo()</a></code></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<pre class="examples"><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>example_isolates</span><span class='op'>)</span> <span class='co'># see all R/SI results at a glance</span>
<span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://docs.ropensci.org/skimr/'>"skimr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='co'># class &lt;rsi&gt; supported in skim() too:</span>
@ -505,7 +497,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># mutate(across(where(is.rsi.eligible), as.rsi))</span>
<span class='op'>}</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -517,11 +509,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -530,8 +522,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

20
docs/reference/catalogue_of_life.html
View File

@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -281,7 +273,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intelligent determination of microorganisms.</p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># Get version info of included data set</span>
<pre class="examples"><span class='co'># Get version info of included data set</span>
<span class='fu'><a href='catalogue_of_life_version.html'>catalogue_of_life_version</a></span><span class='op'>(</span><span class='op'>)</span>
@ -309,7 +301,7 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<span class='co'>#&gt; [1] "Fungi" # Fungi?!</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"C. elegans"</span><span class='op'>)</span>
<span class='co'>#&gt; [1] "Cladosporium elegans" # Because a microorganism was found</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -321,11 +313,11 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -334,8 +326,6 @@ Function <code><a href='as.mo.html'>as.mo()</a></code> to use the data for intel
</body>
</html>

22
docs/reference/catalogue_of_life_version.html
View File

@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Version info of included Catalogue of Life</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/catalogue_of_life.R'><code>R/catalogue_of_life.R</code></a></small>
<div class="hidden name"><code>catalogue_of_life_version.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>This function returns information about the included data from the Catalogue of Life.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<pre class="usage"><span class='fu'>catalogue_of_life_version</span><span class='op'>(</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@ -260,7 +252,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code>catalogue_of_life_version()</code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -282,11 +274,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -295,8 +287,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</body>
</html>

32
docs/reference/eucast_rules.html
View File

@ -59,8 +59,6 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<!-- 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>
@ -72,15 +70,9 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -94,7 +86,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -248,7 +240,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>eucast_rules</span><span class='op'>(</span>
<pre class="usage"><span class='fu'>eucast_rules</span><span class='op'>(</span>
<span class='va'>x</span>,
col_mo <span class='op'>=</span> <span class='cn'>NULL</span>,
info <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/interactive.html'>interactive</a></span><span class='op'>(</span><span class='op'>)</span>,
@ -262,7 +254,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
<span class='va'>...</span>
<span class='op'>)</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></code></pre></div>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='va'>ab</span>, administration <span class='op'>=</span> <span class='st'>"iv"</span>, version_breakpoints <span class='op'>=</span> <span class='fl'>11</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -341,17 +333,17 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><a href='as.rsi.html'>as.rsi()</a></code> for that. <br />
<strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br /></p>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>5 October 2021</a>.</p><h3 class='hasAnchor' id='custom-rules'><a class='anchor' aria-hidden='true' href='#custom-rules'></a>Custom Rules</h3>
<p>The file containing all EUCAST rules is located here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv'>https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <a href='catalogue_of_life.html'>5 October 2021</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Custom Rules</h3>
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre class='sourceCode r'><code><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<p>Custom rules can be created using <code><a href='custom_eucast_rules.html'>custom_eucast_rules()</a></code>, e.g.:</p><pre><span class='va'>x</span> <span class='op'>&lt;-</span> <span class='fu'><a href='custom_eucast_rules.html'>custom_eucast_rules</a></span><span class='op'>(</span><span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"R"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"R"</span>,
<span class='va'>AMC</span> <span class='op'>==</span> <span class='st'>"I"</span> <span class='op'>&amp;</span> <span class='va'>genus</span> <span class='op'>==</span> <span class='st'>"Klebsiella"</span> <span class='op'>~</span> <span class='va'>aminopenicillins</span> <span class='op'>==</span> <span class='st'>"I"</span><span class='op'>)</span>
<span class='fu'>eucast_rules</span><span class='op'>(</span><span class='va'>example_isolates</span>, rules <span class='op'>=</span> <span class='st'>"custom"</span>, custom_rules <span class='op'>=</span> <span class='va'>x</span><span class='op'>)</span>
</code></pre>
</pre>
<h3 class='hasAnchor' id='-other-rules'><a class='anchor' aria-hidden='true' href='#-other-rules'></a>'Other' Rules</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>'Other' Rules</h3>
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol>
@ -388,7 +380,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='va'>a</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span>mo <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"Staphylococcus aureus"</span>,
<span class='st'>"Enterococcus faecalis"</span>,
<span class='st'>"Escherichia coli"</span>,
@ -430,7 +422,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># }</span>
<span class='fu'>eucast_dosage</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"tobra"</span>, <span class='st'>"genta"</span>, <span class='st'>"cipro"</span><span class='op'>)</span>, <span class='st'>"iv"</span><span class='op'>)</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -442,11 +434,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -455,8 +447,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
</body>
</html>

20
docs/reference/index.html
View File

@ -57,8 +57,6 @@
<!-- 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>
@ -70,15 +68,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-index">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -92,7 +84,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -319,7 +311,7 @@
<tr>
<th colspan="2">
<h2 id="section-preparing-data-antimicrobial-resistance" class="hasAnchor"><a href="#section-preparing-data-antimicrobial-resistance" class="anchor"></a>Preparing data: antimicrobial resistance</h2>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/" class="external-link">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
<p class="section-desc"><p>With <code><a href="../reference/as.mic.html">as.mic()</a></code> and <code><a href="../reference/as.disk.html">as.disk()</a></code> you can transform your raw input to valid MIC or disk diffusion values. Use <code><a href="../reference/as.rsi.html">as.rsi()</a></code> for cleaning raw data to let it only contain “R”, “I” and “S”, or to interpret MIC or disk diffusion values as R/SI based on the lastest EUCAST and CLSI guidelines. Afterwards, you can extend antibiotic interpretations by applying <a href="https://www.eucast.org/expert_rules_and_intrinsic_resistance/">EUCAST rules</a> with <code><a href="../reference/eucast_rules.html">eucast_rules()</a></code>.</p></p>
</th>
</tr>
@ -409,7 +401,7 @@
</tr><tr>
<td>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> </p>
<p><code><a href="plot.html">plot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;mic&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;disk&gt;</i>)</a></code> <code><a href="plot.html">plot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">autoplot(<i>&lt;rsi&gt;</i>)</a></code> <code><a href="plot.html">fortify(<i>&lt;rsi&gt;</i>)</a></code> </p>
</td>
<td><p>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></p></td>
</tr><tr>
@ -689,11 +681,11 @@
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -702,8 +694,6 @@
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22
docs/reference/intrinsic_resistant.html
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@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -246,7 +238,7 @@
<p>Data set containing defined intrinsic resistance by EUCAST of all bug-drug combinations.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>intrinsic_resistant</span></code></pre></div>
<pre class="usage"><span class='va'>intrinsic_resistant</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@ -272,7 +264,7 @@
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># \donttest{</span>
<pre class="examples"><span class='co'># \donttest{</span>
<span class='kw'>if</span> <span class='op'>(</span><span class='kw'><a href='https://rdrr.io/r/base/library.html'>require</a></span><span class='op'>(</span><span class='st'><a href='https://dplyr.tidyverse.org'>"dplyr"</a></span><span class='op'>)</span><span class='op'>)</span> <span class='op'>{</span>
<span class='va'>intrinsic_resistant</span> <span class='op'>%&gt;%</span>
<span class='fu'><a href='https://dplyr.tidyverse.org/reference/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>antibiotic</span> <span class='op'>==</span> <span class='st'>"Vancomycin"</span>, <span class='va'>microorganism</span> <span class='op'>%like%</span> <span class='st'>"Enterococcus"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
@ -280,7 +272,7 @@
<span class='co'># [1] "Enterococcus casseliflavus" "Enterococcus gallinarum"</span>
<span class='op'>}</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -292,11 +284,11 @@
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -305,8 +297,6 @@
</body>
</html>

22
docs/reference/microorganisms.codes.html
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@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9050</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data Set with 5,604 Common Microorganism Codes</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.codes.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with <code><a href='mo_source.html'>set_mo_source()</a></code>. They will all be searched when using <code><a href='as.mo.html'>as.mo()</a></code> and consequently all the <code><a href='mo_property.html'>mo_*</a></code> functions.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms.codes</span></code></pre></div>
<pre class="usage"><span class='va'>microorganisms.codes</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@ -266,7 +258,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="read-more-on-our-website-"><a class="anchor" href="#read-more-on-our-website-"></a>Read more on Our Website!</h2>
@ -288,11 +280,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -301,8 +293,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</body>
</html>

22
docs/reference/microorganisms.html
View File

@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -246,7 +238,7 @@
<p>A data set containing the full microbial taxonomy (<strong>last updated: 5 October 2021</strong>) of six kingdoms from the Catalogue of Life (CoL) and the List of Prokaryotic names with Standing in Nomenclature (LPSN). MO codes can be looked up using <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms</span></code></pre></div>
<pre class="usage"><span class='va'>microorganisms</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@ -285,7 +277,7 @@
<p>Please note that entries are only based on the Catalogue of Life and the LPSN (see below). Since these sources incorporate entries based on (recent) publications in the International Journal of Systematic and Evolutionary Microbiology (IJSEM), it can happen that the year of publication is sometimes later than one might expect.</p>
<p>For example, <em>Staphylococcus pettenkoferi</em> was described for the first time in Diagnostic Microbiology and Infectious Disease in 2002 (doi: <a href='https://doi.org/10.1016/s0732-8893(02)00399-1'>10.1016/s0732-8893(02)00399-1</a>
), but it was not before 2007 that a publication in IJSEM followed (doi: <a href='https://doi.org/10.1099/ijs.0.64381-0'>10.1099/ijs.0.64381-0</a>
). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='manual-additions'><a class='anchor' aria-hidden='true' href='#manual-additions'></a>Manual additions</h3>
). Consequently, the <code>AMR</code> package returns 2007 for <code><a href='mo_property.html'>mo_year("S. pettenkoferi")</a></code>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Manual additions</h3>
<p>For convenience, some entries were added manually:</p><ul>
@ -300,7 +292,7 @@
</ul>
<h3 class='hasAnchor' id='direct-download'><a class='anchor' aria-hidden='true' href='#direct-download'></a>Direct download</h3>
<h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Direct download</h3>
<p>This data set is available as 'flat file' for use even without <span style="R">R</span> - you can find the file here:</p><ul>
@ -350,11 +342,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -363,8 +355,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</body>
</html>

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docs/reference/microorganisms.old.html
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@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Data Set with Previously Accepted Taxonomic Names</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/data.R'><code>R/data.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/data.R'><code>R/data.R</code></a></small>
<div class="hidden name"><code>microorganisms.old.Rd</code></div>
</div>
@ -246,12 +238,12 @@
<p>A data set containing old (previously valid or accepted) taxonomic names according to the Catalogue of Life. This data set is used internally by <code><a href='as.mo.html'>as.mo()</a></code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>microorganisms.old</span></code></pre></div>
<pre class="usage"><span class='va'>microorganisms.old</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 14,100 observations and 4 variables:</p><ul>
<p>A <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> with 14,338 observations and 4 variables:</p><ul>
<li><p><code>fullname</code><br /> Old full taxonomic name of the microorganism</p></li>
<li><p><code>fullname_new</code><br /> New full taxonomic name of the microorganism</p></li>
<li><p><code>ref</code><br /> Author(s) and year of concerning scientific publication</p></li>
@ -267,7 +259,7 @@
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="reference-data-publicly-available"><a class="anchor" href="#reference-data-publicly-available"></a>Reference Data Publicly Available</h2>
@ -294,11 +286,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
</div>
</footer>
@ -307,8 +299,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
</body>
</html>

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docs/reference/mo_property.html
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@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9040</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Get Properties of a Microorganism</h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/mo_property.R'><code>R/mo_property.R</code></a></small>
<div class="hidden name"><code>mo_property.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>Use these functions to return a specific property of a microorganism based on the latest accepted taxonomy. All input values will be evaluated internally with <code><a href='as.mo.html'>as.mo()</a></code>, which makes it possible to use microbial abbreviations, codes and names as input. See <em>Examples</em>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<pre class="usage"><span class='fu'>mo_name</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mo_fullname</span><span class='op'>(</span><span class='va'>x</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
@ -300,7 +292,7 @@
<span class='fu'>mo_url</span><span class='op'>(</span><span class='va'>x</span>, open <span class='op'>=</span> <span class='cn'>FALSE</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span>
<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></code></pre></div>
<span class='fu'>mo_property</span><span class='op'>(</span><span class='va'>x</span>, property <span class='op'>=</span> <span class='st'>"fullname"</span>, language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
@ -388,7 +380,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p><img src='figures/logo_col.png' height=40px style=margin-bottom:5px /> <br />
This package contains the complete taxonomic tree of almost all microorganisms (~70,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
This package contains the complete taxonomic tree of almost all microorganisms (~71,000 species) from the authoritative and comprehensive Catalogue of Life (CoL, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a>). The CoL is the most comprehensive and authoritative global index of species currently available. Nonetheless, we supplemented the CoL data with data from the List of Prokaryotic names with Standing in Nomenclature (LPSN, <a href='https://lpsn.dsmz.de'>lpsn.dsmz.de</a>). This supplementation is needed until the <a href='https://github.com/CatalogueOfLife/general'>CoL+ project</a> is finished, which we await.</p>
<p><a href='catalogue_of_life.html'>Click here</a> for more information about the included taxa. Check which versions of the CoL and LPSN were included in this package with <code><a href='catalogue_of_life_version.html'>catalogue_of_life_version()</a></code>.</p>
<h2 class="hasAnchor" id="source"><a class="anchor" href="#source"></a>Source</h2>
@ -400,7 +392,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<li><p>Becker K <em>et al.</em> <strong>Emergence of coagulase-negative staphylococci</strong> 2020. Expert Rev Anti Infect Ther. 18(4):349-366; doi: <a href='https://doi.org/10.1080/14787210.2020.1730813'>10.1080/14787210.2020.1730813</a></p></li>
<li><p>Lancefield RC <strong>A serological differentiation of human and other groups of hemolytic streptococci</strong>. 1933. J Exp Med. 57(4): 571–95; doi: <a href='https://doi.org/10.1084/jem.57.4.571'>10.1084/jem.57.4.571</a></p></li>
<li><p>Catalogue of Life: 2019 Annual Checklist, <a href='http://www.catalogueoflife.org'>http://www.catalogueoflife.org</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (March 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
<li><p>List of Prokaryotic names with Standing in Nomenclature (5 October 2021), doi: <a href='https://doi.org/10.1099/ijsem.0.004332'>10.1099/ijsem.0.004332</a></p></li>
<li><p>US Edition of SNOMED CT from 1 September 2020, retrieved from the Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS), OID 2.16.840.1.114222.4.11.1009, version 12; url: <a href='https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009'>https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009</a></p></li>
</ol>
@ -419,7 +411,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<div class='dont-index'><p>Data set <a href='microorganisms.html'>microorganisms</a></p></div>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># taxonomic tree -----------------------------------------------------------</span>
<pre class="examples"><span class='co'># taxonomic tree -----------------------------------------------------------</span>
<span class='fu'>mo_kingdom</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Bacteria"</span>
<span class='fu'>mo_phylum</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Proteobacteria"</span>
<span class='fu'>mo_class</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span> <span class='co'># "Gammaproteobacteria"</span>
@ -519,7 +511,7 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<span class='fu'>mo_info</span><span class='op'>(</span><span class='st'>"E. coli"</span><span class='op'>)</span>
<span class='co'># }</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -531,11 +523,11 @@ This package contains the complete taxonomic tree of almost all microorganisms (
<footer>
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<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@ -544,8 +536,6 @@ This package contains the complete taxonomic tree of almost all microorganisms (
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46
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@ -58,8 +58,6 @@
<!-- 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>
@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9030</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -238,7 +230,7 @@
<div class="col-md-9 contents">
<div class="page-header">
<h1>Plotting for Classes <code>rsi</code>, <code>mic</code> and <code>disk</code></h1>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/main/R/plot.R'><code>R/plot.R</code></a></small>
<small class="dont-index">Source: <a href='https://github.com/msberends/AMR/blob/master/R/plot.R'><code>R/plot.R</code></a></small>
<div class="hidden name"><code>plot.Rd</code></div>
</div>
@ -246,7 +238,7 @@
<p>Functions to plot classes <code>rsi</code>, <code>mic</code> and <code>disk</code>, with support for base <span style="R">R</span> and <code>ggplot2</code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='co'># S3 method for mic</span>
<pre class="usage"><span class='co'># S3 method for mic</span>
<span class='fu'>plot</span><span class='op'>(</span>
<span class='va'>x</span>,
mo <span class='op'>=</span> <span class='cn'>NULL</span>,
@ -262,7 +254,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for mic</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>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>,
@ -276,6 +268,9 @@
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for mic</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>,
@ -292,7 +287,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for disk</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>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>,
@ -306,6 +301,9 @@
<span class='va'>...</span>
<span class='op'>)</span>
<span class='co'># S3 method for disk</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>,
@ -316,7 +314,7 @@
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>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'>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'>deparse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/substitute.html'>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>,
@ -324,14 +322,17 @@
colours_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>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>,
language <span class='op'>=</span> <span class='fu'><a href='translate.html'>get_locale</a></span><span class='op'>(</span><span class='op'>)</span>,
<span class='va'>...</span>
<span class='op'>)</span></code></pre></div>
<span class='op'>)</span>
<span class='co'># S3 method for rsi</span>
<span class='fu'>fortify</span><span class='op'>(</span><span class='va'>object</span>, <span class='va'>...</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
<table class="ref-arguments">
<colgroup><col class="name" /><col class="desc" /></colgroup>
<tr>
<th>x, object</th>
<td><p>values created with <code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code> or <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
<td><p>values created with <code><a href='as.mic.html'>as.mic()</a></code>, <code><a href='as.disk.html'>as.disk()</a></code> or <code><a href='as.rsi.html'>as.rsi()</a></code> (or their <code>random_*</code> variants, such as <code><a href='random.html'>random_mic()</a></code>)</p></td>
</tr>
<tr>
<th>mo</th>
@ -367,13 +368,14 @@
</tr>
<tr>
<th>...</th>
<td><p>arguments passed on to <code><a href='as.rsi.html'>as.rsi()</a></code></p></td>
<td><p>arguments passed on to methods</p></td>
</tr>
</table>
<h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
<p>The <code><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot()</a></code> functions return a <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot</a></code> model that is extendible with any <code>ggplot2</code> function.</p>
<p>The <code><a href='https://ggplot2.tidyverse.org/reference/fortify.html'>fortify()</a></code> functions return a <a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a> as an extension for usage in the <code><a href='https://ggplot2.tidyverse.org/reference/ggplot.html'>ggplot2::ggplot()</a></code> function.</p>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>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>
@ -392,7 +394,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
<pre class="examples"><span class='va'>some_mic_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_mic</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>
<span class='va'>some_disk_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_disk</a></span><span class='op'>(</span>size <span class='op'>=</span> <span class='fl'>100</span>, mo <span class='op'>=</span> <span class='st'>"Escherichia coli"</span>, ab <span class='op'>=</span> <span class='st'>"cipro"</span><span class='op'>)</span>
<span class='va'>some_rsi_values</span> <span class='op'>&lt;-</span> <span class='fu'><a href='random.html'>random_rsi</a></span><span class='op'>(</span><span class='fl'>50</span>, prob_RSI <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0.30</span>, <span class='fl'>0.55</span>, <span class='fl'>0.05</span><span class='op'>)</span><span class='op'>)</span>
@ -411,7 +413,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<span class='fu'><a href='https://ggplot2.tidyverse.org/reference/autoplot.html'>autoplot</a></span><span class='op'>(</span><span class='va'>some_rsi_values</span><span class='op'>)</span>
<span class='op'>}</span>
<span class='co'># }</span>
</code></pre></div>
</pre>
</div>
<div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
<nav id="toc" data-toggle="toc" class="sticky-top">
@ -423,11 +425,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, <a href="https://www.rug.nl/staff/c.f.luz/" class="external-link">Christian F. Luz</a>, <a href="https://www.rug.nl/staff/a.w.friedrich/" class="external-link">Alexander W. Friedrich</a>, <a href="https://www.rug.nl/staff/b.sinha/" class="external-link">Bhanu N. M. Sinha</a>, <a href="https://www.rug.nl/staff/c.j.albers/" class="external-link">Casper J. Albers</a>, <a href="https://www.rug.nl/staff/c.glasner/" class="external-link">Corinna Glasner</a>.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@ -436,8 +438,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>maturing<
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18
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@ -58,8 +58,6 @@
<!-- mathjax -->
<script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script>
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@ -71,15 +69,9 @@
</head>
<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
<div class="navbar navbar-default navbar-fixed-top" role="navigation">
@ -93,7 +85,7 @@
</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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
</span>
</div>
@ -246,7 +238,7 @@
<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 (2010-2020). Use <code><a href='as.rsi.html'>as.rsi()</a></code> to transform MICs or disks measurements to R/SI values.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='va'>rsi_translation</span></code></pre></div>
<pre class="usage"><span class='va'>rsi_translation</span></pre>
<h2 class="hasAnchor" id="format"><a class="anchor" href="#format"></a>Format</h2>
@ -292,11 +284,11 @@
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
</div>
<div class="pkgdown">
<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
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@ -305,8 +297,6 @@
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@ -58,8 +58,6 @@
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<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>
@ -71,15 +69,9 @@
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<body data-spy="scroll" data-target="#toc">
<div class="container template-reference-topic">
<header>
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@ -93,7 +85,7 @@
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<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="Latest development version">1.7.1.9051</span>
<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.7.1.9053</span>
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@ -246,14 +238,14 @@
<p>For language-dependent output of AMR functions, like <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code> and <code><a href='ab_property.html'>ab_name()</a></code>.</p>
</div>
<div class="ref-usage sourceCode"><pre class='sourceCode r'><code><span class='fu'>get_locale</span><span class='op'>(</span><span class='op'>)</span></code></pre></div>
<pre class="usage"><span class='fu'>get_locale</span><span class='op'>(</span><span class='op'>)</span></pre>
<h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2>
<p>Strings will be translated to foreign languages if they are defined in a local translation file. Additions to this file can be suggested at our repository. The file can be found here: <a href='https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv'>https://github.com/msberends/AMR/blob/main/data-raw/translations.tsv</a>. This file will be read by all functions where a translated output can be desired, like all <code><a href='mo_property.html'>mo_*</a></code> functions (such as <code><a href='mo_property.html'>mo_name()</a></code>, <code><a href='mo_property.html'>mo_gramstain()</a></code>, <code><a href='mo_property.html'>mo_type()</a></code>, etc.) and <code><a href='ab_property.html'>ab_*</a></code> functions (such as <code><a href='ab_property.html'>ab_name()</a></code>, <code><a href='ab_property.html'>ab_group()</a></code>, etc.).</p>
<p>Currently supported languages are: Danish, Dutch, English, French, German, Italian, Portuguese and Spanish. All these languages have translations available for all antimicrobial agents and colloquial microorganism names.</p>
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3 class='hasAnchor' id='changing-the-default-language'><a class='anchor' aria-hidden='true' href='#changing-the-default-language'></a>Changing the Default Language</h3>
<p>Please suggest your own translations <a href='https://github.com/msberends/AMR/issues/new?title=Translations'>by creating a new issue on our repository</a>.</p><h3 class='hasAnchor' id='arguments'><a class='anchor' href='#arguments'></a>Changing the Default Language</h3>
<p>The system language will be used at default (as returned by <code><a href='https://rdrr.io/r/base/Sys.getenv.html'>Sys.getenv("LANG")</a></code> or, if <code>LANG</code> is not set, <code><a href='https://rdrr.io/r/base/locales.html'>Sys.getlocale()</a></code>), if that language is supported. But the language to be used can be overwritten in two ways and will be checked in this order:</p><ol>
@ -277,7 +269,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<p>On our website <a href='https://msberends.github.io/AMR/'>https://msberends.github.io/AMR/</a> you can find <a href='https://msberends.github.io/AMR/articles/AMR.html'>a comprehensive tutorial</a> about how to conduct AMR data analysis, the <a href='https://msberends.github.io/AMR/reference/'>complete documentation of all functions</a> and <a href='https://msberends.github.io/AMR/articles/WHONET.html'>an example analysis using WHONET data</a>.</p>
<h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
<div class="ref-examples sourceCode"><pre class='sourceCode r'><code><span class='co'># The 'language' argument of below functions</span>
<pre class="examples"><span class='co'># The 'language' argument of below functions</span>
<span class='co'># will be set automatically to your system language</span>
<span class='co'># with get_locale()</span>
@ -308,7 +300,7 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<span class='co'># Spanish</span>
<span class='fu'><a href='mo_property.html'>mo_name</a></span><span class='op'>(</span><span class='st'>"CoNS"</span>, language <span class='op'>=</span> <span class='st'>"es"</span><span class='op'>)</span>
<span class='co'>#&gt; "Staphylococcus coagulasa negativo (SCN)"</span>
</code></pre></div>
</pre>
</div>
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<nav id="toc" data-toggle="toc" class="sticky-top">
@ -320,11 +312,11 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
<footer>
<div class="copyright">
<p><p>Developed by <a href="https://www.rug.nl/staff/m.s.berends/" class="external-link">Matthijs S. Berends</a>, Christian F. Luz.</p></p>
<p>Developed by <a href='https://www.rug.nl/staff/m.s.berends/'>Matthijs S. Berends</a>, Dennis Souverein, Erwin E. A. Hassing, Christian F. Luz.</p>
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<p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 1.6.1.9001.</p></p>
<p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p>
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@ -333,8 +325,6 @@ The <a href='lifecycle.html'>lifecycle</a> of this function is <strong>stable</s
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15
man/plot.Rd
View File

@ -4,10 +4,13 @@
\alias{plot}
\alias{plot.mic}
\alias{autoplot.mic}
\alias{fortify.mic}
\alias{plot.disk}
\alias{autoplot.disk}
\alias{fortify.disk}
\alias{plot.rsi}
\alias{autoplot.rsi}
\alias{fortify.rsi}
\title{Plotting for Classes \code{rsi}, \code{mic} and \code{disk}}
\usage{
\method{plot}{mic}(
@ -38,6 +41,8 @@
...
)
\method{fortify}{mic}(object, ...)
\method{plot}{disk}(
x,
main = paste("Disk zones of", deparse(substitute(x))),
@ -66,6 +71,8 @@
...
)
\method{fortify}{disk}(object, ...)
\method{plot}{rsi}(
x,
ylab = "Percentage",
@ -83,9 +90,11 @@
language = get_locale(),
...
)
\method{fortify}{rsi}(object, ...)
}
\arguments{
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.rsi]{as.rsi()}}}
\item{x, object}{values created with \code{\link[=as.mic]{as.mic()}}, \code{\link[=as.disk]{as.disk()}} or \code{\link[=as.rsi]{as.rsi()}} (or their \verb{random_*} variants, such as \code{\link[=random_mic]{random_mic()}})}
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
@ -103,10 +112,12 @@
\item{expand}{a \link{logical} to indicate whether the range on the x axis should be expanded between the lowest and highest value. For MIC values, intermediate values will be factors of 2 starting from the highest MIC value. For disk diameters, the whole diameter range will be filled.}
\item{...}{arguments passed on to \code{\link[=as.rsi]{as.rsi()}}}
\item{...}{arguments passed on to methods}
}
\value{
The \code{autoplot()} functions return a \code{\link[ggplot2:ggplot]{ggplot}} model that is extendible with any \code{ggplot2} function.
The \code{fortify()} functions return a \link{data.frame} as an extension for usage in the \code{\link[ggplot2:ggplot]{ggplot2::ggplot()}} function.
}
\description{
Functions to plot classes \code{rsi}, \code{mic} and \code{disk}, with support for base \R and \code{ggplot2}.