dr. M.S. (Matthijs) Berends 9ebc33a59d (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

..

ab_from_text.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

ab_property.Rd

(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

add_custom_antimicrobials.Rd

Add add_custom_antimicrobial_synonyms() (#307) (#311)

2026-10-10 09:14:07 +02:00

add_custom_microorganisms.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

age_groups.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

age.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

amr_course.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

AMR-deprecated.Rd

Generalise interpretive rules for multi-guideline support (#268) (#283)

2026-05-01 18:38:51 +01:00

AMR-options.Rd

(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

amr-tidymodels.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

AMR.Rd

(v3.0.1.9109) Fix WHONET codes SUD and ROX in clinical_breakpoints, and add sulbactam/durlobactam (#308)

2026-10-10 09:42:25 +02:00

antibiogram.Rd

(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

antimicrobial_selectors.Rd

(v3.0.1.9121) styler

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

antimicrobials.Rd

(v3.0.1.9109) Fix WHONET codes SUD and ROX in clinical_breakpoints, and add sulbactam/durlobactam (#308)

2026-10-10 09:42:25 +02:00

as.ab.Rd

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

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

as.av.Rd

(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

as.disk.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

as.mic.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

as.mo.Rd

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

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

as.sir.Rd

(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

atc_online.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

av_from_text.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

av_property.Rd

(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.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

bug_drug_combinations.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

clinical_breakpoints.Rd

(v3.0.1.9109) Fix WHONET codes SUD and ROX in clinical_breakpoints, and add sulbactam/durlobactam (#308)

2026-10-10 09:42:25 +02:00

count.Rd

(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_interpretive_rules.Rd

(v3.0.1.9109) Fix WHONET codes SUD and ROX in clinical_breakpoints, and add sulbactam/durlobactam (#308)

2026-10-10 09:42:25 +02:00

custom_mdro_guideline.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

dosage.Rd

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

esbl_isolates.Rd

(v3.0.1.9007) fix #246

2026-01-06 23:08:50 +01:00

example_isolates_unclean.Rd

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00

example_isolates.Rd

Add add_if_missing parameter to control NA handling in interpretive rules (#264)

2026-04-21 21:53:43 +02:00

export_ncbi_biosample.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

first_isolate.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

g.test.Rd

(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.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

ggplot_pca.Rd

(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.Rd

(v3.0.1.9088) add version number to intrinsic_resistant

2026-09-03 12:14:25 +02:00

guess_ab_col.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

interpretive_rules.Rd

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

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

intrinsic_resistant.Rd

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

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

italicise_taxonomy.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

join.Rd

(v3.0.1.9059) Update taxonomy of microorganisms

2026-06-23 01:38:13 +02:00

key_antimicrobials.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

kurtosis.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

like.Rd

(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.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

mean_amr_distance.Rd

(v3.0.0.9007) allow any tidyselect language in as.sir()

2025-07-17 14:29:35 +02:00

microorganisms.codes.Rd

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

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

microorganisms.groups.Rd

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

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

microorganisms.Rd

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

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

mo_matching_score.Rd

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

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

mo_property.Rd

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

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

mo_source.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

pca.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

plot.Rd

(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.Rd

(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

random.Rd

(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.Rd

(v3.0.1.9059) Fix WISCA in vignette

2026-06-23 14:38:59 +02:00

sir_combine.Rd

(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

skewness.Rd

(v2.1.1.9233) chore: make all argument texts full sentences

2025-03-31 14:53:24 +02:00

top_n_microorganisms.Rd

improve top_n_microorganisms(): add property_for_each, fix property=NULL, enforce rank order (#297)

2026-06-26 21:40:11 +02:00

translate.Rd

(v2.1.1.9270) Add support for Korean, fix ATCs

2025-05-04 14:24:43 +02:00

WHOCC.Rd

(v3.0.1.9059) Update taxonomy of microorganisms

2026-06-23 01:38:13 +02:00

WHONET.Rd

(v2.1.1.9260) fix antibiogram

2025-04-29 16:15:18 +02:00