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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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8
R/custom_eucast_rules.R
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@@ -89,11 +89,11 @@
#' #> 2 Klebsiella pneumoniae R R S
#' ```
#'
#' ### Usage of multiple antibiotics and antibiotic group names
#' ### Usage of multiple antimicrobials and antimicrobial 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.
#' You can define antimicrobial groups instead of single antimicrobials for the rule consequence, which is the part *after* the tilde (~). In the examples above, the antimicrobial 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":
#' Rules can also be applied to multiple antimicrobials and antimicrobial groups simultaneously. Use the `c()` function to combine multiple antimicrobials. 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")
@@ -104,7 +104,7 @@
#' #> amoxicillin (AMX), ampicillin (AMP), azlocillin (AZL), mezlocillin (MEZ), piperacillin (PIP), piperacillin/tazobactam (TZP)
#' ```
#'
#' These `r length(DEFINED_AB_GROUPS)` antibiotic groups are allowed in the rules (case-insensitive) and can be used in any combination:
#' These `r length(DEFINED_AB_GROUPS)` antimicrobial groups are allowed in the rules (case-insensitive) and can be used in any combination:
#'
#' `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