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4
DESCRIPTION
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@ -1,5 +1,5 @@
Package: AMR Package: AMR
Version: 1.8.2.9049 Version: 1.8.2.9050
Date: 2022-11-13 Date: 2022-11-13
Title: Antimicrobial Resistance Data Analysis Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR) Description: Functions to simplify and standardise antimicrobial resistance (AMR)
@ -52,5 +52,5 @@ BugReports: https://github.com/msberends/AMR/issues
License: GPL-2 | file LICENSE License: GPL-2 | file LICENSE
Encoding: UTF-8 Encoding: UTF-8
LazyData: true LazyData: true
RoxygenNote: 7.2.1 RoxygenNote: 7.2.2
Roxygen: list(markdown = TRUE) Roxygen: list(markdown = TRUE)

2
NEWS.md
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@ -1,4 +1,4 @@
# AMR 1.8.2.9049 # AMR 1.8.2.9050
This version will eventually become v2.0! We're happy to reach a new major milestone soon! This version will eventually become v2.0! We're happy to reach a new major milestone soon!

12
R/ab.R
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@ -29,9 +29,9 @@
#' Transform Input to an Antibiotic ID #' Transform Input to an Antibiotic ID
#' #'
#' Use this function to determine the antibiotic code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names). #' Use this function to determine the antibiotic drug code of one or more antibiotics. The data set [antibiotics] will be searched for abbreviations, official names and synonyms (brand names).
#' @param x a [character] vector to determine to antibiotic ID #' @param x a [character] vector to determine to antibiotic ID
#' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value. #' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antibiotic drug code or name can be retrieved from a single input value.
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode #' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param ... arguments passed on to internal functions #' @param ... arguments passed on to internal functions
#' @rdname as.ab #' @rdname as.ab
@ -47,7 +47,7 @@
#' #'
#' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*. #' Use the [`ab_*`][ab_property()] functions to get properties based on the returned antibiotic ID, see *Examples*.
#' #'
#' Note: the [as.ab()] and [`ab_*`][ab_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. #' Note: the [as.ab()] and [`ab_*`][ab_property()] functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
#' #'
#' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()]. #' You can add your own manual codes to be considered by [as.ab()] and all [`ab_*`][ab_property()] functions, see [add_custom_antimicrobials()].
#' @section Source: #' @section Source:
@ -591,7 +591,7 @@ as.data.frame.ab <- function(x, ...) {
"[<-.ab" <- function(i, j, ..., value) { "[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab) return_after_integrity_check(y, "antimicrobial drug code", AMR_env$AB_lookup$ab)
} }
#' @method [[<- ab #' @method [[<- ab
#' @export #' @export
@ -599,7 +599,7 @@ as.data.frame.ab <- function(x, ...) {
"[[<-.ab" <- function(i, j, ..., value) { "[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab) return_after_integrity_check(y, "antimicrobial drug code", AMR_env$AB_lookup$ab)
} }
#' @method c ab #' @method c ab
#' @export #' @export
@ -608,7 +608,7 @@ c.ab <- function(...) {
x <- list(...)[[1L]] x <- list(...)[[1L]]
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(x) attributes(y) <- attributes(x)
return_after_integrity_check(y, "antimicrobial code", AMR_env$AB_lookup$ab) return_after_integrity_check(y, "antimicrobial drug code", AMR_env$AB_lookup$ab)
} }
#' @method unique ab #' @method unique ab

2
R/ab_from_text.R
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@ -37,7 +37,7 @@
#' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words. #' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode #' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param ... arguments passed on to [as.ab()] #' @param ... arguments passed on to [as.ab()]
#' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. #' @details This function is also internally used by [as.ab()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.ab()] function may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
#' #'
#' ### Argument `type` #' ### Argument `type`
#' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling. #' At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.ab()] internally, it will correct for misspelling.

4
R/ab_property.R
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@ -30,7 +30,7 @@
#' Get Properties of an Antibiotic #' Get Properties of an Antibiotic
#' #'
#' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()]. #' Use these functions to return a specific property of an antibiotic from the [antibiotics] data set. All input values will be evaluated internally with [as.ab()].
#' @param x any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param x any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
#' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b". #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. This will lead to e.g. "polymyxin B" and not "polymyxin b".
#' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`. #' @param property one of the column names of one of the [antibiotics] data set: `vector_or(colnames(antibiotics), sort = FALSE)`.
#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation. #' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.
@ -378,7 +378,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
return(data) return(data)
} }
} else { } else {
# quickly get antibiotic codes # quickly get antibiotic drug codes
vars_ab <- as.ab(data, fast_mode = TRUE) vars_ab <- as.ab(data, fast_mode = TRUE)
vars <- data[!is.na(vars_ab)] vars <- data[!is.na(vars_ab)]
} }

16
R/ab_selectors.R
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@ -29,11 +29,11 @@
#' Antibiotic Selectors #' Antibiotic Selectors
#' #'
#' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()]. #' These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by [cephalosporins()].
#' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value. #' @param ab_class an antimicrobial class or a part of it, such as `"carba"` and `"carbapenems"`. The columns `group`, `atc_group1` and `atc_group2` of the [antibiotics] data set will be searched (case-insensitive) for this value.
#' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"` #' @param filter an [expression] to be evaluated in the [antibiotics] data set, such as `name %like% "trim"`
#' @param only_rsi_columns a [logical] to indicate whether only columns of class `rsi` must be selected (defaults to `FALSE`), see [as.rsi()] #' @param only_rsi_columns a [logical] to indicate whether only columns of class `rsi` must be selected (defaults to `FALSE`), see [as.rsi()]
#' @param only_treatable a [logical] to indicate whether agents that are only for laboratory tests should be excluded (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`) #' @param only_treatable a [logical] to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to `TRUE`), such as gentamicin-high (`GEH`) and imipenem/EDTA (`IPE`)
#' @param ... ignored, only in place to allow future extensions #' @param ... ignored, only in place to allow future extensions
#' @details #' @details
#' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*. #' These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the [Tidyverse selection helpers][tidyselect::language] such as [`everything()`][tidyselect::everything()], but also work in base \R and not only in `dplyr` verbs. Nonetheless, they are very convenient to use with `dplyr` functions such as [`select()`][dplyr::select()], [`filter()`][dplyr::filter()] and [`summarise()`][dplyr::summarise()], see *Examples*.
@ -548,7 +548,7 @@ ab_select_exec <- function(function_name,
if (any(untreatable %in% names(ab_in_data))) { if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) { if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
warning_( warning_(
"in `", function_name, "()`: some agents were ignored since they cannot be used for treating patients: ", "in `", function_name, "()`: some drugs were ignored since they cannot be used for treating patients: ",
vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable], vector_and(ab_name(names(ab_in_data)[names(ab_in_data) %in% untreatable],
language = NULL, language = NULL,
tolower = TRUE tolower = TRUE
@ -564,7 +564,7 @@ ab_select_exec <- function(function_name,
} }
if (length(ab_in_data) == 0) { if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found in the data.") message_("No antimicrobial drugs found in the data.")
return(NULL) return(NULL)
} }
@ -833,13 +833,13 @@ message_agent_names <- function(function_name, agents, ab_group = NULL, examples
if (message_not_thrown_before(function_name, sort(agents))) { if (message_not_thrown_before(function_name, sort(agents))) {
if (length(agents) == 0) { if (length(agents) == 0) {
if (is.null(ab_group)) { if (is.null(ab_group)) {
message_("For `", function_name, "()` no antimicrobial agents found", examples, ".") message_("For `", function_name, "()` no antimicrobial drugs found", examples, ".")
} else if (ab_group == "administrable_per_os") { } else if (ab_group == "administrable_per_os") {
message_("No orally administrable agents found", examples, ".") message_("No orally administrable drugs found", examples, ".")
} else if (ab_group == "administrable_iv") { } else if (ab_group == "administrable_iv") {
message_("No IV administrable agents found", examples, ".") message_("No IV administrable drugs found", examples, ".")
} else { } else {
message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".") message_("No antimicrobial drugs of class '", ab_group, "' found", examples, ".")
} }
} else { } else {
agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'") agents_formatted <- paste0("'", font_bold(agents, collapse = NULL), "'")

6
R/add_custom_antimicrobials.R
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@ -29,7 +29,7 @@
#' Add Custom Antimicrobials to This Package #' Add Custom Antimicrobials to This Package
#' #'
#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial codes to the `AMR` package. #' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug codes to the `AMR` package.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name" #' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, although this requires to load the `AMR` package at every start-up: #' @details Due to how \R works, the [add_custom_antimicrobials()] function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your `.Rprofile` file to circumvent this, although this requires to load the `AMR` package at every start-up:
#' #'
@ -37,7 +37,7 @@
#' # Open .Rprofile file #' # Open .Rprofile file
#' utils::file.edit("~/.Rprofile") #' utils::file.edit("~/.Rprofile")
#' #'
#' # Add custom antibiotic codes: #' # Add custom antibiotic drug codes:
#' library(AMR) #' library(AMR)
#' add_custom_antimicrobials( #' add_custom_antimicrobials(
#' data.frame(ab = "TESTAB", #' data.frame(ab = "TESTAB",
@ -107,7 +107,7 @@ add_custom_antimicrobials <- function(x) {
) )
stop_if( stop_if(
any(x$ab %in% AMR_env$AB_lookup$ab), any(x$ab %in% AMR_env$AB_lookup$ab),
"Antimicrobial code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set." "Antimicrobial drug code(s) ", vector_and(x$ab[x$ab %in% AMR_env$AB_lookup$ab]), " already exist in the internal `antibiotics` data set."
) )
x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE] x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]

20
R/av.R
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@ -27,11 +27,11 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== # # ==================================================================== #
#' Transform Input to an Antiviral Agent ID #' Transform Input to an Antiviral Drug ID
#' #'
#' Use this function to determine the antiviral agent code of one or more antiviral agents. The data set [antivirals] will be searched for abbreviations, official names and synonyms (brand names). #' Use this function to determine the antiviral drug code of one or more antiviral drugs. The data set [antivirals] will be searched for abbreviations, official names and synonyms (brand names).
#' @param x a [character] vector to determine to antiviral agent ID #' @param x a [character] vector to determine to antiviral drug ID
#' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antiviral agent code or name can be retrieved from a single input value. #' @param flag_multiple_results a [logical] to indicate whether a note should be printed to the console that probably more than one antiviral drug code or name can be retrieved from a single input value.
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode #' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param ... arguments passed on to internal functions #' @param ... arguments passed on to internal functions
#' @rdname as.av #' @rdname as.av
@ -45,9 +45,9 @@
#' * Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast) #' * Switching two characters (such as "aycclovir", often the case in clinical data, when doctors typed too fast)
#' * Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc. #' * Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
#' #'
#' Use the [`av_*`][av_property()] functions to get properties based on the returned antiviral agent ID, see *Examples*. #' Use the [`av_*`][av_property()] functions to get properties based on the returned antiviral drug ID, see *Examples*.
#' #'
#' Note: the [as.av()] and [`av_*`][av_property()] functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. #' Note: the [as.av()] and [`av_*`][av_property()] functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
#' @section Source: #' @section Source:
#' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/} #' World Health Organization (WHO) Collaborating Centre for Drug Statistics Methodology: \url{https://www.whocc.no/atc_ddd_index/}
#' #'
@ -482,7 +482,7 @@ as.av <- function(x, flag_multiple_results = TRUE, info = interactive(), ...) {
AMR_env$av_previously_coerced$x_bak[which(AMR_env$av_previously_coerced$x %in% x & is.na(AMR_env$av_previously_coerced$av))]) AMR_env$av_previously_coerced$x_bak[which(AMR_env$av_previously_coerced$x %in% x & is.na(AMR_env$av_previously_coerced$av))])
if (length(x_unknown) > 0 && fast_mode == FALSE) { if (length(x_unknown) > 0 && fast_mode == FALSE) {
warning_( warning_(
"in `as.av()`: these values could not be coerced to a valid antiviral agent ID: ", "in `as.av()`: these values could not be coerced to a valid antiviral drug ID: ",
vector_and(x_unknown), "." vector_and(x_unknown), "."
) )
} }
@ -557,7 +557,7 @@ as.data.frame.av <- function(x, ...) {
"[<-.av" <- function(i, j, ..., value) { "[<-.av" <- function(i, j, ..., value) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av) return_after_integrity_check(y, "antiviral drug code", AMR_env$AV_lookup$av)
} }
#' @method [[<- av #' @method [[<- av
#' @export #' @export
@ -565,7 +565,7 @@ as.data.frame.av <- function(x, ...) {
"[[<-.av" <- function(i, j, ..., value) { "[[<-.av" <- function(i, j, ..., value) {
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(i) attributes(y) <- attributes(i)
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av) return_after_integrity_check(y, "antiviral drug code", AMR_env$AV_lookup$av)
} }
#' @method c av #' @method c av
#' @export #' @export
@ -574,7 +574,7 @@ c.av <- function(...) {
x <- list(...)[[1L]] x <- list(...)[[1L]]
y <- NextMethod() y <- NextMethod()
attributes(y) <- attributes(x) attributes(y) <- attributes(x)
return_after_integrity_check(y, "antiviral agent code", AMR_env$AV_lookup$av) return_after_integrity_check(y, "antiviral drug code", AMR_env$AV_lookup$av)
} }
#' @method unique av #' @method unique av

2
R/av_from_text.R
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@ -37,7 +37,7 @@
#' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words. #' @param thorough_search a [logical] to indicate whether the input must be extensively searched for misspelling and other faulty input values. Setting this to `TRUE` will take considerably more time than when using `FALSE`. At default, it will turn `TRUE` when all input elements contain a maximum of three words.
#' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode #' @param info a [logical] to indicate whether a progress bar should be printed, defaults to `TRUE` only in interactive mode
#' @param ... arguments passed on to [as.av()] #' @param ... arguments passed on to [as.av()]
#' @details This function is also internally used by [as.av()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.av()] function may use very long regular expression to match brand names of antiviral agents. This may fail on some systems. #' @details This function is also internally used by [as.av()], although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the [as.av()] function may use very long regular expression to match brand names of antiviral drugs. This may fail on some systems.
#' #'
#' ### Argument `type` #' ### Argument `type`
#' At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.av()] internally, it will correct for misspelling. #' At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses [as.av()] internally, it will correct for misspelling.

6
R/av_property.R
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@ -27,10 +27,10 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== # # ==================================================================== #
#' Get Properties of an Antiviral Agent #' Get Properties of an Antiviral Drug
#' #'
#' Use these functions to return a specific property of an antiviral agent from the [antivirals] data set. All input values will be evaluated internally with [as.av()]. #' Use these functions to return a specific property of an antiviral drug from the [antivirals] data set. All input values will be evaluated internally with [as.av()].
#' @param x any (vector of) text that can be coerced to a valid antiviral agent code with [as.av()] #' @param x any (vector of) text that can be coerced to a valid antiviral drug code with [as.av()]
#' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character]. #' @param tolower a [logical] to indicate whether the first [character] of every output should be transformed to a lower case [character].
#' @param property one of the column names of one of the [antivirals] data set: `vector_or(colnames(antivirals), sort = FALSE)`. #' @param property one of the column names of one of the [antivirals] data set: `vector_or(colnames(antivirals), sort = FALSE)`.
#' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation. #' @param language language of the returned text, defaults to system language (see [get_AMR_locale()]) and can also be set with `getOption("AMR_locale")`. Use `language = NULL` or `language = ""` to prevent translation.

6
R/custom_eucast_rules.R
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@ -91,7 +91,7 @@
#' #'
#' ### Usage of antibiotic group names #' ### Usage of antibiotic group names
#' #'
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule. #' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.
#' #'
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")` #' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
#' @returns A [list] containing the custom rules #' @returns A [list] containing the custom rules
@ -174,8 +174,8 @@ custom_eucast_rules <- function(...) {
stop_if( stop_if(
any(is.na(result_group)), any(is.na(result_group)),
"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"", "this result of rule ", i, " could not be translated to a single antimicrobial drug/group: \"",
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ", as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial drug, or be one of: ",
vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), "." vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), "."
) )
result_value <- as.character(result)[[3]] result_value <- as.character(result)[[3]]

6
R/data.R
View File

@ -45,7 +45,7 @@
#' - `oral_units`\cr Units of `oral_ddd` #' - `oral_units`\cr Units of `oral_ddd`
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for `r sum(!is.na(antibiotics$iv_ddd))` drugs
#' - `iv_units`\cr Units of `iv_ddd` #' - `iv_units`\cr Units of `iv_ddd`
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use [ab_loinc()] to retrieve them quickly, see [ab_property()]. #' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use [ab_loinc()] to retrieve them quickly, see [ab_property()].
#' #'
#' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables: #' ### For the [antivirals] data set: a [tibble][tibble::tibble] with `r nrow(antivirals)` observations and `r ncol(antivirals)` variables:
#' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available #' - `av`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
@ -58,7 +58,7 @@
#' - `oral_units`\cr Units of `oral_ddd` #' - `oral_units`\cr Units of `oral_ddd`
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment #' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
#' - `iv_units`\cr Units of `iv_ddd` #' - `iv_units`\cr Units of `iv_ddd`
#' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. #' - `loinc`\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.
#' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`. #' @details Properties that are based on an ATC code are only available when an ATC is available. These properties are: `atc_group1`, `atc_group2`, `oral_ddd`, `oral_units`, `iv_ddd` and `iv_units`.
#' #'
#' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available. #' Synonyms (i.e. trade names) were derived from the PubChem Compound ID (column `cid`) and consequently only available where a CID is available.
@ -272,7 +272,7 @@
#' EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with [eucast_dosage()]. #' EUCAST breakpoints used in this package are based on the dosages in this data set. They can be retrieved with [eucast_dosage()].
#' @format A [tibble][tibble::tibble] with `r format(nrow(dosage), big.mark = ",")` observations and `r ncol(dosage)` variables: #' @format A [tibble][tibble::tibble] with `r format(nrow(dosage), big.mark = ",")` observations and `r ncol(dosage)` variables:
#' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available #' - `ab`\cr Antibiotic ID as used in this package (such as `AMC`), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
#' - `name`\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO #' - `name`\cr Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO
#' - `type`\cr Type of the dosage, either `r vector_or(dosage$type)` #' - `type`\cr Type of the dosage, either `r vector_or(dosage$type)`
#' - `dose`\cr Dose, such as "2 g" or "25 mg/kg" #' - `dose`\cr Dose, such as "2 g" or "25 mg/kg"
#' - `dose_times`\cr Number of times a dose must be administered #' - `dose_times`\cr Number of times a dose must be administered

4
R/eucast_rules.R
View File

@ -65,9 +65,9 @@ format_eucast_version_nr <- function(version, markdown = TRUE) {
#' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time. #' @param verbose a [logical] to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.
#' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`. #' @param version_breakpoints the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either `r vector_or(names(EUCAST_VERSION_BREAKPOINTS), reverse = TRUE)`.
#' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`. #' @param version_expertrules the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either `r vector_or(names(EUCAST_VERSION_EXPERT_RULES), reverse = TRUE)`.
#' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of `NA` (the default) for this argument will remove results for these three agents, while e.g. a value of `"R"` will make the results for these agents resistant. Use `NULL` or `FALSE` to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`. #' @param ampc_cephalosporin_resistance a [character] value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to `NA`. Currently only works when `version_expertrules` is `3.2` and higher; these version of '*EUCAST Expert Rules on Enterobacterales*' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of `NA` (the default) for this argument will remove results for these three drugs, while e.g. a value of `"R"` will make the results for these drugs resistant. Use `NULL` or `FALSE` to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using `TRUE` is equal to using `"R"`. \cr For *EUCAST Expert Rules* v3.2, this rule applies to: `r vector_and(gsub("[^a-zA-Z ]+", "", unlist(strsplit(EUCAST_RULES_DF[which(EUCAST_RULES_DF$reference.version %in% c(3.2, 3.3) & EUCAST_RULES_DF$reference.rule %like% "ampc"), "this_value"][1], "|", fixed = TRUE))), quotes = "*")`.
#' @param ... column name of an antibiotic, see section *Antibiotics* below #' @param ... column name of an antibiotic, see section *Antibiotics* below
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
#' @param administration route of administration, either `r vector_or(dosage$administration)` #' @param administration route of administration, either `r vector_or(dosage$administration)`
#' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param only_rsi_columns a [logical] to indicate whether only antibiotic columns must be detected that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param custom_rules custom rules to apply, created with [custom_eucast_rules()] #' @param custom_rules custom rules to apply, created with [custom_eucast_rules()]

4
R/first_isolate.R
View File

@ -107,14 +107,14 @@
#' #'
#' 1. Using `type = "points"` and argument `points_threshold` (default) #' 1. Using `type = "points"` and argument `points_threshold` (default)
#' #'
#' This method weighs *all* antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as `0.5` points, a difference from S to R (or vice versa) counts as `1` point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate. #' This method weighs *all* antimicrobial drugs available in the data set. Any difference from I to S or R (or vice versa) counts as `0.5` points, a difference from S to R (or vice versa) counts as `1` point. When the sum of points exceeds `points_threshold`, which defaults to `2`, an isolate will be selected as a first weighted isolate.
#' #'
#' All antimicrobials are internally selected using the [all_antimicrobials()] function. The output of this function does not need to be passed to the [first_isolate()] function. #' All antimicrobials are internally selected using the [all_antimicrobials()] function. The output of this function does not need to be passed to the [first_isolate()] function.
#' #'
#' #'
#' 2. Using `type = "keyantimicrobials"` and argument `ignore_I` #' 2. Using `type = "keyantimicrobials"` and argument `ignore_I`
#' #'
#' This method only weighs specific antimicrobial agents, called *key antimicrobials*. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With `ignore_I = FALSE`, also differences from I to S or R (or vice versa) will lead to this. #' This method only weighs specific antimicrobial drugs, called *key antimicrobials*. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With `ignore_I = FALSE`, also differences from I to S or R (or vice versa) will lead to this.
#' #'
#' Key antimicrobials are internally selected using the [key_antimicrobials()] function, but can also be added manually as a variable to the data and set in the `col_keyantimicrobials` argument. Another option is to pass the output of the [key_antimicrobials()] function directly to the `col_keyantimicrobials` argument. #' Key antimicrobials are internally selected using the [key_antimicrobials()] function, but can also be added manually as a variable to the data and set in the `col_keyantimicrobials` argument. Another option is to pass the output of the [key_antimicrobials()] function directly to the `col_keyantimicrobials` argument.
#' #'

2
R/ggplot_pca.R
View File

@ -78,7 +78,7 @@
#' filter(n() >= 30) %>% # filter on only 30 results per group #' filter(n() >= 30) %>% # filter on only 30 results per group
#' summarise_if(is.rsi, resistance) # then get resistance of all drugs #' summarise_if(is.rsi, resistance) # then get resistance of all drugs
#' #'
#' # now conduct PCA for certain antimicrobial agents #' # now conduct PCA for certain antimicrobial drugs
#' pca_result <- resistance_data %>% #' pca_result <- resistance_data %>%
#' pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) #' pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
#' #'

2
R/guess_ab_col.R
View File

@ -339,7 +339,7 @@ get_ab_from_namespace <- function(x, cols_ab) {
# separate drugs, such as `AMX` # separate drugs, such as `AMX`
val <- as.ab(val) val <- as.ab(val)
} else { } else {
stop_("unknown antimicrobial agent (group): ", val, call = FALSE) stop_("unknown antimicrobial drug (group): ", val, call = FALSE)
} }
x_new <- c(x_new, val) x_new <- c(x_new, val)
} }

18
R/key_antimicrobials.R
View File

@ -33,20 +33,20 @@
#' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically #' @param x a [data.frame] with antibiotics columns, like `AMX` or `amox`. Can be left blank to determine automatically
#' @param y,z [character] vectors to compare #' @param y,z [character] vectors to compare
#' @inheritParams first_isolate #' @inheritParams first_isolate
#' @param universal names of **broad-spectrum** antimicrobial agents, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param universal names of **broad-spectrum** antimicrobial drugs, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antimicrobial drugs
#' @param gram_negative names of antibiotic agents for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param gram_negative names of antibiotic drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param gram_positive names of antibiotic drugs for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @param antifungal names of antifungal agents for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents. #' @param antifungal names of antifungal drugs for **fungi**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antifungal drugs
#' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`) #' @param only_rsi_columns a [logical] to indicate whether only columns must be included that were transformed to class `rsi` (see [as.rsi()]) on beforehand (defaults to `FALSE`)
#' @param ... ignored, only in place to allow future extensions #' @param ... ignored, only in place to allow future extensions
#' @details #' @details
#' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*. #' The [key_antimicrobials()] and [all_antimicrobials()] functions are context-aware. This means that the `x` argument can be left blank if used inside a [data.frame] call, see *Examples*.
#' #'
#' The function [key_antimicrobials()] returns a [character] vector with 12 antimicrobial results for every isolate. The function [all_antimicrobials()] returns a [character] vector with all antimicrobial results for every isolate. These vectors can then be compared using [antimicrobials_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antimicrobials()] and ignored by [antimicrobials_equal()]. #' The function [key_antimicrobials()] returns a [character] vector with 12 antimicrobial results for every isolate. The function [all_antimicrobials()] returns a [character] vector with all antimicrobial drug results for every isolate. These vectors can then be compared using [antimicrobials_equal()], to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (`"."`) by [key_antimicrobials()] and ignored by [antimicrobials_equal()].
#' #'
#' Please see the [first_isolate()] function how these important functions enable the 'phenotype-based' method for determination of first isolates. #' Please see the [first_isolate()] function how these important functions enable the 'phenotype-based' method for determination of first isolates.
#' #'
#' The default antimicrobial agents used for **all rows** (set in `universal`) are: #' The default antimicrobial drugs used for **all rows** (set in `universal`) are:
#' #'
#' - Ampicillin #' - Ampicillin
#' - Amoxicillin/clavulanic acid #' - Amoxicillin/clavulanic acid
@ -55,7 +55,7 @@
#' - Piperacillin/tazobactam #' - Piperacillin/tazobactam
#' - Trimethoprim/sulfamethoxazole #' - Trimethoprim/sulfamethoxazole
#' #'
#' The default antimicrobial agents used for **Gram-negative bacteria** (set in `gram_negative`) are: #' The default antimicrobial drugs used for **Gram-negative bacteria** (set in `gram_negative`) are:
#' #'
#' - Cefotaxime #' - Cefotaxime
#' - Ceftazidime #' - Ceftazidime
@ -64,7 +64,7 @@
#' - Meropenem #' - Meropenem
#' - Tobramycin #' - Tobramycin
#' #'
#' The default antimicrobial agents used for **Gram-positive bacteria** (set in `gram_positive`) are: #' The default antimicrobial drugs used for **Gram-positive bacteria** (set in `gram_positive`) are:
#' #'
#' - Erythromycin #' - Erythromycin
#' - Oxacillin #' - Oxacillin
@ -74,7 +74,7 @@
#' - Vancomycin #' - Vancomycin
#' #'
#' #'
#' The default antimicrobial agents used for **fungi** (set in `antifungal`) are: #' The default antimicrobial drugs used for **fungi** (set in `antifungal`) are:
#' #'
#' - Anidulafungin #' - Anidulafungin
#' - Caspofungin #' - Caspofungin

4
R/mdro.R
View File

@ -918,7 +918,7 @@ mdro <- function(x = NULL,
) )
} }
) )
# for PDR; all agents are R (or I if combine_SI = FALSE) # for PDR; all drugs are R (or I if combine_SI = FALSE)
x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE]), x_transposed <- as.list(as.data.frame(t(x[rows, lst_vector, drop = FALSE]),
stringsAsFactors = FALSE stringsAsFactors = FALSE
)) ))
@ -1171,7 +1171,7 @@ mdro <- function(x = NULL,
) )
} }
# PDR (=4): all agents are R # PDR (=4): all drugs are R
x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4 x[which(x$classes_affected == 999 & x$classes_in_guideline == x$classes_available), "MDRO"] <- 4
if (isTRUE(verbose)) { if (isTRUE(verbose)) {
x[which(x$MDRO == 4), "reason"] <- paste( x[which(x$MDRO == 4), "reason"] <- paste(

2
R/mo_property.R
View File

@ -34,7 +34,7 @@
#' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"` #' @param property one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`, or must be `"shortname"`
#' @inheritParams as.mo #' @inheritParams as.mo
#' @param ... other arguments passed on to [as.mo()], such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input' #' @param ... other arguments passed on to [as.mo()], such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'
#' @param ab any (vector of) text that can be coerced to a valid antibiotic code with [as.ab()] #' @param ab any (vector of) text that can be coerced to a valid antibiotic drug code with [as.ab()]
#' @param open browse the URL using [`browseURL()`][utils::browseURL()] #' @param open browse the URL using [`browseURL()`][utils::browseURL()]
#' @details All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010: #' @details All functions will, at default, keep old taxonomic properties. Please refer to this example, knowing that *Escherichia blattae* was renamed to *Shimwellia blattae* in 2010:
#' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming) #' - `mo_name("Escherichia blattae")` will return `"Shimwellia blattae"` (with a message about the renaming)

2
R/pca.R
View File

@ -54,7 +54,7 @@
#' filter(n() >= 30) %>% # filter on only 30 results per group #' filter(n() >= 30) %>% # filter on only 30 results per group
#' summarise_if(is.rsi, resistance) # then get resistance of all drugs #' summarise_if(is.rsi, resistance) # then get resistance of all drugs
#' #'
#' # now conduct PCA for certain antimicrobial agents #' # now conduct PCA for certain antimicrobial drugs
#' pca_result <- resistance_data %>% #' pca_result <- resistance_data %>%
#' pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) #' pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)
#' #'

2
R/plot.R
View File

@ -33,7 +33,7 @@
#' @param x,object values created with [as.mic()], [as.disk()] or [as.rsi()] (or their `random_*` variants, such as [random_mic()]) #' @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 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 ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details* #' @param guideline interpretation guideline to use, defaults to the latest included EUCAST guideline, see *Details*
#' @param main,title title of the plot #' @param main,title title of the plot
#' @param xlab,ylab axis title #' @param xlab,ylab axis title

4
R/random.R
View File

@ -29,10 +29,10 @@
#' Random MIC Values/Disk Zones/RSI Generation #' Random MIC Values/Disk Zones/RSI Generation
#' #'
#' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible. #' These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
#' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank. #' @param size desired size of the returned vector. If used in a [data.frame] call or `dplyr` verb, will get the current (group) size if left blank.
#' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()] #' @param mo any [character] that can be coerced to a valid microorganism code with [as.mo()]
#' @param ab any [character] that can be coerced to a valid antimicrobial agent code with [as.ab()] #' @param ab any [character] that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param prob_RSI a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value) #' @param prob_RSI a vector of length 3: the probabilities for "R" (1st value), "S" (2nd value) and "I" (3rd value)
#' @param ... ignored, only in place to allow future extensions #' @param ... ignored, only in place to allow future extensions
#' @details The base \R function [sample()] is used for generating values. #' @details The base \R function [sample()] is used for generating values.

8
R/rsi.R
View File

@ -33,7 +33,7 @@
#' @rdname as.rsi #' @rdname as.rsi
#' @param x vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres) #' @param x vector of values (for class [`mic`]: MIC values in mg/L, for class [`disk`]: a disk diffusion radius in millimetres)
#' @param mo any (vector of) text that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically #' @param mo any (vector of) text that can be coerced to valid microorganism codes with [as.mo()], can be left empty to determine it automatically
#' @param ab any (vector of) text that can be coerced to a valid antimicrobial code with [as.ab()] #' @param ab any (vector of) text that can be coerced to a valid antimicrobial drug code with [as.ab()]
#' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*. #' @param uti (Urinary Tract Infection) A vector with [logical]s (`TRUE` or `FALSE`) to specify whether a UTI specific interpretation from the guideline should be chosen. For using [as.rsi()] on a [data.frame], this can also be a column containing [logical]s or when left blank, the data set will be searched for a column 'specimen', and rows within this column containing 'urin' (such as 'urine', 'urina') will be regarded isolates from a UTI. See *Examples*.
#' @inheritParams first_isolate #' @inheritParams first_isolate
#' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details* #' @param guideline defaults to EUCAST `r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))` (the latest implemented EUCAST guideline in the [rsi_translation] data set), supports EUCAST (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "EUCAST")$guideline)))`) and CLSI (`r min(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`-`r max(as.integer(gsub("[^0-9]", "", subset(rsi_translation, guideline %like% "CLSI")$guideline)))`), see *Details*
@ -78,7 +78,7 @@
#' #'
#' ### Machine-Readable Interpretation Guidelines #' ### Machine-Readable Interpretation Guidelines
#' #'
#' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` 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. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. #' The repository of this package [contains a machine-readable version](https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt) of all guidelines. This is a CSV file consisting of `r format(nrow(AMR::rsi_translation), big.mark = ",")` rows and `r ncol(AMR::rsi_translation)` 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 drug and the microorganism. **This allows for easy implementation of these rules in laboratory information systems (LIS)**. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
#' #'
#' ### Other #' ### Other
#' #'
@ -95,7 +95,7 @@
#' - **I = Susceptible, Increased exposure**\cr #' - **I = Susceptible, Increased exposure**\cr
#' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. #' A microorganism is categorised as *Susceptible, Increased exposure* when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
#' #'
#' This AMR package honours this (new) insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates. #' This AMR package honours this insight. Use [susceptibility()] (equal to [proportion_SI()]) to determine antimicrobial susceptibility and [count_susceptible()] (equal to [count_SI()]) to count susceptible isolates.
#' @return Ordered [factor] with new class `rsi` #' @return Ordered [factor] with new class `rsi`
#' @aliases rsi #' @aliases rsi
#' @export #' @export
@ -258,7 +258,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
if (!is.null(cur_col)) { if (!is.null(cur_col)) {
ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE)) ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE))
if (!is.na(ab)) { if (!is.na(ab)) {
# this is a valid antibiotic code # this is a valid antibiotic drug code
message_( message_(
"Column '", font_bold(cur_col), "' is as.rsi()-eligible (despite only having empty values), since it seems to be ", "Column '", font_bold(cur_col), "' is as.rsi()-eligible (despite only having empty values), since it seems to be ",
ab_name(ab, language = NULL, tolower = TRUE), " (", ab, ")" ab_name(ab, language = NULL, tolower = TRUE), " (", ab, ")"

2
R/translate.R
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@ -32,7 +32,7 @@
#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()]. #' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
#' @param x text to translate #' @param x text to translate
#' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. #' @param language language to choose. Use one of these supported language names or ISO-639-1 codes: `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`.
#' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial agents and colloquial microorganism names. #' @details The currently `r length(LANGUAGES_SUPPORTED)` supported languages are `r vector_or(paste0(sapply(LANGUAGES_SUPPORTED_NAMES, function(x) x[[1]]), " (" , LANGUAGES_SUPPORTED, ")"), quotes = FALSE, sort = FALSE)`. All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
#' #'
#' **To silence language notes when this package loads** on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this: #' **To silence language notes when this package loads** on a non-English operating system, you can set the option `AMR_locale` in your `.Rprofile` file like this:
#' #'

4
R/vctrs.R
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@ -67,7 +67,7 @@ vec_cast.character.ab <- function(x, to, ...) {
as.character(x) as.character(x)
} }
vec_cast.ab.character <- function(x, to, ...) { vec_cast.ab.character <- function(x, to, ...) {
return_after_integrity_check(x, "antimicrobial code", as.character(AMR_env$AB_lookup$ab)) return_after_integrity_check(x, "antimicrobial drug code", as.character(AMR_env$AB_lookup$ab))
} }
# S3: av # S3: av
@ -81,7 +81,7 @@ vec_cast.character.av <- function(x, to, ...) {
as.character(x) as.character(x)
} }
vec_cast.av.character <- function(x, to, ...) { vec_cast.av.character <- function(x, to, ...) {
return_after_integrity_check(x, "antiviral agent code", as.character(AMR_env$AV_lookup$av)) return_after_integrity_check(x, "antiviral drug code", as.character(AMR_env$AV_lookup$av))
} }
# S3: mo # S3: mo

6
README.md
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@ -1,8 +1,8 @@
% AMR (for R)
# `AMR` (for R) # `AMR` (for R)
<img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center" height="300px" /> <a href="https://msberends.github.io/AMR/"><img src="https://msberends.github.io/AMR/AMR_intro.svg" align="center"></a>
----
This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)). This work was published in the Journal of Statistical Software (Volume 104(3); [DOI 10.18637/jss.v104.i03](https://doi.org/10.18637/jss.v104.i03)) and formed the basis of two PhD theses ([DOI 10.33612/diss.177417131](https://doi.org/10.33612/diss.177417131) and [DOI 10.33612/diss.192486375](https://doi.org/10.33612/diss.192486375)).

2
_pkgdown.yml
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@ -61,7 +61,7 @@ footer:
home: home:
sidebar: sidebar:
structure: [toc, links, authors, citation] structure: [toc, links, authors]
navbar: navbar:
title: "AMR (for R)" title: "AMR (for R)"

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data-raw/AMR_intro.ai
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14
index.md
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@ -1,5 +1,19 @@
# The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a> # The `AMR` Package for R <a href="https://msberends.github.io/AMR/"><img src="./logo.svg" align="right" height="139" /></a>
* Works on Windows, macOS and Linux with **all versions of R** since R-3.0
* Provides the **full microbiological taxonomy** and data on **all antimicrobial drugs**
* Applies all recent **CLSI and EUCAST clinical breakpoints** for MICs and disk zones
* Corrects for duplicate isolates, **calculates and predicts AMR** per antibiotic class
* Integrates with **WHONET**, ATC, **EARS-Net**, PubChem, **LOINC** and **SNOMED CT**
* Completely **dependency-free**, highly suitable for places with **limited resources**
<div style="display: flex;">
<p style="text-align:left; width: 50%;"><small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small></p>
<p style="text-align:right; width: 50%;"><small><a href="https://doi.org/10.18637/jss.v104.i03">https://doi.org/10.18637/jss.v104.i03</a></small></p>
</div>
----
### Introduction ### Introduction
The `AMR` package is a [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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 AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. The `AMR` package is a [free and open-source](#copyright) R package with [zero dependencies](https://en.wikipedia.org/wiki/Dependency_hell) 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 AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting.

2
man/ab_from_text.Rd
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@ -36,7 +36,7 @@ A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts. Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antimicrobial drugs, doses and forms of administration found in the texts.
} }
\details{ \details{
This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. This function is also internally used by \code{\link[=as.ab]{as.ab()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.ab]{as.ab()}} function may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
\subsection{Argument \code{type}}{ \subsection{Argument \code{type}}{
At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling. At default, the function will search for antimicrobial drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.ab]{as.ab()}} internally, it will correct for misspelling.

2
man/ab_property.Rd
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@ -56,7 +56,7 @@ set_ab_names(
) )
} }
\arguments{ \arguments{
\item{x}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}} \item{x}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.} \item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}

4
man/add_custom_antimicrobials.Rd
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@ -13,7 +13,7 @@ clear_custom_antimicrobials()
\item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"} \item{x}{a \link{data.frame} resembling the \link{antibiotics} data set, at least containing columns "ab" and "name"}
} }
\description{ \description{
With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial codes to the \code{AMR} package. With \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} you can add your own custom antimicrobial drug codes to the \code{AMR} package.
} }
\details{ \details{
Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up: Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}} function has to be run in every \R session - added antimicrobials are not stored between sessions and are thus lost when \R is exited. It is possible to save the antimicrobial additions to your \code{.Rprofile} file to circumvent this, although this requires to load the \code{AMR} package at every start-up:
@ -21,7 +21,7 @@ Due to how \R works, the \code{\link[=add_custom_antimicrobials]{add_custom_anti
\if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file \if{html}{\out{<div class="sourceCode r">}}\preformatted{# Open .Rprofile file
utils::file.edit("~/.Rprofile") utils::file.edit("~/.Rprofile")
# Add custom antibiotic codes: # Add custom antibiotic drug codes:
library(AMR) library(AMR)
add_custom_antimicrobials( add_custom_antimicrobials(
data.frame(ab = "TESTAB", data.frame(ab = "TESTAB",

4
man/antibiotic_class_selectors.Rd
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@ -104,7 +104,7 @@ not_intrinsic_resistant(
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \code{rsi} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}} \item{only_rsi_columns}{a \link{logical} to indicate whether only columns of class \code{rsi} must be selected (defaults to \code{FALSE}), see \code{\link[=as.rsi]{as.rsi()}}}
\item{only_treatable}{a \link{logical} to indicate whether agents that are only for laboratory tests should be excluded (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})} \item{only_treatable}{a \link{logical} to indicate whether antimicrobial drugs should be excluded that are only for laboratory tests (defaults to \code{TRUE}), such as gentamicin-high (\code{GEH}) and imipenem/EDTA (\code{IPE})}
\item{...}{ignored, only in place to allow future extensions} \item{...}{ignored, only in place to allow future extensions}
@ -118,7 +118,7 @@ not_intrinsic_resistant(
(internally) a \link{character} vector of column names, with additional class \code{"ab_selector"} (internally) a \link{character} vector of column names, with additional class \code{"ab_selector"}
} }
\description{ \description{
These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial agent, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by \code{\link[=cephalosporins]{cephalosporins()}}. These functions allow for filtering rows and selecting columns based on antibiotic test results that are of a specific antibiotic class or group, without the need to define the columns or antibiotic abbreviations. In short, if you have a column name that resembles an antimicrobial drug, it will be picked up by any of these functions that matches its pharmaceutical class: "cefazolin", "CZO" and "J01DB04" will all be picked up by \code{\link[=cephalosporins]{cephalosporins()}}.
} }
\details{ \details{
These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}. These functions can be used in data set calls for selecting columns and filtering rows. They are heavily inspired by the \link[tidyselect:language]{Tidyverse selection helpers} such as \code{\link[tidyselect:everything]{everything()}}, but also work in base \R and not only in \code{dplyr} verbs. Nonetheless, they are very convenient to use with \code{dplyr} functions such as \code{\link[dplyr:select]{select()}}, \code{\link[dplyr:filter]{filter()}} and \code{\link[dplyr:summarise]{summarise()}}, see \emph{Examples}.

4
man/antibiotics.Rd
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@ -21,7 +21,7 @@
\item \code{oral_units}\cr Units of \code{oral_ddd} \item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs \item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral (intravenous) treatment, currently available for 146 drugs
\item \code{iv_units}\cr Units of \code{iv_ddd} \item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}. \item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug. Use \code{\link[=ab_loinc]{ab_loinc()}} to retrieve them quickly, see \code{\link[=ab_property]{ab_property()}}.
} }
} }
@ -37,7 +37,7 @@
\item \code{oral_units}\cr Units of \code{oral_ddd} \item \code{oral_units}\cr Units of \code{oral_ddd}
\item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment \item \code{iv_ddd}\cr Defined Daily Dose (DDD), parenteral treatment
\item \code{iv_units}\cr Units of \code{iv_ddd} \item \code{iv_units}\cr Units of \code{iv_ddd}
\item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial agent. \item \code{loinc}\cr All LOINC codes (Logical Observation Identifiers Names and Codes) associated with the name of the antimicrobial drug.
} }
} }

6
man/as.ab.Rd
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@ -13,7 +13,7 @@ is.ab(x)
\arguments{ \arguments{
\item{x}{a \link{character} vector to determine to antibiotic ID} \item{x}{a \link{character} vector to determine to antibiotic ID}
\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antibiotic code or name can be retrieved from a single input value.} \item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antibiotic drug code or name can be retrieved from a single input value.}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode} \item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
@ -23,7 +23,7 @@ is.ab(x)
A \link{character} \link{vector} with additional class \code{\link{ab}} A \link{character} \link{vector} with additional class \code{\link{ab}}
} }
\description{ \description{
Use this function to determine the antibiotic code of one or more antibiotics. The data set \link{antibiotics} will be searched for abbreviations, official names and synonyms (brand names). Use this function to determine the antibiotic drug code of one or more antibiotics. The data set \link{antibiotics} will be searched for abbreviations, official names and synonyms (brand names).
} }
\details{ \details{
All entries in the \link{antibiotics} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes. All entries in the \link{antibiotics} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
@ -38,7 +38,7 @@ All these properties will be searched for the user input. The \code{\link[=as.ab
Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on the returned antibiotic ID, see \emph{Examples}. Use the \code{\link[=ab_property]{ab_*}} functions to get properties based on the returned antibiotic ID, see \emph{Examples}.
Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. Note: the \code{\link[=as.ab]{as.ab()}} and \code{\link[=ab_property]{ab_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}. You can add your own manual codes to be considered by \code{\link[=as.ab]{as.ab()}} and all \code{\link[=ab_property]{ab_*}} functions, see \code{\link[=add_custom_antimicrobials]{add_custom_antimicrobials()}}.
} }

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man/as.av.Rd
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@ -4,16 +4,16 @@
\alias{as.av} \alias{as.av}
\alias{av} \alias{av}
\alias{is.av} \alias{is.av}
\title{Transform Input to an Antiviral Agent ID} \title{Transform Input to an Antiviral Drug ID}
\usage{ \usage{
as.av(x, flag_multiple_results = TRUE, info = interactive(), ...) as.av(x, flag_multiple_results = TRUE, info = interactive(), ...)
is.av(x) is.av(x)
} }
\arguments{ \arguments{
\item{x}{a \link{character} vector to determine to antiviral agent ID} \item{x}{a \link{character} vector to determine to antiviral drug ID}
\item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antiviral agent code or name can be retrieved from a single input value.} \item{flag_multiple_results}{a \link{logical} to indicate whether a note should be printed to the console that probably more than one antiviral drug code or name can be retrieved from a single input value.}
\item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode} \item{info}{a \link{logical} to indicate whether a progress bar should be printed, defaults to \code{TRUE} only in interactive mode}
@ -23,7 +23,7 @@ is.av(x)
A \link{character} \link{vector} with additional class \code{\link{ab}} A \link{character} \link{vector} with additional class \code{\link{ab}}
} }
\description{ \description{
Use this function to determine the antiviral agent code of one or more antiviral agents. The data set \link{antivirals} will be searched for abbreviations, official names and synonyms (brand names). Use this function to determine the antiviral drug code of one or more antiviral drugs. The data set \link{antivirals} will be searched for abbreviations, official names and synonyms (brand names).
} }
\details{ \details{
All entries in the \link{antivirals} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes. All entries in the \link{antivirals} data set have three different identifiers: a human readable EARS-Net code (column \code{ab}, used by ECDC and WHONET), an ATC code (column \code{atc}, used by WHO), and a CID code (column \code{cid}, Compound ID, used by PubChem). The data set contains more than 5,000 official brand names from many different countries, as found in PubChem. Not that some drugs contain multiple ATC codes.
@ -36,9 +36,9 @@ All these properties will be searched for the user input. The \code{\link[=as.av
\item Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc. \item Digitalised paper records, leaving artefacts like 0/o/O (zero and O's), B/8, n/r, etc.
} }
Use the \code{\link[=av_property]{av_*}} functions to get properties based on the returned antiviral agent ID, see \emph{Examples}. Use the \code{\link[=av_property]{av_*}} functions to get properties based on the returned antiviral drug ID, see \emph{Examples}.
Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} functions may use very long regular expression to match brand names of antimicrobial agents. This may fail on some systems. Note: the \code{\link[=as.av]{as.av()}} and \code{\link[=av_property]{av_*}} functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.
} }
\section{Source}{ \section{Source}{

6
man/as.rsi.Rd
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@ -77,7 +77,7 @@ rsi_interpretation_history(clean = FALSE)
\item{mo}{any (vector of) text that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically} \item{mo}{any (vector of) text that can be coerced to valid microorganism codes with \code{\link[=as.mo]{as.mo()}}, can be left empty to determine it automatically}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}} \item{guideline}{defaults to EUCAST 2022 (the latest implemented EUCAST guideline in the \link{rsi_translation} data set), supports EUCAST (2013-2022) and CLSI (2013-2022), see \emph{Details}}
@ -142,7 +142,7 @@ After using \code{\link[=as.rsi]{as.rsi()}}, you can use the \code{\link[=eucast
\subsection{Machine-Readable Interpretation Guidelines}{ \subsection{Machine-Readable Interpretation Guidelines}{
The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial agent and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed. The repository of this package \href{https://github.com/msberends/AMR/blob/main/data-raw/rsi_translation.txt}{contains a machine-readable version} of all guidelines. This is a CSV file consisting of 18,308 rows and 11 columns. This file is machine-readable, since it contains one row for every unique combination of the test method (MIC or disk diffusion), the antimicrobial drug and the microorganism. \strong{This allows for easy implementation of these rules in laboratory information systems (LIS)}. Note that it only contains interpretation guidelines for humans - interpretation guidelines from CLSI for animals were removed.
} }
\subsection{Other}{ \subsection{Other}{
@ -166,7 +166,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
} }
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }
\section{Reference Data Publicly Available}{ \section{Reference Data Publicly Available}{

2
man/av_from_text.Rd
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@ -36,7 +36,7 @@ A \link{list}, or a \link{character} if \code{collapse} is not \code{NULL}
Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antiviral drugs, doses and forms of administration found in the texts. Use this function on e.g. clinical texts from health care records. It returns a \link{list} with all antiviral drugs, doses and forms of administration found in the texts.
} }
\details{ \details{
This function is also internally used by \code{\link[=as.av]{as.av()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.av]{as.av()}} function may use very long regular expression to match brand names of antiviral agents. This may fail on some systems. This function is also internally used by \code{\link[=as.av]{as.av()}}, although it then only searches for the first drug name and will throw a note if more drug names could have been returned. Note: the \code{\link[=as.av]{as.av()}} function may use very long regular expression to match brand names of antiviral drugs. This may fail on some systems.
\subsection{Argument \code{type}}{ \subsection{Argument \code{type}}{
At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.av]{as.av()}} internally, it will correct for misspelling. At default, the function will search for antiviral drug names. All text elements will be searched for official names, ATC codes and brand names. As it uses \code{\link[=as.av]{as.av()}} internally, it will correct for misspelling.

6
man/av_property.Rd
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@ -13,7 +13,7 @@
\alias{av_ddd_units} \alias{av_ddd_units}
\alias{av_info} \alias{av_info}
\alias{av_url} \alias{av_url}
\title{Get Properties of an Antiviral Agent} \title{Get Properties of an Antiviral Drug}
\usage{ \usage{
av_name(x, language = get_AMR_locale(), tolower = FALSE, ...) av_name(x, language = get_AMR_locale(), tolower = FALSE, ...)
@ -40,7 +40,7 @@ av_url(x, open = FALSE, ...)
av_property(x, property = "name", language = get_AMR_locale(), ...) av_property(x, property = "name", language = get_AMR_locale(), ...)
} }
\arguments{ \arguments{
\item{x}{any (vector of) text that can be coerced to a valid antiviral agent code with \code{\link[=as.av]{as.av()}}} \item{x}{any (vector of) text that can be coerced to a valid antiviral drug code with \code{\link[=as.av]{as.av()}}}
\item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.} \item{language}{language of the returned text, defaults to system language (see \code{\link[=get_AMR_locale]{get_AMR_locale()}}) and can also be set with \code{getOption("AMR_locale")}. Use \code{language = NULL} or \code{language = ""} to prevent translation.}
@ -63,7 +63,7 @@ av_property(x, property = "name", language = get_AMR_locale(), ...)
} }
} }
\description{ \description{
Use these functions to return a specific property of an antiviral agent from the \link{antivirals} data set. All input values will be evaluated internally with \code{\link[=as.av]{as.av()}}. Use these functions to return a specific property of an antiviral drug from the \link{antivirals} data set. All input values will be evaluated internally with \code{\link[=as.av]{as.av()}}.
} }
\details{ \details{
All output \link[=translate]{will be translated} where possible. All output \link[=translate]{will be translated} where possible.

2
man/count.Rd
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@ -81,7 +81,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
} }
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }
\section{Combination Therapy}{ \section{Combination Therapy}{

2
man/custom_eucast_rules.Rd
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@ -74,7 +74,7 @@ eucast_rules(df, rules = "custom", custom_rules = y, info = FALSE)
\subsection{Usage of antibiotic group names}{ \subsection{Usage of antibiotic group names}{
It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule. It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part \emph{after} the tilde. In above examples, the antibiotic group \code{aminopenicillins} is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.
\itemize{ \itemize{
\item "aminoglycosides"\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high) \item "aminoglycosides"\cr(amikacin, amikacin/fosfomycin, amphotericin B-high, apramycin, arbekacin, astromicin, bekanamycin, dibekacin, framycetin, gentamicin, gentamicin-high, habekacin, hygromycin, isepamicin, kanamycin, kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin, pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin, streptoduocin, streptomycin, streptomycin-high, tobramycin and tobramycin-high)
\item "aminopenicillins"\cr(amoxicillin and ampicillin) \item "aminopenicillins"\cr(amoxicillin and ampicillin)

2
man/dosage.Rd
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@ -8,7 +8,7 @@
A \link[tibble:tibble]{tibble} with 169 observations and 9 variables: A \link[tibble:tibble]{tibble} with 169 observations and 9 variables:
\itemize{ \itemize{
\item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available \item \code{ab}\cr Antibiotic ID as used in this package (such as \code{AMC}), using the official EARS-Net (European Antimicrobial Resistance Surveillance Network) codes where available
\item \code{name}\cr Official name of the antimicrobial agent as used by WHONET/EARS-Net or the WHO \item \code{name}\cr Official name of the antimicrobial drug as used by WHONET/EARS-Net or the WHO
\item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti" \item \code{type}\cr Type of the dosage, either "high_dosage", "standard_dosage" or "uncomplicated_uti"
\item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg" \item \code{dose}\cr Dose, such as "2 g" or "25 mg/kg"
\item \code{dose_times}\cr Number of times a dose must be administered \item \code{dose_times}\cr Number of times a dose must be administered

4
man/eucast_rules.Rd
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@ -50,7 +50,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".} \item{version_expertrules}{the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".}
\item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of \code{NA} (the default) for this argument will remove results for these three agents, while e.g. a value of \code{"R"} will make the results for these agents resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.} \item{ampc_cephalosporin_resistance}{a \link{character} value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to \code{NA}. Currently only works when \code{version_expertrules} is \code{3.2} and higher; these version of '\emph{EUCAST Expert Rules on Enterobacterales}' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three drugs. A value of \code{NA} (the default) for this argument will remove results for these three drugs, while e.g. a value of \code{"R"} will make the results for these drugs resistant. Use \code{NULL} or \code{FALSE} to not alter results for these three drugs of AmpC de-repressed cephalosporin-resistant mutants. Using \code{TRUE} is equal to using \code{"R"}. \cr For \emph{EUCAST Expert Rules} v3.2, this rule applies to: \emph{Citrobacter braakii}, \emph{Citrobacter freundii}, \emph{Citrobacter gillenii}, \emph{Citrobacter murliniae}, \emph{Citrobacter rodenticum}, \emph{Citrobacter sedlakii}, \emph{Citrobacter werkmanii}, \emph{Citrobacter youngae}, \emph{Enterobacter}, \emph{Hafnia alvei}, \emph{Klebsiella aerogenes}, \emph{Morganella morganii}, \emph{Providencia} and \emph{Serratia}.}
\item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} \item{only_rsi_columns}{a \link{logical} to indicate whether only antibiotic columns must be detected that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
@ -58,7 +58,7 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 11)
\item{...}{column name of an antibiotic, see section \emph{Antibiotics} below} \item{...}{column name of an antibiotic, see section \emph{Antibiotics} below}
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
\item{administration}{route of administration, either "im", "iv" or "oral"} \item{administration}{route of administration, either "im", "iv" or "oral"}
} }

4
man/first_isolate.Rd
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@ -151,12 +151,12 @@ This is a more reliable method, since it also \emph{weighs} the antibiogram (ant
\enumerate{ \enumerate{
\item Using \code{type = "points"} and argument \code{points_threshold} (default) \item Using \code{type = "points"} and argument \code{points_threshold} (default)
This method weighs \emph{all} antimicrobial agents available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate. This method weighs \emph{all} antimicrobial drugs available in the data set. Any difference from I to S or R (or vice versa) counts as \code{0.5} points, a difference from S to R (or vice versa) counts as \code{1} point. When the sum of points exceeds \code{points_threshold}, which defaults to \code{2}, an isolate will be selected as a first weighted isolate.
All antimicrobials are internally selected using the \code{\link[=all_antimicrobials]{all_antimicrobials()}} function. The output of this function does not need to be passed to the \code{\link[=first_isolate]{first_isolate()}} function. All antimicrobials are internally selected using the \code{\link[=all_antimicrobials]{all_antimicrobials()}} function. The output of this function does not need to be passed to the \code{\link[=first_isolate]{first_isolate()}} function.
\item Using \code{type = "keyantimicrobials"} and argument \code{ignore_I} \item Using \code{type = "keyantimicrobials"} and argument \code{ignore_I}
This method only weighs specific antimicrobial agents, called \emph{key antimicrobials}. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S or R (or vice versa) will lead to this. This method only weighs specific antimicrobial drugs, called \emph{key antimicrobials}. Any difference from S to R (or vice versa) in these key antimicrobials will select an isolate as a first weighted isolate. With \code{ignore_I = FALSE}, also differences from I to S or R (or vice versa) will lead to this.
Key antimicrobials are internally selected using the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function, but can also be added manually as a variable to the data and set in the \code{col_keyantimicrobials} argument. Another option is to pass the output of the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function directly to the \code{col_keyantimicrobials} argument. Key antimicrobials are internally selected using the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function, but can also be added manually as a variable to the data and set in the \code{col_keyantimicrobials} argument. Another option is to pass the output of the \code{\link[=key_antimicrobials]{key_antimicrobials()}} function directly to the \code{col_keyantimicrobials} argument.
} }

2
man/ggplot_pca.Rd
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@ -123,7 +123,7 @@ if (require("dplyr")) {
filter(n() >= 30) \%>\% # filter on only 30 results per group filter(n() >= 30) \%>\% # filter on only 30 results per group
summarise_if(is.rsi, resistance) # then get resistance of all drugs summarise_if(is.rsi, resistance) # then get resistance of all drugs
# now conduct PCA for certain antimicrobial agents # now conduct PCA for certain antimicrobial drugs
pca_result <- resistance_data \%>\% pca_result <- resistance_data \%>\%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)

18
man/key_antimicrobials.Rd
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@ -37,13 +37,13 @@ antimicrobials_equal(
\item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.} \item{col_mo}{column name of the IDs of the microorganisms (see \code{\link[=as.mo]{as.mo()}}), defaults to the first column of class \code{\link{mo}}. Values will be coerced using \code{\link[=as.mo]{as.mo()}}.}
\item{universal}{names of \strong{broad-spectrum} antimicrobial agents, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.} \item{universal}{names of \strong{broad-spectrum} antimicrobial drugs, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antimicrobial drugs}
\item{gram_negative}{names of antibiotic agents for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.} \item{gram_negative}{names of antibiotic drugs for \strong{Gram-positives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
\item{gram_positive}{names of antibiotic agents for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.} \item{gram_positive}{names of antibiotic drugs for \strong{Gram-negatives}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antibiotic drugs}
\item{antifungal}{names of antifungal agents for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default agents.} \item{antifungal}{names of antifungal drugs for \strong{fungi}, case-insensitive. Set to \code{NULL} to ignore. See \emph{Details} for the default antifungal drugs}
\item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})} \item{only_rsi_columns}{a \link{logical} to indicate whether only columns must be included that were transformed to class \code{rsi} (see \code{\link[=as.rsi]{as.rsi()}}) on beforehand (defaults to \code{FALSE})}
@ -63,11 +63,11 @@ These functions can be used to determine first weighted isolates by considering
\details{ \details{
The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}. The \code{\link[=key_antimicrobials]{key_antimicrobials()}} and \code{\link[=all_antimicrobials]{all_antimicrobials()}} functions are context-aware. This means that the \code{x} argument can be left blank if used inside a \link{data.frame} call, see \emph{Examples}.
The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}. The function \code{\link[=key_antimicrobials]{key_antimicrobials()}} returns a \link{character} vector with 12 antimicrobial results for every isolate. The function \code{\link[=all_antimicrobials]{all_antimicrobials()}} returns a \link{character} vector with all antimicrobial drug results for every isolate. These vectors can then be compared using \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}, to check if two isolates have generally the same antibiogram. Missing and invalid values are replaced with a dot (\code{"."}) by \code{\link[=key_antimicrobials]{key_antimicrobials()}} and ignored by \code{\link[=antimicrobials_equal]{antimicrobials_equal()}}.
Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates. Please see the \code{\link[=first_isolate]{first_isolate()}} function how these important functions enable the 'phenotype-based' method for determination of first isolates.
The default antimicrobial agents used for \strong{all rows} (set in \code{universal}) are: The default antimicrobial drugs used for \strong{all rows} (set in \code{universal}) are:
\itemize{ \itemize{
\item Ampicillin \item Ampicillin
\item Amoxicillin/clavulanic acid \item Amoxicillin/clavulanic acid
@ -77,7 +77,7 @@ The default antimicrobial agents used for \strong{all rows} (set in \code{univer
\item Trimethoprim/sulfamethoxazole \item Trimethoprim/sulfamethoxazole
} }
The default antimicrobial agents used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are: The default antimicrobial drugs used for \strong{Gram-negative bacteria} (set in \code{gram_negative}) are:
\itemize{ \itemize{
\item Cefotaxime \item Cefotaxime
\item Ceftazidime \item Ceftazidime
@ -87,7 +87,7 @@ The default antimicrobial agents used for \strong{Gram-negative bacteria} (set i
\item Tobramycin \item Tobramycin
} }
The default antimicrobial agents used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are: The default antimicrobial drugs used for \strong{Gram-positive bacteria} (set in \code{gram_positive}) are:
\itemize{ \itemize{
\item Erythromycin \item Erythromycin
\item Oxacillin \item Oxacillin
@ -97,7 +97,7 @@ The default antimicrobial agents used for \strong{Gram-positive bacteria} (set i
\item Vancomycin \item Vancomycin
} }
The default antimicrobial agents used for \strong{fungi} (set in \code{antifungal}) are: The default antimicrobial drugs used for \strong{fungi} (set in \code{antifungal}) are:
\itemize{ \itemize{
\item Anidulafungin \item Anidulafungin
\item Caspofungin \item Caspofungin

2
man/mdro.Rd
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@ -184,7 +184,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
} }
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }
\examples{ \examples{

2
man/mo_property.Rd
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@ -266,7 +266,7 @@ mo_property(
\item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'} \item{...}{other arguments passed on to \code{\link[=as.mo]{as.mo()}}, such as 'minimum_matching_score', 'ignore_pattern', and 'remove_from_input'}
\item{ab}{any (vector of) text that can be coerced to a valid antibiotic code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any (vector of) text that can be coerced to a valid antibiotic drug code with \code{\link[=as.ab]{as.ab()}}}
\item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}} \item{open}{browse the URL using \code{\link[utils:browseURL]{browseURL()}}}

2
man/pca.Rd
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@ -74,7 +74,7 @@ if (require("dplyr")) {
filter(n() >= 30) \%>\% # filter on only 30 results per group filter(n() >= 30) \%>\% # filter on only 30 results per group
summarise_if(is.rsi, resistance) # then get resistance of all drugs summarise_if(is.rsi, resistance) # then get resistance of all drugs
# now conduct PCA for certain antimicrobial agents # now conduct PCA for certain antimicrobial drugs
pca_result <- resistance_data \%>\% pca_result <- resistance_data \%>\%
pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT) pca(AMC, CXM, CTX, CAZ, GEN, TOB, TMP, SXT)

2
man/plot.Rd
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@ -99,7 +99,7 @@
\item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}} \item{mo}{any (vector of) text that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{any (vector of) text that can be coerced to a valid antimicrobial code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any (vector of) text that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{guideline}{interpretation guideline to use, defaults to the latest included EUCAST guideline, see \emph{Details}} \item{guideline}{interpretation guideline to use, defaults to the latest included EUCAST guideline, see \emph{Details}}

2
man/proportion.Rd
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@ -153,7 +153,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
} }
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }
\examples{ \examples{

4
man/random.Rd
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@ -18,7 +18,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
\item{mo}{any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}} \item{mo}{any \link{character} that can be coerced to a valid microorganism code with \code{\link[=as.mo]{as.mo()}}}
\item{ab}{any \link{character} that can be coerced to a valid antimicrobial agent code with \code{\link[=as.ab]{as.ab()}}} \item{ab}{any \link{character} that can be coerced to a valid antimicrobial drug code with \code{\link[=as.ab]{as.ab()}}}
\item{...}{ignored, only in place to allow future extensions} \item{...}{ignored, only in place to allow future extensions}
@ -28,7 +28,7 @@ random_rsi(size = NULL, prob_RSI = c(0.33, 0.33, 0.33), ...)
class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \code{disk} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}}) class \code{mic} for \code{\link[=random_mic]{random_mic()}} (see \code{\link[=as.mic]{as.mic()}}) and class \code{disk} for \code{\link[=random_disk]{random_disk()}} (see \code{\link[=as.disk]{as.disk()}})
} }
\description{ \description{
These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial agent, the generated results will reflect reality as much as possible. These functions can be used for generating random MIC values and disk diffusion diameters, for AMR data analysis practice. By providing a microorganism and antimicrobial drug, the generated results will reflect reality as much as possible.
} }
\details{ \details{
The base \R function \code{\link[=sample]{sample()}} is used for generating values. The base \R function \code{\link[=sample]{sample()}} is used for generating values.

2
man/resistance_predict.Rd
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@ -122,7 +122,7 @@ A microorganism is categorised as \emph{Susceptible, standard dosing regimen}, w
A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection. A microorganism is categorised as \emph{Susceptible, Increased exposure} when there is a high likelihood of therapeutic success because exposure to the agent is increased by adjusting the dosing regimen or by its concentration at the site of infection.
} }
This AMR package honours this (new) insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates. This AMR package honours this insight. Use \code{\link[=susceptibility]{susceptibility()}} (equal to \code{\link[=proportion_SI]{proportion_SI()}}) to determine antimicrobial susceptibility and \code{\link[=count_susceptible]{count_susceptible()}} (equal to \code{\link[=count_SI]{count_SI()}}) to count susceptible isolates.
} }
\examples{ \examples{

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man/translate.Rd
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@ -25,7 +25,7 @@ translate_AMR(x, language = get_AMR_locale())
For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}. For language-dependent output of AMR functions, like \code{\link[=mo_name]{mo_name()}}, \code{\link[=mo_gramstain]{mo_gramstain()}}, \code{\link[=mo_type]{mo_type()}} and \code{\link[=ab_name]{ab_name()}}.
} }
\details{ \details{
The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial agents and colloquial microorganism names. The currently 16 supported languages are English (en), Chinese (zh), Danish (da), Dutch (nl), French (fr), German (de), Greek (el), Italian (it), Japanese (ja), Polish (pl), Portuguese (pt), Russian (ru), Spanish (es), Swedish (sv), Turkish (tr) or Ukrainian (uk). All these languages have translations available for all antimicrobial drugs and colloquial microorganism names.
\strong{To silence language notes when this package loads} on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this: \strong{To silence language notes when this package loads} on a non-English operating system, you can set the option \code{AMR_locale} in your \code{.Rprofile} file like this:

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