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