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(v2.1.1.9255) fix examples

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dr. M.S. (Matthijs) Berends
2025-04-26 16:35:14 +02:00
parent 92316d5ddc
commit d166aa2c1d
5 changed files with 6 additions and 13 deletions
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10
R/sir.R
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@ -146,7 +146,7 @@
#' options(AMR_breakpoint_type = "animal")
#' ```
#'
#' ###### TODO #187 When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints.
###### TODO #187 When applying veterinary breakpoints (by setting `host` or by setting `breakpoint_type = "animal"`), the [CLSI VET09 guideline](https://clsi.org/standards/products/veterinary-medicine/documents/vet09/) will be applied to cope with missing animal species-specific breakpoints.
#'
#' ### After Interpretation
#'
@ -994,12 +994,7 @@ as.sir.data.frame <- function(x,
sir_logs_all <- lapply(result_list, function(x) x$log)
sir_logs_all <- Filter(Negate(is.null), sir_logs_all) # remove NULLs early
if (length(sir_logs_all) > 0) {
rbindlist <- import_fn("rbindlist", "data.table", error_on_fail = FALSE)
if (!is.null(rbindlist)) {
sir_logs_all <- rbindlist(sir_logs_all, fill = TRUE, ignore.attr = TRUE)
} else {
sir_logs_all <- do.call(rbind, sir_logs_all)
}
sir_logs_all <- do.call(rbind_AMR, sir_logs_all)
AMR_env$sir_interpretation_history <- rbind_AMR(AMR_env$sir_interpretation_history, sir_logs_all)
}
@ -1857,6 +1852,7 @@ sir_interpretation_history <- function(clean = FALSE) {
meet_criteria(clean, allow_class = "logical", has_length = 1)
out <- AMR_env$sir_interpretation_history
out$outcome <- as.sir(out$outcome)
out$site <- as.character(out$site)
if (isTRUE(clean)) {
AMR_env$sir_interpretation_history <- AMR_env$sir_interpretation_history[0, , drop = FALSE]
}