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(v2.1.1.9160) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-26 20:28:33 +01:00
parent 0c3ea4b538
commit 22e66741cc
13 changed files with 38 additions and 50 deletions
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10
R/custom_antimicrobials.R
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@@ -69,11 +69,8 @@
#' @export
#' @examples
#' \donttest{
#'
#' # returns NA and throws a warning (which is suppressed here):
#' suppressWarnings(
#' as.ab("testab")
#' )
#' # returns a wildly guessed result:
#' as.ab("testab")
#'
#' # now add a custom entry - it will be considered by as.ab() and
#' # all ab_*() functions
@@ -109,6 +106,7 @@
#' ab_name("J01CR50")
#'
#' # even antimicrobial selectors work
#' # see ?amr_selector
#' x <- data.frame(
#' random_column = "some value",
#' coflu = as.sir("S"),
@@ -155,7 +153,7 @@ add_custom_antimicrobials <- function(x) {
}
AMR_env$AB_lookup <- unique(rbind_AMR(AMR_env$AB_lookup, new_df))
AMR_env$ab_previously_coerced <- AMR_env$ab_previously_coerced[which(!AMR_env$ab_previously_coerced$ab %in% x$ab), , drop = FALSE]
AMR_env$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.")
}