# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (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. # # # # 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 rsi_translation # (sourcing "data-raw/_internals.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_intrinsic_resistance/"), "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_intrinsic_resistance/"), "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_intrinsic_resistance/")) 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, version = "Catalogue of Life: {year} Annual Checklist", url_CoL = "http://www.catalogueoflife.org", url_LPSN = "https://lpsn.dsmz.de", 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"))