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(v2.1.1.9151) update readme
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@ -55,8 +55,8 @@
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#' @section Full list of supported (antimicrobial) classes:
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#'
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#' `r paste0(" * ", na.omit(sapply(DEFINED_AB_GROUPS, function(ab) ifelse(tolower(gsub("^AB_", "", ab)) %in% ls(envir = asNamespace("AMR")), paste0("[", tolower(gsub("^AB_", "", ab)), "()] can select: \\cr ", vector_and(paste0(ab_name(eval(parse(text = ab), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), " (", eval(parse(text = ab), envir = asNamespace("AMR")), ")"), quotes = FALSE, sort = TRUE)), character(0)), USE.NAMES = FALSE)), "\n", collapse = "")`
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#' @rdname antimicrobial_class_selectors
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#' @name antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @name antimicrobial_selectors
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#' @return When used inside selecting or filtering, this returns a [character] vector of column names, with additional class `"amr_selector"`. When used individually, this returns an ['ab' vector][as.ab()] with all possible antimicrobials that the function would be able to select or filter.
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#' @export
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#' @inheritSection AMR Reference Data Publicly Available
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@ -243,7 +243,7 @@ amr_class <- function(amr_class,
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amr_select_exec(NULL, only_sir_columns = only_sir_columns, amr_class_args = amr_class, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @details The [amr_selector()] function can be used to internally filter the [antibiotics] data set on any results, see *Examples*. It allows for filtering on a (part of) a certain name, and/or a group name or even a minimum of DDDs for oral treatment. This function yields the highest flexibility, but is also the least user-friendly, since it requires a hard-coded filter to set.
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#' @export
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amr_selector <- function(filter,
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@ -280,7 +280,7 @@ amr_selector <- function(filter,
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)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -289,7 +289,7 @@ aminoglycosides <- function(only_sir_columns = FALSE, only_treatable = TRUE, ret
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amr_select_exec("aminoglycosides", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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aminopenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -297,7 +297,7 @@ aminopenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("aminopenicillins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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antifungals <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -305,7 +305,7 @@ antifungals <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("antifungals", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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antimycobacterials <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -313,7 +313,7 @@ antimycobacterials <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("antimycobacterials", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -322,7 +322,7 @@ betalactams <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_
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amr_select_exec("betalactams", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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betalactams_with_inhibitor <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -330,7 +330,7 @@ betalactams_with_inhibitor <- function(only_sir_columns = FALSE, return_all = TR
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amr_select_exec("betalactams_with_inhibitor", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -339,7 +339,7 @@ carbapenems <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_
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amr_select_exec("carbapenems", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -347,7 +347,7 @@ cephalosporins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("cephalosporins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins_1st <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -355,7 +355,7 @@ cephalosporins_1st <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("cephalosporins_1st", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins_2nd <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -363,7 +363,7 @@ cephalosporins_2nd <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("cephalosporins_2nd", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins_3rd <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -371,7 +371,7 @@ cephalosporins_3rd <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("cephalosporins_3rd", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins_4th <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -379,7 +379,7 @@ cephalosporins_4th <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("cephalosporins_4th", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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cephalosporins_5th <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -387,7 +387,7 @@ cephalosporins_5th <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("cephalosporins_5th", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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fluoroquinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -395,7 +395,7 @@ fluoroquinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("fluoroquinolones", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -403,7 +403,7 @@ glycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("glycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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isoxazolylpenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -411,7 +411,7 @@ isoxazolylpenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, .
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amr_select_exec("isoxazolylpenicillins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -420,7 +420,7 @@ lincosamides <- function(only_sir_columns = FALSE, only_treatable = TRUE, return
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amr_select_exec("lincosamides", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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lipoglycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -428,7 +428,7 @@ lipoglycopeptides <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("lipoglycopeptides", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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macrolides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -436,7 +436,7 @@ macrolides <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("macrolides", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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monobactams <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -444,7 +444,7 @@ monobactams <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("monobactams", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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nitrofurans <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -452,7 +452,7 @@ nitrofurans <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("nitrofurans", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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oxazolidinones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -460,7 +460,7 @@ oxazolidinones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("oxazolidinones", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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penicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -468,7 +468,7 @@ penicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("penicillins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -476,7 +476,7 @@ phenicols <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("phenicols", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -485,7 +485,7 @@ polymyxins <- function(only_sir_columns = FALSE, only_treatable = TRUE, return_a
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amr_select_exec("polymyxins", only_sir_columns = only_sir_columns, only_treatable = only_treatable, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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quinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -493,7 +493,7 @@ quinolones <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("quinolones", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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rifamycins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -501,7 +501,7 @@ rifamycins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("rifamycins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -509,7 +509,7 @@ streptogramins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("streptogramins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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tetracyclines <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -517,7 +517,7 @@ tetracyclines <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("tetracyclines", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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trimethoprims <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -525,7 +525,7 @@ trimethoprims <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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amr_select_exec("trimethoprims", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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ureidopenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -533,7 +533,7 @@ ureidopenicillins <- function(only_sir_columns = FALSE, return_all = TRUE, ...)
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amr_select_exec("ureidopenicillins", only_sir_columns = only_sir_columns, return_all = return_all)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @details The [administrable_per_os()] and [administrable_iv()] functions also rely on the [antibiotics] data set - antimicrobials will be matched where a DDD (defined daily dose) for resp. oral and IV treatment is available in the [antibiotics] data set.
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#' @export
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administrable_per_os <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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||||
@ -575,7 +575,7 @@ administrable_per_os <- function(only_sir_columns = FALSE, return_all = TRUE, ..
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)
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}
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#' @rdname antimicrobial_class_selectors
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#' @rdname antimicrobial_selectors
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#' @export
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administrable_iv <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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meet_criteria(only_sir_columns, allow_class = "logical", has_length = 1)
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@ -602,7 +602,7 @@ administrable_iv <- function(only_sir_columns = FALSE, return_all = TRUE, ...) {
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||||
)
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||||
}
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||||
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||||
#' @rdname antimicrobial_class_selectors
|
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#' @rdname antimicrobial_selectors
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#' @inheritParams eucast_rules
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#' @details The [not_intrinsic_resistant()] function can be used to only select antimicrobials that pose no intrinsic resistance for the microorganisms in the data set. For example, if a data set contains only microorganism codes or names of *E. coli* and *K. pneumoniae* and contains a column "vancomycin", this column will be removed (or rather, unselected) using this function. It currently applies `r format_eucast_version_nr(names(EUCAST_VERSION_EXPERT_RULES[1]))` to determine intrinsic resistance, using the [eucast_rules()] function internally. Because of this determination, this function is quite slow in terms of performance.
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#' @export
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||||
|
||||
@ -34,7 +34,7 @@
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#'
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#' Adhering to previously described approaches (see *Source*) and especially the Bayesian WISCA model (Weighted-Incidence Syndromic Combination Antibiogram) by Bielicki *et al.*, these functions provide flexible output formats including plots and tables, ideal for integration with R Markdown and Quarto reports.
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#' @param x a [data.frame] containing at least a column with microorganisms and columns with antimicrobial results (class 'sir', see [as.sir()])
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#' @param antibiotics vector of any antimicrobial name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antimicrobial selectors][antimicrobial_class_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as `"TZP+TOB"` or `"cipro + genta"`, given that columns resembling such antimicrobials exist in `x`. See *Examples*.
|
||||
#' @param antibiotics vector of any antimicrobial name or code (will be evaluated with [as.ab()], column name of `x`, or (any combinations of) [antimicrobial selectors][antimicrobial_selectors] such as [aminoglycosides()] or [carbapenems()]. For combination antibiograms, this can also be set to values separated with `"+"`, such as `"TZP+TOB"` or `"cipro + genta"`, given that columns resembling such antimicrobials exist in `x`. See *Examples*.
|
||||
#' @param mo_transform a character to transform microorganism input - must be `"name"`, `"shortname"` (default), `"gramstain"`, or one of the column names of the [microorganisms] data set: `r vector_or(colnames(microorganisms), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input or `NA` to consider all microorganisms 'unknown'.
|
||||
#' @param ab_transform a character to transform antimicrobial input - must be one of the column names of the [antibiotics] data set (defaults to `"name"`): `r vector_or(colnames(antibiotics), sort = FALSE, quotes = TRUE)`. Can also be `NULL` to not transform the input.
|
||||
#' @param syndromic_group a column name of `x`, or values calculated to split rows of `x`, e.g. by using [ifelse()] or [`case_when()`][dplyr::case_when()]. See *Examples*.
|
||||
|
||||
Reference in New Issue
Block a user