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- New sir_combine() to combine SIR results of multiple antimicrobials into one variable; antibiogram(), wisca() and the count/proportion functions now use the same engine (antibiogram() and wisca() output unchanged)
- With multiple antimicrobials, count_*() and proportion_*() now follow the documented combination therapy rules: resistance() is the proportion of failing combinations, count_all() excludes isolates with an unknown combination result, and WT/NWT/NS/NI are handled correctly
- where() is now decided at runtime instead of at installation, fixing antibiogram() and wisca() without tidyselect (e.g. CRAN binaries without dplyr)
- Imports from data.table and cli moved to .onLoad(); data.table functions are only used while it is loaded; the like() example no longer unloads data.table, which crashed R
- Static test that fails on code outside functions depending on suggested packages
- New check-without-dplyr workflow: installs AMR with all suggested packages, removes dplyr (and tidyselect), then runs all unit tests and examples against the installed package
- g.test() now returns the degrees of freedom as 'parameter', so they are printed
- Fix R CMD check NOTEs (hidden .claude folder, lost braces in inherited g.test and ggplot_pca docs)
Adds add_custom_antimicrobial_synonyms() to add local names, such as trade names, to existing antimicrobials, also via the AMR_custom_ab option. Matching is language-independent; as.ab() now returns NA with a warning for input that is not valid UTF-8.
* 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
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Co-authored-by: Claude <noreply@anthropic.com>
