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251 lines
8.5 KiB
R
Executable File
251 lines
8.5 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 CODE: #
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# https://github.com/msberends/AMR #
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# #
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# PLEASE CITE THIS SOFTWARE AS: #
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# Berends MS, Luz CF, Friedrich AW, et al. (2022). #
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# AMR: An R Package for Working with Antimicrobial Resistance Data. #
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# Journal of Statistical Software, 104(3), 1-31. #
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# https://doi.org/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://amr-for-r.org #
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# ==================================================================== #
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# add new version numbers here, and add the rules themselves to "data-raw/interpretive_rules.tsv" and clinical_breakpoints
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# (sourcing "data-raw/_pre_commit_checks.R" will process the TSV file)
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EUCAST_VERSION_BREAKPOINTS <- list(
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"16.0" = list(
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version_txt = "v16.0",
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year = 2026,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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),
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"15.0" = list(
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version_txt = "v15.0",
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year = 2025,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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),
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"14.0" = list(
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version_txt = "v14.0",
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year = 2024,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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),
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"13.1" = list(
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version_txt = "v13.1",
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year = 2023,
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title = "'EUCAST Clinical Breakpoint Tables'",
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url = "https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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),
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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/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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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/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/"
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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/bacteria/document-archive/"
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)
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)
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EUCAST_VERSION_EXPERT_RULES <- list(
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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/bacteria/important-additional-information/expert-rules/"
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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/bacteria/important-additional-information/expert-rules/"
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),
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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/bacteria/important-additional-information/expert-rules/"
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)
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)
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EUCAST_VERSION_EXPECTED_PHENOTYPES <- list(
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"1.2" = list(
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version_txt = "v1.2",
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year = 2023,
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title = "'EUCAST Expected Resistant Phenotypes'",
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url = "https://www.eucast.org/bacteria/important-additional-information/expert-rules/"
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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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name = "Global Biodiversity Information Facility (GBIF), via Catalogue of Life (COL)",
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accessed_date = as.Date("2026-05-07"),
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# take the citation from https://www.gbif.org/dataset/7ddf754f-d193-4cc9-b351-99906754a03b#citation
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citation = "Banki, O. *et al.* (2026). Catalogue of Life (2026-04-18 XR). Catalogue of Life Foundation, Amsterdam, Netherlands. \\doi{10.48580/dgxjw}.",
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url = "https://www.gbif.org"
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),
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LPSN = list(
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name = "List of Prokaryotic names with Standing in Nomenclature (LPSN)",
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accessed_date = as.Date("2026-05-07"),
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citation = "Freese, HM *et al.* (2026). **TYGS and LPSN in 2025: a Global Core Biodata Resource for genome-based classification and nomenclature of prokaryotes within DSMZ Digital Diversity.** Nucleic Acids Research, 54, D884–D891; \\doi{10.1093/nar/gkaf1110}.",
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url = "https://lpsn.dsmz.de"
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),
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MycoBank = list(
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name = "MycoBank",
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accessed_date = as.Date("2026-05-07"),
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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}.",
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url = "https://www.mycobank.org"
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),
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BacDive = list(
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name = "BacDive",
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accessed_date = as.Date("2026-05-07"),
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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}.",
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url = "https://bacdive.dsmz.de"
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),
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SNOMED = list(
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name = "Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT)",
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accessed_date = as.Date("2024-07-16"),
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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 'Microorganism', OID 2.16.840.1.114222.4.11.1009 (v12).",
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url = "https://www.cdc.gov/phin/php/phinvads/"
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),
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LOINC = list(
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name = "Logical Observation Identifiers Names and Codes (LOINC)",
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accessed_date = as.Date("2023-10-19"),
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citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.76 (18 September, 2023).",
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url = "https://loinc.org"
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),
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ATC_DDD = list(
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name = "ATC/DDD Index",
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accessed_date = as.Date("2025-05-04"),
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citation = "WHO Collaborating Centre for Drug Statistics Methodology, Guidelines for ATC classification and DDD assignment, Oslo",
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url = "https://atcddd.fhi.no/atc_ddd_index/"
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)
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)
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globalVariables(c(
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".GenericCallEnv",
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".mo",
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".rowid",
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".syndromic_group",
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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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"antimicrobials",
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"atc_group1",
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"atc_group2",
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"base_ab",
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"beta_posterior_1",
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"beta_posterior_2",
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"ci_max",
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"ci_min",
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"clinical_breakpoints",
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"code",
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"cols",
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"count",
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"coverage",
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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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"gamma_posterior",
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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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"host_index",
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"host_match",
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"input",
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"input_given",
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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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"lower",
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"lower_ci",
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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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"n",
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"n_susceptible",
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"n_tested",
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"n_total",
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"name",
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"new",
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"numerator",
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"observations",
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"old",
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"old_name",
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"p_susceptible",
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"pattern",
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"R",
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"rank_index",
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"ref_tbl",
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"reference.rule",
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"reference.rule_group",
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"reference.version",
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"rule.provider",
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"rowid",
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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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"SI",
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"sir",
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"species",
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"syndromic_group",
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"total",
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"total_rows",
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"txt",
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"type",
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"upper",
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"upper_ci",
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"uti_index",
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"value",
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"varname",
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"where",
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"x",
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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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