dr. M.S. (Matthijs) Berends 95756d224d Merge branch 'main' into breakpoints ...

# Conflicts:
#	DESCRIPTION
#	NEWS.md
#	R/sysdata.rda
#	data/antibiotics.rda
#	data/antimicrobials.rda

2026-11-09 20:46:50 +01:00

..

aa_amr-package.R

Format the month of the taxonomy update in English regardless of the system locale

2026-10-15 10:34:06 +02:00

aa_globals.R

(v3.0.1.9151) Fix inconsistencies in the plotting functions and correct the translations of the interpretation categories

2026-10-15 22:25:20 +02:00

aa_helper_functions.R

(v3.0.1.9153) Speed up mdro(), as.sir(), wisca() and wisca_plot() and the binding of mo vectors, fix PDR in the CMI 2012 guideline of mdro() being assigned to the wrong rows, and limit the stratified WISCA example to the 5 most common species

2026-10-16 06:08:26 +02:00

aa_helper_pm_functions.R

(v3.0.1.9153) Speed up mdro(), as.sir(), wisca() and wisca_plot() and the binding of mo vectors, fix PDR in the CMI 2012 guideline of mdro() being assigned to the wrong rows, and limit the stratified WISCA example to the 5 most common species

2026-10-16 06:08:26 +02:00

aa_options.R

Store all screening breakpoints under screening agents, and add these agents to antimicrobials (#328)

2026-11-02 17:31:46 +01:00

aa_session_cache.R

(v3.1.0.9017) Add labels_taxonomy() for taxonomic names in italics in plot labels, add type = "plotmath" to italicise_taxonomy(), and only italicise species names after a genus

2026-11-09 20:45:07 +01:00

ab_from_text.R

new eucast breakpoints parsing

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

ab_property.R

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

ab.R

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

age.R

new eucast breakpoints parsing

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

amr_course.R

new eucast breakpoints parsing

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

amr_selectors.R

(v3.0.1.9121) styler

2026-10-12 11:42:06 +02:00

antibiogram.R

(v3.1.0.9011) Use top_n_microorganisms() in the WISCA examples of the index, manual and vignette, and reword the WISCA prior weight warning to also cover small groups (#337)

2026-10-30 12:45:56 +01:00

atc_online.R

new eucast breakpoints parsing

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

av_from_text.R

new eucast breakpoints parsing

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

av_property.R

new eucast breakpoints parsing

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

av.R

(v3.0.1.9103) Replace dead EC Union Register URLs; URL check no longer includes closing braces

2026-10-04 19:53:40 +02:00

availability.R

new eucast breakpoints parsing

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

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

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

custom_antimicrobials.R

(v3.0.1.9112) Fix detection of non-UTF-8 input in as.ab() and add_custom_antimicrobial_synonyms() on R 4.2 and older, where enc2utf8() escapes invalid bytes

2026-10-10 12:49:13 +02:00

custom_interpretive_rules.R

(v3.0.1.9128) Revamp console output of interpretive_rules() with cli styling and guideline-dependent SIR colours, make it 11 to 18 times faster with identical results, and fix counts of values that were not actually written (#259)

2026-10-13 12:27:38 +02:00

custom_mdro_guideline.R

new eucast breakpoints parsing

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

custom_microorganisms.R

Improve the session caches of as.ab(), as.mo() and all mo_*() functions (#313) (#314)

2026-10-07 14:29:48 +02:00

data.R

Make anaerobes more specific than a Gram stain in rank_index

2026-11-03 08:37:55 +01:00

disk.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

export_biosample.R

new eucast breakpoints parsing

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

first_isolate.R

new eucast breakpoints parsing

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

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

get_episode.R

new eucast breakpoints parsing

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

ggplot_pca.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

ggplot_sir.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

guess_ab_col.R

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

interpretive_rules.R

v3.1.0

2026-10-16 14:11:02 +02:00

italicise_taxonomy.R

(v3.1.0.9017) Add labels_taxonomy() for taxonomic names in italics in plot labels, add type = "plotmath" to italicise_taxonomy(), and only italicise species names after a genus

2026-11-09 20:45:07 +01:00

join_microorganisms.R

new eucast breakpoints parsing

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

key_antimicrobials.R

new eucast breakpoints parsing

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

kurtosis.R

new eucast breakpoints parsing

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

like.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

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

mean_amr_distance.R

new eucast breakpoints parsing

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

mic.R

Store EUCAST MIC breakpoints exactly as published, and compare dilutions in as.sir() (#331)

2026-11-02 16:56:51 +01:00

mo_matching_score.R

new eucast breakpoints parsing

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

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

mo_source.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

mo.R

(v3.1.0.9009) Fix the misaligned arrows in the message on taxonomically renamed microorganisms in colour-supporting consoles, by padding on the visible width instead of using format() (fixes #336)

2026-10-30 09:59:01 +01:00

pca.R

v3.1.0

2026-10-16 14:11:02 +02:00

plotting.R

(v3.1.0.9017) Add labels_taxonomy() for taxonomic names in italics in plot labels, add type = "plotmath" to italicise_taxonomy(), and only italicise species names after a genus

2026-11-09 20:45:07 +01:00

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

random.R

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

resistance_predict.R

new eucast breakpoints parsing

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

sir_calc.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

sir_combine.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

sir_df.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

sir.R

Set the order of sites in as.sir(), and add the veterinary sites

2026-11-02 20:20:05 +01:00

skewness.R

new eucast breakpoints parsing

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

sysdata.rda

(v3.1.0.9017) Add labels_taxonomy() for taxonomic names in italics in plot labels, add type = "plotmath" to italicise_taxonomy(), and only italicise species names after a genus

2026-11-09 20:45:07 +01:00

tidymodels.R

(v3.1.0.9004) Document the columns argument of the tidymodels steps to fix the Rd usage warning in R CMD check

2026-10-17 18:23:06 +02:00

top_n_microorganisms.R

new eucast breakpoints parsing

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

translate.R

(v3.0.1.9137) Add the guideline argument to count_df(), proportion_df(), sir_df(), ggplot_sir(), geom_sir(), and labels_sir_count(), so that with CLSI the 'I' category is merged with R, and describe in the documentation of get_AMR_locale() that LANG takes precedence over LANGUAGE

2026-10-15 08:25:37 +02:00

vctrs.R

(v3.0.1.9153) Speed up mdro(), as.sir(), wisca() and wisca_plot() and the binding of mo vectors, fix PDR in the CMI 2012 guideline of mdro() being assigned to the wrong rows, and limit the stratified WISCA example to the 5 most common species

2026-10-16 06:08:26 +02:00

whocc.R

new eucast breakpoints parsing

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

zz_deprecated.R

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

zzz.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