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aa_globals.R
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aa_globals.R
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# ==================================================================== #
# TITLE: #
# AMR: An R Package for Working with Antimicrobial Resistance Data #
# #
# SOURCE CODE: #
# https://github.com/msberends/AMR #
# #
# PLEASE CITE THIS SOFTWARE AS: #
# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
# AMR: An R Package for Working with Antimicrobial Resistance Data. #
# Journal of Statistical Software, 104(3), 1-31. #
# https://doi.org/10.18637/jss.v104.i03 #
# #
# 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. #
# #
# 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. #
# #
# Visit our website for the full manual and a complete tutorial about #
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
# (sourcing "data-raw/_pre_commit_checks.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,
title = "'EUCAST Clinical Breakpoint Tables'",
url = "https://www.eucast.org/clinical_breakpoints/"
),
"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(
"3.3" = 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(
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"
),
"3.1" = 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"
# )
# )
TAXONOMY_VERSION <- list(
GBIF = list(
name = "Global Biodiversity Information Facility (GBIF)",
accessed_date = as.Date("2024-06-24"),
citation = "GBIF Secretariat (2023). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
url = "https://www.gbif.org"
),
LPSN = list(
name = "List of Prokaryotic names with Standing in Nomenclature (LPSN)",
accessed_date = as.Date("2024-06-24"),
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"
),
MycoBank = list(
name = "MycoBank",
accessed_date = as.Date("2024-06-24"),
citation = "Vincent, R *et al* (2013). **MycoBank gearing up for new horizons.** IMA Fungus, 4(2), 371-9; \\doi{10.5598/imafungus.2013.04.02.16}.",
url = "https://www.mycobank.org"
),
BacDive = list(
name = "BacDive",
accessed_date = as.Date("2024-07-16"),
citation = "Reimer, LC *et al.* (2022). ***BacDive* in 2022: the knowledge base for standardized bacterial and archaeal data.** Nucleic Acids Res., 50(D1):D741-D74; \\doi{10.1093/nar/gkab961}.",
url = "https://bacdive.dsmz.de"
),
SNOMED = list(
name = "Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT)",
accessed_date = as.Date("2024-07-16"),
citation = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS). US Edition of SNOMED CT from 1 September 2020. Value Set Name 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
url = "https://phinvads.cdc.gov"
),
LOINC = list(
name = "Logical Observation Identifiers Names and Codes (LOINC)",
accessed_date = as.Date("2023-10-19"),
citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023).",
url = "https://loinc.org"
)
)
globalVariables(c(
".GenericCallEnv",
".mo",
".rowid",
".syndromic_group",
"ab",
"ab_txt",
"affect_ab_name",
"affect_mo_name",
"angle",
"antibiotic",
"antibiotics",
"atc_group1",
"atc_group2",
"base_ab",
"ci_max",
"ci_min",
"clinical_breakpoints",
"code",
"cols",
"count",
"data",
"disk",
"dosage",
"dose",
"dose_times",
"fullname",
"fullname_lower",
"g_species",
"genus",
"gr",
"group",
"guideline",
"hjust",
"host_index",
"host_match",
"input",
"intrinsic_resistant",
"isolates",
"lang",
"language",
"lookup",
"method",
"mic ",
"mic",
"microorganism",
"microorganisms",
"microorganisms.codes",
"mo",
"n",
"name",
"new",
"numerator",
"observations",
"old",
"old_name",
"pattern",
"R",
"rank_index",
"ref_tbl",
"reference.rule",
"reference.rule_group",
"reference.version",
"rowid",
"rule_group",
"rule_name",
"se_max",
"se_min",
"SI",
"sir",
"species",
"syndromic_group",
"total",
"txt",
"type",
"uti_index",
"value",
"varname",
"x",
"xvar",
"y",
"year",
"yvar"
))