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cleanup and new intro logo

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dr. M.S. (Matthijs) Berends
2022-11-13 13:44:25 +01:00
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12
R/ab.R
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@ -29,9 +29,9 @@
#' 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 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 ... arguments passed on to internal functions
#' @rdname as.ab
@ -47,7 +47,7 @@
#'
#' 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()].
#' @section Source:
@ -591,7 +591,7 @@ as.data.frame.ab <- function(x, ...) {
"[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
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
#' @export
@ -599,7 +599,7 @@ as.data.frame.ab <- function(x, ...) {
"[[<-.ab" <- function(i, j, ..., value) {
y <- NextMethod()
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
#' @export
@ -608,7 +608,7 @@ c.ab <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
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

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 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()]
#' @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`
#' 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
#'
#' 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 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.
@ -378,7 +378,7 @@ set_ab_names <- function(data, ..., property = "name", language = get_AMR_locale
return(data)
}
} else {
# quickly get antibiotic codes
# quickly get antibiotic drug codes
vars_ab <- as.ab(data, fast_mode = TRUE)
vars <- data[!is.na(vars_ab)]
}

16
R/ab_selectors.R
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@ -29,11 +29,11 @@
#' 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 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_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
#' @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*.
@ -548,7 +548,7 @@ ab_select_exec <- function(function_name,
if (any(untreatable %in% names(ab_in_data))) {
if (message_not_thrown_before(function_name, "ab_class", "untreatable", entire_session = TRUE)) {
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],
language = NULL,
tolower = TRUE
@ -564,7 +564,7 @@ ab_select_exec <- function(function_name,
}
if (length(ab_in_data) == 0) {
message_("No antimicrobial agents found in the data.")
message_("No antimicrobial drugs found in the data.")
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 (length(agents) == 0) {
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") {
message_("No orally administrable agents found", examples, ".")
message_("No orally administrable drugs found", examples, ".")
} else if (ab_group == "administrable_iv") {
message_("No IV administrable agents found", examples, ".")
message_("No IV administrable drugs found", examples, ".")
} else {
message_("No antimicrobial agents of class '", ab_group, "' found", examples, ".")
message_("No antimicrobial drugs of class '", ab_group, "' found", examples, ".")
}
} else {
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
#'
#' 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"
#' @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
#' utils::file.edit("~/.Rprofile")
#'
#' # Add custom antibiotic codes:
#' # Add custom antibiotic drug codes:
#' library(AMR)
#' add_custom_antimicrobials(
#' data.frame(ab = "TESTAB",
@ -107,7 +107,7 @@ add_custom_antimicrobials <- function(x) {
)
stop_if(
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]

20
R/av.R
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@ -27,11 +27,11 @@
# 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).
#' @param x a [character] vector to determine to antiviral agent 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.
#' 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 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 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 ... arguments passed on to internal functions
#' @rdname as.av
@ -45,9 +45,9 @@
#' * 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.
#'
#' 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:
#' 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))])
if (length(x_unknown) > 0 && fast_mode == FALSE) {
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), "."
)
}
@ -557,7 +557,7 @@ as.data.frame.av <- function(x, ...) {
"[<-.av" <- function(i, j, ..., value) {
y <- NextMethod()
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
#' @export
@ -565,7 +565,7 @@ as.data.frame.av <- function(x, ...) {
"[[<-.av" <- function(i, j, ..., value) {
y <- NextMethod()
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
#' @export
@ -574,7 +574,7 @@ c.av <- function(...) {
x <- list(...)[[1L]]
y <- NextMethod()
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

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 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()]
#' @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`
#' 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/ #
# ==================================================================== #
#' 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()].
#' @param x any (vector of) text that can be coerced to a valid antiviral agent code 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 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 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.

6
R/custom_eucast_rules.R
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@ -91,7 +91,7 @@
#'
#' ### 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 = "")`
#' @returns A [list] containing the custom rules
@ -174,8 +174,8 @@ custom_eucast_rules <- function(...) {
stop_if(
any(is.na(result_group)),
"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"",
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ",
"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 drug, or be one of: ",
vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), "."
)
result_value <- as.character(result)[[3]]

6
R/data.R
View File

@ -45,7 +45,7 @@
#' - `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_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:
#' - `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`
#' - `iv_ddd`\cr Defined Daily Dose (DDD), parenteral treatment
#' - `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`.
#'
#' 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()].
#' @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
#' - `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)`
#' - `dose`\cr Dose, such as "2 g" or "25 mg/kg"
#' - `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 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 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 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 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()]

4
R/first_isolate.R
View File

@ -107,14 +107,14 @@
#'
#' 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.
#'
#'
#' 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.
#'

2
R/ggplot_pca.R
View File

@ -78,7 +78,7 @@
#' filter(n() >= 30) %>% # filter on only 30 results per group
#' 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(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`
val <- as.ab(val)
} else {
stop_("unknown antimicrobial agent (group): ", val, call = FALSE)
stop_("unknown antimicrobial drug (group): ", val, call = FALSE)
}
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 y,z [character] vectors to compare
#' @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 gram_negative names of antibiotic agents for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
#' @param gram_positive names of antibiotic agents for **Gram-negatives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default agents.
#' @param antifungal names of antifungal agents for **fungi**, 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 drugs for **Gram-positives**, case-insensitive. Set to `NULL` to ignore. See *Details* for the default antibiotic drugs
#' @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 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 ... ignored, only in place to allow future extensions
#' @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 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.
#'
#' 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
#' - Amoxicillin/clavulanic acid
@ -55,7 +55,7 @@
#' - Piperacillin/tazobactam
#' - 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
#' - Ceftazidime
@ -64,7 +64,7 @@
#' - Meropenem
#' - 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
#' - Oxacillin
@ -74,7 +74,7 @@
#' - Vancomycin
#'
#'
#' The default antimicrobial agents used for **fungi** (set in `antifungal`) are:
#' The default antimicrobial drugs used for **fungi** (set in `antifungal`) are:
#'
#' - Anidulafungin
#' - 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]),
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$classes_available), "MDRO"] <- 4
if (isTRUE(verbose)) {
x[which(x$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"`
#' @inheritParams as.mo
#' @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()]
#' @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)

2
R/pca.R
View File

@ -54,7 +54,7 @@
#' filter(n() >= 30) %>% # filter on only 30 results per group
#' 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(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 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 main,title title of the plot
#' @param xlab,ylab axis title

4
R/random.R
View File

@ -29,10 +29,10 @@
#' 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 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 ... ignored, only in place to allow future extensions
#' @details The base \R function [sample()] is used for generating values.

8
R/rsi.R
View File

@ -33,7 +33,7 @@
#' @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 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*.
#' @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*
@ -78,7 +78,7 @@
#'
#' ### 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
#'
@ -95,7 +95,7 @@
#' - **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.
#'
#' 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`
#' @aliases rsi
#' @export
@ -258,7 +258,7 @@ is.rsi.eligible <- function(x, threshold = 0.05) {
if (!is.null(cur_col)) {
ab <- suppressWarnings(as.ab(cur_col, fast_mode = TRUE, info = FALSE))
if (!is.na(ab)) {
# this is a valid antibiotic code
# this is a valid antibiotic drug code
message_(
"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, ")"

2
R/translate.R
View File

@ -32,7 +32,7 @@
#' For language-dependent output of AMR functions, like [mo_name()], [mo_gramstain()], [mo_type()] and [ab_name()].
#' @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)`.
#' @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:
#'

4
R/vctrs.R
View File

@ -67,7 +67,7 @@ vec_cast.character.ab <- function(x, to, ...) {
as.character(x)
}
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
@ -81,7 +81,7 @@ vec_cast.character.av <- function(x, to, ...) {
as.character(x)
}
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