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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
parent 496c08d851
commit 7ca44fb756
56 changed files with 4623 additions and 4607 deletions
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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