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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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11
R/zzz.R
11
R/zzz.R
@@ -112,6 +112,17 @@ AMR_env$cross_icon <- if (isTRUE(base::l10n_info()$`UTF-8`)) "\u00d7" else "x"
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AMR_env$AB_lookup <- cbind(AMR::antimicrobials, AB_LOOKUP)
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AMR_env$AV_lookup <- cbind(AMR::antivirals, AV_LOOKUP)
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# Transitional: create INTERPRETIVE_RULES_DF alias if sysdata.rda predates the rename from EUCAST_RULES_DF.
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# Remove this block once data-raw/_pre_commit_checks.R has been re-run.
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ns <- asNamespace("AMR")
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if (!exists("INTERPRETIVE_RULES_DF", envir = ns, inherits = FALSE) &&
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exists("EUCAST_RULES_DF", envir = ns, inherits = FALSE)) {
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df <- get("EUCAST_RULES_DF", envir = ns)
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df$rule.provider <- "EUCAST"
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df <- df[, c("rule.provider", setdiff(colnames(df), "rule.provider")), drop = FALSE]
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assignInNamespace("INTERPRETIVE_RULES_DF", df, ns = "AMR")
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}
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}
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.onAttach <- function(libname, pkgname) {
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