AMR/man at 844e2581ee7d3f1aba372fdd67c4bd5d5eb7d040 - AMR

ab_from_text.Rd

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

ab_property.Rd

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +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

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

AMR-options.Rd

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +02:00

amr-tidymodels.Rd

(v3.1.0.9004) Document the columns argument of the tidymodels steps to fix the Rd usage warning in R CMD check

2026-10-17 18:23:06 +02:00

AMR.Rd

Format the month of the taxonomy update in English regardless of the system locale

2026-10-15 10:34:06 +02:00

antibiogram.Rd

(v3.0.1.9154) Shorten an example comment of wisca() to fix the Rd line widths NOTE

2026-10-16 06:32:46 +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

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +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

(v3.0.1.9148) 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

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

(v3.0.1.9147) 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

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

(v3.0.1.9149) 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

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

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +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

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +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

(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

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

(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.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

(v3.1.0.9003) Rewrite the manual index on the website for findability: sections ordered by task (cleaning data, interpreting results as SIR, analysing data), titles before function names, a filter field that also finds topics mentioning a term, and colours prepared for dark mode; also make the tidymodels extensions public in the manual and use consistent help page titles

2026-10-17 09:36:10 +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