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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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@@ -42,9 +42,9 @@ pre_commit_lst <- list()
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usethis::ui_info(paste0("Updating internal package data"))
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# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
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pre_commit_lst$EUCAST_RULES_DF <- utils::read.delim(
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file = "data-raw/eucast_rules.tsv",
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# See 'data-raw/interpretive_rules.tsv' for the interpretive rules reference file
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pre_commit_lst$INTERPRETIVE_RULES_DF <- utils::read.delim(
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file = "data-raw/interpretive_rules.tsv",
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skip = 9,
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sep = "\t",
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stringsAsFactors = FALSE,
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@@ -364,7 +364,7 @@ pre_commit_lst$MO_RELEVANT_GENERA <- c(
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)
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# antibiotic groups
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# (these will also be used for eucast_rules() and understanding data-raw/eucast_rules.tsv)
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# (these will also be used for interpretive_rules() and understanding data-raw/interpretive_rules.tsv)
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pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
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filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
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pull(ab)
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