mirror of
https://github.com/msberends/AMR.git
synced 2026-11-16 00:10:57 +01:00
dr. M.S. (Matthijs) Berends
53d0704271
- 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)
47 lines
770 B
Plaintext
Executable File
47 lines
770 B
Plaintext
Executable File
^.*\.RData$
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^\.Renviron$
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^\.Rprofile$
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^\.Rproj\.user$
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^\.zenodo\.json$
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^_noinclude$
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^_pkgdown\.yml$
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^appveyor\.yml$
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^codecov\.yml$
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^CLAUDE\.md$
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^\.claude$
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^cran-comments\.md$
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^CRAN-RELEASE$
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^\.github$
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^doc$
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^docs$
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^git_.*\.sh$
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^index\.md$
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^index\.Rmd$
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^installed_deps$
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^Meta$
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^pkgdown$
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^public$
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^data-raw$
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^\.lintr$
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^tests/testthat/_snaps$
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^vignettes/AMR\.Rmd$
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^vignettes/AMR_intro\.png$
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^vignettes/AMR_with_tidymodels\.Rmd$
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^vignettes/benchmarks\.Rmd$
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^vignettes/benchmarks\.Rmd\.not$
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^vignettes/datasets\.Rmd$
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^vignettes/EUCAST\.Rmd$
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^vignettes/MDR\.Rmd$
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^vignettes/PCA\.Rmd$
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^vignettes/resistance_predict\.Rmd$
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^vignettes/WHONET\.Rmd$
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^vignettes/WISCA\.Rmd$
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^logo.svg$
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^CRAN-SUBMISSION$
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^PythonPackage$
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^README\.Rmd$
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^tools$
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\.no_include$
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