AMR/man
Dr. Matthijs Berends f065945d7b
Update clinical breakpoints and fix some `as.mo()` bugs (#117)
* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
2023-06-22 15:10:59 +02:00
..
figures website update 2022-12-11 11:44:29 +01:00
AMR-deprecated.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
AMR-options.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
AMR.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
WHOCC.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
WHONET.Rd fix for `antibiogram()`, transform `WHONET` data set to `sir` 2023-02-22 15:40:05 +01:00
ab_from_text.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
ab_property.Rd improve `as.mo()` 2023-05-24 15:55:53 +02:00
add_custom_antimicrobials.Rd check for 2.0 2023-03-12 13:02:37 +01:00
add_custom_microorganisms.Rd unit testing R4.3 2023-05-26 20:37:00 +02:00
age.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
age_groups.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
antibiogram.Rd add oxygen tolerance 2023-05-11 21:56:27 +02:00
antibiotic_class_selectors.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
antibiotics.Rd updated microorganism codes 2023-05-26 16:10:01 +02:00
as.ab.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
as.av.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
as.disk.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
as.mic.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
as.mo.Rd updated microorganism codes 2023-05-26 16:10:01 +02:00
as.sir.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
atc_online.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
av_from_text.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
av_property.Rd improve `as.mo()` 2023-05-24 15:55:53 +02:00
availability.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
bug_drug_combinations.Rd fix for antibiograms on R < 3.5 2023-02-24 09:43:10 +01:00
clinical_breakpoints.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
count.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
custom_eucast_rules.Rd add oxygen tolerance 2023-05-11 21:56:27 +02:00
dosage.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
eucast_rules.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
example_isolates.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
example_isolates_unclean.Rd bring back `antibiogram()`, without deps 2023-02-10 16:18:00 +01:00
first_isolate.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
g.test.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
get_episode.Rd update NEWS 2023-03-11 14:43:31 +01:00
ggplot_pca.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
ggplot_sir.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
guess_ab_col.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
intrinsic_resistant.Rd bring back `antibiogram()`, without deps 2023-02-10 16:18:00 +01:00
italicise_taxonomy.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
join.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
key_antimicrobials.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
kurtosis.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
like.Rd fix documentation 2023-03-16 08:55:37 +01:00
mdro.Rd fix documentation 2023-03-16 08:55:37 +01:00
mean_amr_distance.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
microorganisms.Rd updated microorganism codes 2023-05-26 16:10:01 +02:00
microorganisms.codes.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
mo_matching_score.Rd fix coercing `NA` to custom codes, fixes #107 2023-05-08 13:04:18 +02:00
mo_property.Rd updated microorganism codes 2023-05-26 16:10:01 +02:00
mo_source.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
pca.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
plot.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
proportion.Rd documentation for 'data.table' AB selectors 2023-03-11 16:54:02 +01:00
random.Rd Update clinical breakpoints and fix some `as.mo()` bugs (#117) 2023-06-22 15:10:59 +02:00
resistance_predict.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00
skewness.Rd documentation, unit tests 2023-01-24 10:20:27 +01:00
translate.Rd make `rsi` work in more cases, documentation update 2023-02-22 14:38:57 +01:00