AMR/man at eb6d07e1fe019695f801a403929f6e519e7e9e77 - AMR

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

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

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

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

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

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

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

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

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

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_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

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.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

(v3.0.1.9132) 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.Rd

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.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

(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.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

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.Rd

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.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

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.Rd

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

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

(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

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