dr. M.S. (Matthijs) Berends fcfaa87f5d (v3.0.1.9147) Keep EUCAST blocking rows for infections other than UTI where EUCAST only gives a UTI breakpoint, e.g. breakpoints in brackets for aminoglycosides in Acinetobacter, and let as.sir() with unknown uti consistently prefer non-UTI breakpoints, use UTI breakpoints only if no others exist and note this in sir_interpretation_history() every time ...

The pruning of blocking rows in the EUCAST reproduction script now compares UTI status too, and the script is fixed for the renamed column of the as.ab() coercion cache. In clinical_breakpoints, only the blocking rows were replaced (356 organism/agent/method combinations newly blocked, none unblocked); other changes of a full rebuild, caused by taxonomy updates in the WHONET-based rows, are not included.

2026-10-15 14:55:57 +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

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

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

aa_helper_functions.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

aa_helper_pm_functions.R

new eucast breakpoints parsing

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

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

(v3.0.1.9132) 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_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

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

2026-10-15 10:31:07 +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

Document all values of rank_index in the clinical_breakpoints data set, including species groups, and the stored value of EUCAST's off-scale S breakpoint

2026-10-15 10:37:40 +02:00

disk.R

new eucast breakpoints parsing

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

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

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

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

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

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

(v3.0.1.9125) 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

pca.R

new eucast breakpoints parsing

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

plotting.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

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

(v3.0.1.9147) Keep EUCAST blocking rows for infections other than UTI where EUCAST only gives a UTI breakpoint, e.g. breakpoints in brackets for aminoglycosides in Acinetobacter, and let as.sir() with unknown uti consistently prefer non-UTI breakpoints, use UTI breakpoints only if no others exist and note this in sir_interpretation_history() every time

2026-10-15 14:55:57 +02:00

skewness.R

new eucast breakpoints parsing

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

sysdata.rda

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

2026-10-15 10:31:07 +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

implement EUCAST >= 2019 directly from their source files

2026-10-01 14:53:00 +01:00

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