P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2025-09-06 04:09:39 +02:00
Code Releases Activity

cleanup and new intro logo

Browse Source
This commit is contained in:
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
Download Patch File Download Diff File Expand all files Collapse all files

6
R/custom_eucast_rules.R
View File

@@ -91,7 +91,7 @@
#'
#' ### Usage of antibiotic group names
#'
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the agents that will be matched when running the rule.
#' It is possible to define antibiotic groups instead of single antibiotics for the rule consequence, the part *after* the tilde. In above examples, the antibiotic group `aminopenicillins` is used to include ampicillin and amoxicillin. The following groups are allowed (case-insensitive). Within parentheses are the drugs that will be matched when running the rule.
#'
#' `r paste0(" * ", sapply(DEFINED_AB_GROUPS, function(x) paste0("\"", tolower(gsub("^AB_", "", x)), "\"\\cr(", vector_and(ab_name(eval(parse(text = x), envir = asNamespace("AMR")), language = NULL, tolower = TRUE), quotes = FALSE), ")"), USE.NAMES = FALSE), "\n", collapse = "")`
#' @returns A [list] containing the custom rules
@@ -174,8 +174,8 @@ custom_eucast_rules <- function(...) {
stop_if(
any(is.na(result_group)),
"this result of rule ", i, " could not be translated to a single antimicrobial agent/group: \"",
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial agent, or be one of: ",
"this result of rule ", i, " could not be translated to a single antimicrobial drug/group: \"",
as.character(result)[[2]], "\".\n\nThe input can be a name or code of an antimicrobial drug, or be one of: ",
vector_or(tolower(gsub("AB_", "", DEFINED_AB_GROUPS)), quotes = FALSE), "."
)
result_value <- as.character(result)[[3]]