mirror of https://github.com/msberends/AMR.git
168 lines
5.5 KiB
R
Executable File
168 lines
5.5 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# add new version numbers here, and add the rules themselves to "data-raw/eucast_rules.tsv" and clinical_breakpoints
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# (sourcing "data-raw/_pre_commit_hook.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list(
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"12.0" = list(
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version_txt = "v12.0",
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year = 2022,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/clinical_breakpoints/"
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),
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"11.0" = list(
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version_txt = "v11.0",
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year = 2021,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/clinical_breakpoints/"
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),
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"10.0" = list(
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version_txt = "v10.0",
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year = 2020,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/ast_of_bacteria/previous_versions_of_documents/"
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)
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)
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EUCAST_VERSION_EXPERT_RULES <- list(
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"3.1" = list(
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version_txt = "v3.1",
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year = 2016,
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title = "'EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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),
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"3.2" = list(
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version_txt = "v3.2",
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year = 2020,
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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),
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"3.3" = list(
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version_txt = "v3.3",
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year = 2021,
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title = "'EUCAST Expert Rules' and 'EUCAST Intrinsic Resistance and Unusual Phenotypes'",
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url = "https://www.eucast.org/expert_rules_and_expected_phenotypes/"
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)
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)
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TAXONOMY_VERSION <- list(
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GBIF = list(
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accessed_date = as.Date("2022-12-11"),
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citation = "GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
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url = "https://www.gbif.org"
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),
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LPSN = list(
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accessed_date = as.Date("2022-12-11"),
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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}.",
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url = "https://lpsn.dsmz.de"
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),
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SNOMED = list(
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accessed_date = as.Date("2021-07-01"),
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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).",
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url = "https://phinvads.cdc.gov"
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),
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LOINC = list(
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accessed_date = as.Date("2022-10-30"),
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citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022).",
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url = "https://loinc.org"
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)
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)
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globalVariables(c(
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".rowid",
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"ab",
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"ab_txt",
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"affect_ab_name",
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"affect_mo_name",
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"angle",
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"antibiotic",
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"antibiotics",
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"atc_group1",
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"atc_group2",
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"base_ab",
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"ci_min",
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"ci_max",
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"code",
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"cols",
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"count",
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"data",
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"disk",
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"dosage",
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"dose",
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"dose_times",
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"fullname",
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"fullname_lower",
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"g_species",
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"genus",
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"gr",
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"group",
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"guideline",
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"hjust",
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"input",
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"intrinsic_resistant",
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"isolates",
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"lang",
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"language",
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"lookup",
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"method",
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"mic",
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"mic ",
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"microorganism",
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"microorganisms",
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"microorganisms.codes",
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"mo",
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"name",
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"new",
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"observations",
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"old",
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"old_name",
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"pattern",
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"R",
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"rank_index",
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"reference.rule",
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"reference.rule_group",
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"reference.version",
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"rowid",
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"sir",
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"clinical_breakpoints",
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"rule_group",
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"rule_name",
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"se_max",
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"se_min",
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"species",
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"total",
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"txt",
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"type",
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"value",
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"varname",
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"xvar",
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"y",
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"year",
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"yvar"
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))
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