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Update clinical breakpoints and fix some as.mo() bugs (#117)

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* Updates clinical breakpoints EUCAST/CLSI 2023, fixes #102, fixes #112, fixes #113, fixes #114, fixes #115
* docs
* implement ecoffs
* unit tests
This commit is contained in:
Dr. Matthijs Berends
2023-06-22 15:10:59 +02:00
committed by GitHub
parent 9591688811
commit f065945d7b
55 changed files with 43056 additions and 18400 deletions
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30
R/aa_globals.R
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@ -30,6 +30,12 @@
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
EUCAST_VERSION_BREAKPOINTS <- list(
"13.0" = list(
version_txt = "v13.0",
year = 2023,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
"12.0" = list(
version_txt = "v12.0",
year = 2022,
@ -50,10 +56,10 @@ EUCAST_VERSION_BREAKPOINTS <- list(
)
)
EUCAST_VERSION_EXPERT_RULES <- list(
"3.1" = list(
version_txt = "v3.1",
year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
"3.3" = list(
version_txt = "v3.3",
year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
),
"3.2" = list(
@ -62,10 +68,18 @@ EUCAST_VERSION_EXPERT_RULES <- list(
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
),
"3.3" = list(
version_txt = "v3.3",
year = 2021,
title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
"3.1" = list(
version_txt = "v3.1",
year = 2016,
title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
)
)
EUCAST_VERSION_RESISTANTPHENOTYPES <- list(
"1.2" = list(
version_txt = "v1.2",
year = 2023,
title = "'Expected Resistant Phenotypes'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
)
)