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

..

testthat

(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

2026-10-11 20:36:31 +02:00

testthat.R

new eucast breakpoints parsing

2026-08-20 13:29:16 +01:00

tinytest.R.old

(v3.0.1.9114) Fix errors without cli and on R 3.0, and make the tinytest pipeline actually run the unit tests

2026-10-10 14:54:15 +02:00