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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions
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16
R/custom_antimicrobials.R
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@@ -30,14 +30,14 @@
#' Add Custom Antimicrobials
#'
#' With [add_custom_antimicrobials()] you can add your own custom antimicrobial drug names and codes.
#' @param x a [data.frame] resembling the [antibiotics] data set, at least containing columns "ab" and "name"
#' @param x a [data.frame] resembling the [antimicrobials] data set, at least containing columns "ab" and "name"
#' @details **Important:** 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.
#'
#' There are two ways to circumvent this and automate the process of adding antimicrobials:
#'
#' **Method 1:** Using the package option [`AMR_custom_ab`][AMR-options], which is the preferred method. To use this method:
#'
#' 1. Create a data set in the structure of the [antibiotics] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_ab.rds"`, or any remote location.
#' 1. Create a data set in the structure of the [antimicrobials] data set (containing at the very least columns "ab" and "name") and save it with [saveRDS()] to a location of choice, e.g. `"~/my_custom_ab.rds"`, or any remote location.
#'
#' 2. Set the file location to the package option [`AMR_custom_ab`][AMR-options]: `options(AMR_custom_ab = "~/my_custom_ab.rds")`. This can even be a remote file location, such as an https URL. Since options are not saved between \R sessions, it is best to save this option to the `.Rprofile` file so that it will be loaded on start-up of \R. To do this, open the `.Rprofile` file using e.g. `utils::file.edit("~/.Rprofile")`, add this text and save the file:
#'
@@ -79,7 +79,7 @@
#' ab = "TESTAB",
#' name = "Test Antibiotic",
#' # you can add any property present in the
#' # 'antibiotics' data set, such as 'group':
#' # 'antimicrobials' data set, such as 'group':
#' group = "Test Group"
#' )
#' )
@@ -123,11 +123,11 @@ add_custom_antimicrobials <- function(x) {
)
stop_if(
any(x$ab %in% AMR_env$AB_lookup$ab),
"Antimicrobial drug code(s) ", vector_and(x$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$ab]), " already exist in the internal `antimicrobials` data set."
)
# remove any extra class/type, such as grouped tbl, or data.table:
x <- as.data.frame(x, stringsAsFactors = FALSE)
# keep only columns available in the antibiotics data set
# keep only columns available in the antimicrobials data set
x <- x[, colnames(AMR_env$AB_lookup)[colnames(AMR_env$AB_lookup) %in% colnames(x)], drop = FALSE]
x$generalised_name <- generalise_antibiotic_name(x$name)
x$generalised_all <- as.list(x$generalised_name)
@@ -155,16 +155,16 @@ add_custom_antimicrobials <- function(x) {
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% c(x$ab, x$generalised_name) & !AMR_env$ab_previously_coerced$x %in% c(x$ab, x$generalised_name)), , drop = FALSE]
class(AMR_env$AB_lookup$ab) <- c("ab", "character")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antibiotics` data set.")
message_("Added ", nr2char(nrow(x)), " record", ifelse(nrow(x) > 1, "s", ""), " to the internal `antimicrobials` data set.")
}
#' @rdname add_custom_antimicrobials
#' @export
clear_custom_antimicrobials <- function() {
n <- nrow(AMR_env$AB_lookup)
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
AMR_env$AB_lookup <- cbind(AMR::antimicrobials, AB_LOOKUP)
n2 <- nrow(AMR_env$AB_lookup)
AMR_env$custom_ab_codes <- character(0)
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(AMR_env$ab_previously_coerced$ab %in% AMR_env$AB_lookup$ab), , drop = FALSE]
message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `antibiotics` data set.")
message_("Cleared ", nr2char(n - n2), " custom record", ifelse(n - n2 > 1, "s", ""), " from the internal `antimicrobials` data set.")
}