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(v2.1.1.9163) cleanup

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dr. M.S. (Matthijs) Berends
2025-02-27 14:04:29 +01:00
parent 68efddab3d
commit 07efc292bc
73 changed files with 2187 additions and 1715 deletions
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22
R/custom_eucast_rules.R
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@@ -90,16 +90,16 @@
#' ```
#'
#' ### Usage of multiple antibiotics and antibiotic group names
#'
#'
#' You can define antibiotic groups instead of single antibiotics for the rule consequence, which is the part *after* the tilde (~). In the examples above, the antibiotic group `aminopenicillins` includes both ampicillin and amoxicillin.
#'
#'
#' Rules can also be applied to multiple antibiotics and antibiotic groups simultaneously. Use the `c()` function to combine multiple antibiotics. For instance, the following example sets all aminopenicillins and ureidopenicillins to "R" if column TZP (piperacillin/tazobactam) is "R":
#'
#'
#' ```r
#' x <- custom_eucast_rules(TZP == "R" ~ c(aminopenicillins, ureidopenicillins) == "R")
#' x
#' #> A set of custom EUCAST rules:
#' #>
#' #>
#' #> 1. If TZP is "R" then set to "R":
#' #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
#' ```
@@ -169,7 +169,7 @@ custom_eucast_rules <- function(...) {
"the result of rule ", i, " (the part after the `~`) must contain `==`, such as in `... ~ ampicillin == \"R\"`, see `?custom_eucast_rules`"
)
result_group <- as.character(result)[[2]]
result_group<- as.character(str2lang(result_group))
result_group <- as.character(str2lang(result_group))
result_group <- result_group[result_group != "c"]
result_group_agents <- character(0)
for (j in seq_len(length(result_group))) {
@@ -178,13 +178,15 @@ custom_eucast_rules <- function(...) {
result_group[j] <- paste0(result_group[j], "s")
}
if (paste0("AB_", toupper(result_group[j])) %in% DEFINED_AB_GROUPS) {
result_group_agents <- c(result_group_agents,
eval(parse(text = paste0("AB_", toupper(result_group[j]))), envir = asNamespace("AMR")))
result_group_agents <- c(
result_group_agents,
eval(parse(text = paste0("AB_", toupper(result_group[j]))), envir = asNamespace("AMR"))
)
} else {
out_group <- tryCatch(
suppressWarnings(as.ab(result_group[j],
fast_mode = TRUE,
flag_multiple_results = FALSE
fast_mode = TRUE,
flag_multiple_results = FALSE
)),
error = function(e) NA_character_
)
@@ -194,7 +196,7 @@ custom_eucast_rules <- function(...) {
}
}
result_group_agents <- result_group_agents[!is.na(result_group_agents)]
stop_if(
length(result_group_agents) == 0,
"this result of rule ", i, " could not be translated to a single antimicrobial drug/group: \"",