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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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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