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styled, unit test fix

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dr. M.S. (Matthijs) Berends
2022-08-28 10:31:50 +02:00
parent 4cb1db4554
commit 4d050aef7c
147 changed files with 10897 additions and 8169 deletions
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214
R/aa_globals.R
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@@ -9,7 +9,7 @@
# (c) 2018-2022 Berends MS, Luz CF et al. #
# Developed at the University of Groningen, the Netherlands, in #
# collaboration with non-profit organisations Certe Medical #
# Diagnostics & Advice, and University Medical Center Groningen. #
# Diagnostics & Advice, and University Medical Center Groningen. #
# #
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
@@ -24,34 +24,50 @@
# ==================================================================== #
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and rsi_translation
# (sourcing "data-raw/pre-commit-hook.R" will process the TSV file)
EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(version_txt = "v11.0",
year = 2021,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"),
"10.0" = list(version_txt = "v10.0",
year = 2020,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"))
EUCAST_VERSION_EXPERT_RULES <- list("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/"),
"3.2" = list(version_txt = "v3.2",
year = 2020,
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'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"))
# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
EUCAST_VERSION_BREAKPOINTS <- list(
"11.0" = list(
version_txt = "v11.0",
year = 2021,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
"10.0" = list(
version_txt = "v10.0",
year = 2020,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"
)
)
EUCAST_VERSION_EXPERT_RULES <- list(
"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/"
),
"3.2" = list(
version_txt = "v3.2",
year = 2020,
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'",
url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
)
)
SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
current_source = "US Edition of SNOMED CT from 1 September 2020",
current_version = 12,
current_oid = "2.16.840.1.114222.4.11.1009",
value_set_name = "Microorganism",
url = "https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009")
SNOMED_VERSION <- list(
title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)",
current_source = "US Edition of SNOMED CT from 1 September 2020",
current_version = 12,
current_oid = "2.16.840.1.114222.4.11.1009",
value_set_name = "Microorganism",
url = "https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009"
)
CATALOGUE_OF_LIFE <- list(
year = 2019,
@@ -61,73 +77,75 @@ CATALOGUE_OF_LIFE <- list(
yearmonth_LPSN = "5 October 2021"
)
globalVariables(c(".rowid",
"ab",
"ab_txt",
"affect_ab_name",
"affect_mo_name",
"angle",
"antibiotic",
"antibiotics",
"atc_group1",
"atc_group2",
"base_ab",
"code",
"cols",
"count",
"data",
"disk",
"dosage",
"dose",
"dose_times",
"fullname",
"fullname_lower",
"g_species",
"genus",
"gr",
"group",
"guideline",
"hjust",
"input",
"intrinsic_resistant",
"isolates",
"lang",
"language",
"lookup",
"method",
"mic",
"mic ",
"microorganism",
"microorganisms",
"microorganisms.codes",
"microorganisms.old",
"mo",
"name",
"new",
"observations",
"old",
"old_name",
"pattern",
"R",
"rank_index",
"reference.rule",
"reference.rule_group",
"reference.version",
"rowid",
"rsi",
"rsi_translation",
"rule_group",
"rule_name",
"se_max",
"se_min",
"species",
"species_id",
"total",
"txt",
"type",
"value",
"varname",
"xvar",
"y",
"year",
"yvar"))
globalVariables(c(
".rowid",
"ab",
"ab_txt",
"affect_ab_name",
"affect_mo_name",
"angle",
"antibiotic",
"antibiotics",
"atc_group1",
"atc_group2",
"base_ab",
"code",
"cols",
"count",
"data",
"disk",
"dosage",
"dose",
"dose_times",
"fullname",
"fullname_lower",
"g_species",
"genus",
"gr",
"group",
"guideline",
"hjust",
"input",
"intrinsic_resistant",
"isolates",
"lang",
"language",
"lookup",
"method",
"mic",
"mic ",
"microorganism",
"microorganisms",
"microorganisms.codes",
"microorganisms.old",
"mo",
"name",
"new",
"observations",
"old",
"old_name",
"pattern",
"R",
"rank_index",
"reference.rule",
"reference.rule_group",
"reference.version",
"rowid",
"rsi",
"rsi_translation",
"rule_group",
"rule_name",
"se_max",
"se_min",
"species",
"species_id",
"total",
"txt",
"type",
"value",
"varname",
"xvar",
"y",
"year",
"yvar"
))