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mirror of https://github.com/msberends/AMR.git synced 2026-05-31 19:01:42 +02:00

Generalise interpretive rules for multi-guideline support (#268)

- Rename data-raw/eucast_rules.tsv → interpretive_rules.tsv; add rule.provider
  column (value: "EUCAST") to distinguish future CLSI rows
- Rename EUCAST_RULES_DF → INTERPRETIVE_RULES_DF in _pre_commit_checks.R;
  filter by rule.provider == guideline when applying rules in interpretive_rules()
- Rename custom_eucast_rules() → custom_interpretive_rules() with new S3 class
  "custom_interpretive_rules"; old function becomes a deprecated wrapper in
  zz_deprecated.R; backward-compat S3 dispatch shims added for old class
- Remove stop_if(guideline == "CLSI", ...) so clsi_rules() no longer errors
- Add .onLoad shim in zzz.R to create INTERPRETIVE_RULES_DF from EUCAST_RULES_DF
  for transitional compatibility until sysdata.rda is regenerated

https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP
This commit is contained in:
Claude
2026-04-30 21:29:26 +00:00
parent f7e9294bea
commit befbccc304
10 changed files with 1687 additions and 106 deletions

View File

@@ -70,6 +70,13 @@ as.data.frame.deprecated_amr_dataset <- function(x, ...) {
# - `antibiotics` in `antibiogram()`
# - `converse_capped_values` in `as.sir()`
#' @rdname AMR-deprecated
#' @export
custom_eucast_rules <- function(...) {
deprecation_warning("custom_eucast_rules", "custom_interpretive_rules", is_function = TRUE)
custom_interpretive_rules(...)
}
#' @rdname AMR-deprecated
#' @export
ab_class <- function(...) {