dr. M.S. (Matthijs) Berends 30021a9831 (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_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

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

aa_session_cache.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

ab_from_text.R

new eucast breakpoints parsing

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

ab_property.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

ab.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

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

(v3.0.1.9153) 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

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

(v3.0.1.9149) Fix WHONET codes in microorganisms.codes that referred to unrelated microorganisms, let codes refer to the name they were named after and add a source column, and replace the fuzzy matching of WHONET names by exact matching with a guard against unreviewed remaps

2026-10-15 21:08:04 +02:00

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

(v3.0.1.9128) 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

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

italicise_taxonomy.R

new eucast breakpoints parsing

2026-08-20 13:29:16 +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

(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

mean_amr_distance.R

new eucast breakpoints parsing

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

mic.R

new eucast breakpoints parsing

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

mo_matching_score.R

new eucast breakpoints parsing

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

mo_property.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

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

(v3.0.1.9153) 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

pca.R

new eucast breakpoints parsing

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

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

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

(v3.0.1.9129) 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

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

(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

skewness.R

new eucast breakpoints parsing

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

sysdata.rda

(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

tidymodels.R

Show translated pathogen names instead of microorganism codes in grouped traditional antibiograms, including for unknown species

2026-10-15 10:31:07 +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

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

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