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133 lines
6.4 KiB
133 lines
6.4 KiB
# ==================================================================== # |
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# TITLE # |
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# Antimicrobial Resistance (AMR) Data Analysis for R # |
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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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# LICENCE # |
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# (c) 2018-2022 Berends MS, Luz CF et al. # |
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# Developed at the University of Groningen, the Netherlands, in # |
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# collaboration with non-profit organisations Certe Medical # |
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# Diagnostics & Advice, and University Medical Center Groningen. # |
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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 rsi_translation |
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# (sourcing "data-raw/_internals.R" will process the TSV file) |
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EUCAST_VERSION_BREAKPOINTS <- list("11.0" = list(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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"10.0" = list(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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EUCAST_VERSION_EXPERT_RULES <- list("3.1" = list(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_intrinsic_resistance/"), |
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"3.2" = list(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_intrinsic_resistance/"), |
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"3.3" = list(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_intrinsic_resistance/")) |
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SNOMED_VERSION <- list(title = "Public Health Information Network Vocabulary Access and Distribution System (PHIN VADS)", |
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current_source = "US Edition of SNOMED CT from 1 September 2020", |
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current_version = 12, |
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current_oid = "2.16.840.1.114222.4.11.1009", |
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value_set_name = "Microorganism", |
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url = "https://phinvads.cdc.gov/vads/ViewValueSet.action?oid=2.16.840.1.114222.4.11.1009") |
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CATALOGUE_OF_LIFE <- list( |
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year = 2019, |
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version = "Catalogue of Life: {year} Annual Checklist", |
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url_CoL = "http://www.catalogueoflife.org", |
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url_LPSN = "https://lpsn.dsmz.de", |
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yearmonth_LPSN = "5 October 2021" |
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) |
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globalVariables(c(".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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"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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"microorganisms.old", |
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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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"rsi", |
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"rsi_translation", |
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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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"species_id", |
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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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