3 Commits

Include renames

Author	SHA1	Message	Date
dr. M.S. (Matthijs) Berends	8b01bcb23c	(v3.0.1.9135) Fix get_mo_source() removing the mo_source file at the default location, returning the wrong mo_source, and throwing an error after the original file was moved, and run the unit tests in CI also in a real interactive session and with a user setup, a Dutch locale, and CLSI as default guideline, with tests that no longer assume an English locale or EUCAST	2026-10-14 23:34:45 +02:00
dr. M.S. (Matthijs) Berends	8b3bc220ed	(v3.0.1.9130) Add workflow to check reverse dependencies against the development version on every push to main, list WT/NWT for ECOFFs as breaking change, and update cran-comments.md for v3.1.0	2026-10-13 22:25:28 +02:00
dr. M.S. (Matthijs) Berends	53d0704271	(v3.0.1.9116) New sir_combine() for combination therapy as one engine for antibiogram(), wisca(), count_*() and proportion_*() (#321), and make all suggested packages runtime-only with a new CI workflow without dplyr ... - 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)	2026-10-11 20:36:31 +02:00