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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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1a1a3abed1e6fce82b9df08147527c442ab44989
AMR
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T
History
dr. M.S. (Matthijs) Berends
1a1a3abed1
(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
..
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
(v3.0.1.9132) 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
(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
(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
(v3.0.1.9129) 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
