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fix SIR interpretation

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dr. M.S. (Matthijs) Berends
2024-05-31 09:50:54 +02:00
parent ba4dc20cf3
commit 60c6c21e45
6 changed files with 128 additions and 66 deletions
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65
R/custom_eucast_rules.R
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@@ -30,7 +30,7 @@
#' Define Custom EUCAST Rules
#'
#' Define custom EUCAST rules for your organisation or specific analysis and use the output of this function in [eucast_rules()].
#' @param ... rules in [formula][base::tilde] notation, see *Examples*
#' @param ... rules in [formula][base::tilde] notation, see below for instructions, and in *Examples*
#' @details
#' Some organisations have their own adoption of EUCAST rules. This function can be used to define custom EUCAST rules to be used in the [eucast_rules()] function.
#' @section How it works:
@@ -89,11 +89,24 @@
#' #> 2 Klebsiella pneumoniae R R S
#' ```
#'
#' ### Usage of antibiotic group names
#' ### 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)
#' ```
#'
#' 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.
#' These `r length(DEFINED_AB_GROUPS)` antibiotic 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 = "")`
#' `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
#' @export
#' @examples
@@ -156,24 +169,34 @@ 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]]
if (paste0("AB_", toupper(result_group), "S") %in% DEFINED_AB_GROUPS) {
# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
result_group <- paste0(result_group, "s")
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))) {
if (paste0("AB_", toupper(result_group[j]), "S") %in% DEFINED_AB_GROUPS) {
# support for e.g. 'aminopenicillin' if user meant 'aminopenicillins'
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")))
} else {
out_group <- tryCatch(
suppressWarnings(as.ab(result_group[j],
fast_mode = TRUE,
flag_multiple_results = FALSE
)),
error = function(e) NA_character_
)
if (!all(is.na(out_group))) {
result_group_agents <- c(result_group_agents, out_group)
}
}
}
if (paste0("AB_", toupper(result_group)) %in% DEFINED_AB_GROUPS) {
result_group <- eval(parse(text = paste0("AB_", toupper(result_group))), envir = asNamespace("AMR"))
} else {
result_group <- tryCatch(
suppressWarnings(as.ab(result_group,
fast_mode = TRUE,
flag_multiple_results = FALSE
)),
error = function(e) NA_character_
)
}
result_group_agents <- result_group_agents[!is.na(result_group_agents)]
stop_if(
any(is.na(result_group)),
length(result_group_agents) == 0,
"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), "."
@@ -186,7 +209,7 @@ custom_eucast_rules <- function(...) {
)
result_value <- as.sir(result_value)
out[[i]]$result_group <- result_group
out[[i]]$result_group <- result_group_agents
out[[i]]$result_value <- result_value
}