AMR/R/aa_globals.R

168 lines
5.5 KiB
R
Raw Normal View History

2018-02-21 11:52:31 +01:00
# ==================================================================== #
# TITLE #
2022-10-05 09:12:22 +02:00
# AMR: An R Package for Working with Antimicrobial Resistance Data #
2018-02-21 11:52:31 +01:00
# #
2019-01-02 23:24:07 +01:00
# SOURCE #
2020-07-08 14:48:06 +02:00
# https://github.com/msberends/AMR #
2018-02-21 11:52:31 +01:00
# #
2022-10-05 09:12:22 +02:00
# CITE AS #
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
# Data. Journal of Statistical Software, 104(3), 1-31. #
# doi:10.18637/jss.v104.i03 #
# #
2022-12-27 15:16:15 +01:00
# Developed at the University of Groningen and the University Medical #
# Center Groningen in The Netherlands, in collaboration with many #
# colleagues from around the world, see our website. #
2018-02-21 11:52:31 +01:00
# #
2019-01-02 23:24:07 +01:00
# This R package is free software; you can freely use and distribute #
# it for both personal and commercial purposes under the terms of the #
# GNU General Public License version 2.0 (GNU GPL-2), as published by #
# the Free Software Foundation. #
# We created this package for both routine data analysis and academic #
# research and it was publicly released in the hope that it will be #
# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
2020-10-08 11:16:03 +02:00
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
2018-02-21 11:52:31 +01:00
# ==================================================================== #
2023-01-21 23:47:20 +01:00
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
2022-08-28 10:31:50 +02:00
# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
EUCAST_VERSION_BREAKPOINTS <- list(
2022-11-14 15:20:39 +01:00
"12.0" = list(
version_txt = "v12.0",
year = 2022,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
2022-08-28 10:31:50 +02:00
"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/"
)
)
2021-03-11 21:42:30 +01:00
2022-10-05 09:12:22 +02:00
TAXONOMY_VERSION <- list(
GBIF = list(
2022-12-12 00:14:56 +01:00
accessed_date = as.Date("2022-12-11"),
citation = "GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
2022-10-05 09:12:22 +02:00
url = "https://www.gbif.org"
),
LPSN = list(
2022-12-12 00:14:56 +01:00
accessed_date = as.Date("2022-12-11"),
2022-10-05 09:12:22 +02:00
citation = "Parte, AC *et al.* (2020). **List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ.** International Journal of Systematic and Evolutionary Microbiology, 70, 5607-5612; \\doi{10.1099/ijsem.0.004332}.",
url = "https://lpsn.dsmz.de"
),
SNOMED = list(
accessed_date = as.Date("2021-07-01"),
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microoganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
url = "https://phinvads.cdc.gov"
2022-10-30 14:31:45 +01:00
),
LOINC = list(
accessed_date = as.Date("2022-10-30"),
citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022).",
url = "https://loinc.org"
2022-10-05 09:12:22 +02:00
)
2021-03-11 21:42:30 +01:00
)
2022-08-28 10:31:50 +02:00
globalVariables(c(
".rowid",
"ab",
"ab_txt",
"affect_ab_name",
"affect_mo_name",
"angle",
"antibiotic",
"antibiotics",
"atc_group1",
"atc_group2",
"base_ab",
2022-10-22 10:20:09 +02:00
"ci_min",
"ci_max",
2022-08-28 10:31:50 +02:00
"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",
"mo",
"name",
"new",
"observations",
"old",
"old_name",
"pattern",
"R",
"rank_index",
"reference.rule",
"reference.rule_group",
"reference.version",
"rowid",
2023-01-21 23:47:20 +01:00
"sir",
"clinical_breakpoints",
2022-08-28 10:31:50 +02:00
"rule_group",
"rule_name",
"se_max",
"se_min",
"species",
"total",
"txt",
"type",
"value",
"varname",
"xvar",
"y",
"year",
"yvar"
))