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mirror of https://github.com/msberends/AMR.git synced 2025-07-11 05:02:06 +02:00

(v2.1.1.9186) replace antibiotics with antimicrobials!

This commit is contained in:
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
140 changed files with 4870 additions and 4702 deletions

17
R/zzz.R
View File

@ -91,7 +91,7 @@ AMR_env$cli_abort <- import_fn("cli_abort", "cli", error_on_fail = FALSE)
AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
.onLoad <- function(lib, pkg) {
.onLoad <- function(libname, pkgname) {
# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
# without the need to depend on other packages. This was suggested by the
# developers of the vctrs package:
@ -203,15 +203,22 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
# reference data - they have additional data to improve algorithm speed
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
if (NROW(AB_LOOKUP) != NROW(AMR::antibiotics)) {
if (NROW(AB_LOOKUP) != NROW(AMR::antimicrobials)) {
# antibiotics data set was updated - run create_AB_AV_lookup() again
AB_LOOKUP <- create_AB_AV_lookup(AMR::antibiotics)
AB_LOOKUP <- create_AB_AV_lookup(AMR::antimicrobials)
}
AMR_env$AB_lookup <- cbind(AMR::antibiotics, AB_LOOKUP)
# deprecated antibiotics data set
makeActiveBinding("antibiotics", function() {
deprecation_warning(old = "antibiotics", new = "antimicrobials", is_function = FALSE, is_dataset = TRUE)
AMR::antimicrobials
}, env = asNamespace(pkgname))
AMR_env$AB_lookup <- cbind(AMR::antimicrobials, AB_LOOKUP)
AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
}
.onAttach <- function(lib, pkg) {
.onAttach <- function(libname, pkgname) {
# if custom ab option is available, load it
if (!is.null(getOption("AMR_custom_ab")) && file.exists(getOption("AMR_custom_ab", default = ""))) {
if (getOption("AMR_custom_ab") %unlike% "[.]rds$") {