AMR/R at 4115db67fa14b2ad27bdd67906e7bf883dc0bcdd - AMR

aa_amr-package.R

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

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

(v3.0.1.9115) Fix interpretation of capped MICs without an S category (off-scale S breakpoint) or without breakpoints in as.sir(), and correct the documented default of capped_mic_handling (#295 )

2026-10-11 15:40:09 +02:00

aa_session_cache.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

ab_from_text.R

new eucast breakpoints parsing

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

ab_property.R

new eucast breakpoints parsing

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

ab.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

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

(v3.0.1.9121) styler

2026-10-12 11:42:06 +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

new eucast breakpoints parsing

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

count.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

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

EUCAST import: blocking rows, note restrictions, PK-PD and parser fixes (#310 )

2026-10-02 06:01:58 +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

new eucast breakpoints parsing

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

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

(v3.0.1.9116) 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

mdro.R

new eucast breakpoints parsing

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

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

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

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

mo_source.R

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

2026-10-07 14:29:48 +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

(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

proportion.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

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

(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

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

sir_df.R

new eucast breakpoints parsing

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

sir.R

(v3.0.1.9115) Fix interpretation of capped MICs without an S category (off-scale S breakpoint) or without breakpoints in as.sir(), and correct the documented default of capped_mic_handling (#295 )

2026-10-11 15:40:09 +02:00

skewness.R

new eucast breakpoints parsing

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

sysdata.rda

(v3.0.1.9126) Improve translations of combination names and antimicrobial groups in 20 languages (not en, nl, uk, fr)

2026-10-12 22:56:12 +02:00

tidymodels.R

implement EUCAST >= 2019 directly from their source files

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

top_n_microorganisms.R

new eucast breakpoints parsing

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

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

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

new eucast breakpoints parsing

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

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