dr. M.S. (Matthijs) Berends b74501663b Merge branch 'main' into breakpoints

2026-11-09 22:11:08 +01:00

..

helper-functions.R

new eucast breakpoints parsing

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

helper-microorganisms.R

(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

test-_deprecated.R

(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

test-_misc.R

(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

test-ab_from_text.R

(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

test-ab_property.R

(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

test-ab.R

new eucast breakpoints parsing

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

test-age.R

new eucast breakpoints parsing

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

test-amr_selectors.R

new eucast breakpoints parsing

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

test-antibiogram.R

(v3.1.0.9014) Fix the CI: replace a test unsupported by tinytest, run R 3.0 on Ubuntu 24.04, and use Python 3.12 for the PyPI package, since ubuntu-latest moved to Ubuntu 26.04

2026-10-30 14:55:00 +01:00

test-atc_online.R

new eucast breakpoints parsing

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

test-av_from_text.R

new eucast breakpoints parsing

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

test-av_property.R

new eucast breakpoints parsing

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

test-av.R

new eucast breakpoints parsing

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

test-availability.R

new eucast breakpoints parsing

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

test-bug_drug_combinations.R

Let aggregated analyses follow the guideline for the 'I' category in count_df(), proportion_df(), sir_df(), the plotting functions, antibiogram(), wisca(), and bug_drug_combinations(), deprecate combine_SI in favour of guideline, fix format() on bug_drug_combinations() counting I as resistant, and add a shared section 'Interpretation of SIR'

2026-10-15 09:58:21 +02:00

test-count.R

Let aggregated analyses follow the guideline for the 'I' category in count_df(), proportion_df(), sir_df(), the plotting functions, antibiogram(), wisca(), and bug_drug_combinations(), deprecate combine_SI in favour of guideline, fix format() on bug_drug_combinations() counting I as resistant, and add a shared section 'Interpretation of SIR'

2026-10-15 09:58:21 +02:00

test-custom_antimicrobials.R

(v3.0.1.9132) Make translating around 50 times faster and coercion of unknown input in as.ab() up to 70 times faster with identical results, use DOIs instead of PubMed URLs, shorten an example line, and reword cran-comments.md

2026-10-14 20:17:28 +02:00

test-custom_microorganisms.R

new eucast breakpoints parsing

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

test-data-microorganisms.R

Update taxonomy of microorganisms (2026-10) (#312)

2026-10-07 12:55:12 +02:00

test-data.R

Apply the EUCAST breakpoints of Vibrio to the species that EUCAST states only

2026-11-03 17:14:15 +01:00

test-disk.R

new eucast breakpoints parsing

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

test-first_isolate.R

new eucast breakpoints parsing

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

test-g.test.R

(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

test-get_episode.R

new eucast breakpoints parsing

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

test-ggplot_sir.R

(v3.1.0.9021) Show the number of tested isolates on susceptible-only bars, and split ggplot_sir() by antimicrobial if it is not shown in the plot

2026-11-09 22:10:01 +01:00

test-guess_ab_col.R

new eucast breakpoints parsing

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

test-interpretive_rules.R

(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

test-italicise_taxonomy.R

(v3.1.0.9018) Italicise taxonomic names in all plotting functions using labels_taxonomy(), and fix ggplot_pca() with explicit groups

2026-11-09 21:28:37 +01:00

test-join_microorganisms.R

new eucast breakpoints parsing

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

test-key_antimicrobials.R

new eucast breakpoints parsing

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

test-kurtosis.R

new eucast breakpoints parsing

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

test-like.R

new eucast breakpoints parsing

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

test-mdro.R

Return the serovar in mo_shortname() for Salmonella, keep Salmonella groups apart from streptococci, abbreviate all Lancefield groups, and apply the Typhi rule in mdro() (#341)

2026-11-04 07:57:20 +01:00

test-mean_amr_distance.R

new eucast breakpoints parsing

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

test-mic.R

new eucast breakpoints parsing

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

test-mo_property.R

Return the serovar in mo_shortname() for Salmonella, keep Salmonella groups apart from streptococci, abbreviate all Lancefield groups, and apply the Typhi rule in mdro() (#341)

2026-11-04 07:57:20 +01:00

test-mo_source.R

(v3.0.1.9136) Fix the CI entry with a Dutch locale by using a UTF-8 locale that is installed on the runner, and skip the mo_source tests with skip_if() so that the tinytest harness for old R versions supports them

2026-10-15 00:11:07 +02:00

test-mo.R

(v3.0.1.9148) Store zone diameters without S category as blocking rows for EUCAST and as R-only rows for CLSI instead of capping them at 50 mm, let as.mo() return the complex for names such as 'Acinetobacter calcoaceticus-baumannii complex', make the breakpoint reproduction scripts stop on unchecked data defects and year-independent, and document that as.disk() returns NA above 50 mm

2026-10-15 17:05:41 +02:00

test-pca.R

(v3.1.0.9018) Italicise taxonomic names in all plotting functions using labels_taxonomy(), and fix ggplot_pca() with explicit groups

2026-11-09 21:28:37 +01:00

test-plotting.R

(v3.0.1.9152) Let a named colours_SIR without S, I or R use the default colours for these, which fixes the example of ggplot_sir() with colours = c(SI = "yellow"), let ggplot_sir() pass the facet as a value to facet_sir(), and make the test of the eucast_I default independent of the AMR_guideline option

2026-10-16 04:34:52 +02:00

test-proportion.R

Let aggregated analyses follow the guideline for the 'I' category in count_df(), proportion_df(), sir_df(), the plotting functions, antibiogram(), wisca(), and bug_drug_combinations(), deprecate combine_SI in favour of guideline, fix format() on bug_drug_combinations() counting I as resistant, and add a shared section 'Interpretation of SIR'

2026-10-15 09:58:21 +02:00

test-random.R

(v3.0.1.9129) Add guideline argument to random_mic() and random_disk() so that values are based on one guideline version, make guideline years in examples, vignettes and website always the latest, and reword NEWS

2026-10-13 21:43:19 +02:00

test-session_cache.R

(v3.0.1.9134) Add session cache assertions for separate as.ab() and as.mo() calls, for get_mo_source() without a file, and for real cache hits, which detect the cache being emptied in interactive sessions

2026-10-14 22:49:00 +02:00

test-sir_combine.R

(v3.0.1.9123) Add method argument to sir_combine() for resistance within a group (most_resistant), and restore the AMR 3.0.1 behaviour of count_*() and proportion_*() for multiple antimicrobials (#321)

2026-10-12 21:37:13 +02:00

test-sir.R

Apply the EUCAST breakpoints of Vibrio to the species that EUCAST states only

2026-11-03 17:14:15 +01:00

test-skewness.R

new eucast breakpoints parsing

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

test-tidymodels.R

new eucast breakpoints parsing

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

test-top_n_microorganisms.R

new eucast breakpoints parsing

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

test-translate.R

(v3.0.1.9125) Fix translations being translated again (e.g. Ticarcillinee, groupee) and untranslated parts of combination names, and let as.mo() recognise translated names in the set language, cached per language

2026-10-12 22:25:57 +02:00

test-vctrs.R

new eucast breakpoints parsing

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

test-zzz.R

(v3.0.1.9117) Fix static test in test-zzz.R to run without testthat (R 3.0/4.0 tinytest)

2026-10-11 22:15:43 +02:00