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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 * Fix namespace load failure: remove assignInNamespace from .onLoad (#268) assignInNamespace cannot add NEW bindings to a locked package namespace (R locks namespace bindings before .onLoad runs). Replace the .onLoad shim with a runtime fallback inside interpretive_rules(): if INTERPRETIVE_RULES_DF is absent (pre-regeneration sysdata.rda), derive it from EUCAST_RULES_DF by adding the rule.provider column. This also fixes the screening_abx line to reuse the already-resolved interpretive_rules_df_total instead of a bare INTERPRETIVE_RULES_DF reference. https://claude.ai/code/session_01D46BTsfJSPo3HnLWp3PRkP * fixes * fixes --------- Co-authored-by: Claude <noreply@anthropic.com>
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@@ -27,7 +27,7 @@
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# how to conduct AMR data analysis: https://amr-for-r.org #
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# ==================================================================== #
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
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# add new version numbers here, and add the rules themselves to "data-raw/interpretive_rules.tsv" and clinical_breakpoints
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# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list(
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"16.0" = list(
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@@ -221,6 +221,7 @@ globalVariables(c(
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"reference.rule",
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"reference.rule_group",
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"reference.version",
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"rule.provider",
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"rowid",
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"rule_group",
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"rule_name",
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