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SERVICE NOTICE: This instance will be decommissioned 1 december of this year (2026). Please migrate your projects to our new repository:
https://gitrepo.service.rug.nl
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AMR
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a108548cd4de242868392b6c2762c96f1f5f0f5e
AMR
/
man
T
History
dr. M.S. (Matthijs) Berends
a108548cd4
Merge remote-tracking branch 'origin/main' into breakpoints
2026-11-04 19:26:35 +01:00
..
ab_from_text.Rd
(v3.0.1.9059) Fix WISCA in vignette
2026-06-23 14:38:59 +02:00
ab_property.Rd
(v3.1.0.9003) 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
Store all screening breakpoints under screening agents, and add these agents to antimicrobials (
#328
)
2026-11-02 17:31:46 +01:00
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
Store all screening breakpoints under screening agents, and add these agents to antimicrobials (
#328
)
2026-11-02 17:31:46 +01:00
antibiogram.Rd
(v3.1.0.9011) Use top_n_microorganisms() in the WISCA examples of the index, manual and vignette, and reword the WISCA prior weight warning to also cover small groups (
#337
)
2026-10-30 12:45:56 +01:00
antimicrobial_selectors.Rd
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
antimicrobials.Rd
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
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
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
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
Apply the EUCAST breakpoints of Vibrio to the species that EUCAST states only
2026-11-03 17:14:15 +01:00
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
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
custom_mdro_guideline.Rd
Set the order of sites in as.sir(), and add the veterinary sites
2026-11-02 20:20:05 +01:00
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
(v3.1.0.9013) Add species groups and complexes to the intrinsic_resistant data set for every antimicrobial to which all their species are intrinsically resistant (
fixes
#338
)
2026-10-30 13:37:25 +01:00
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
Return the serovar in mo_shortname() for Salmonella, keep Salmonella groups apart from streptococci, abbreviate all Lancefield groups, and apply the Typhi rule in mdro() (
#341
)
2026-11-04 07:57:20 +01:00
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
