mirror of https://github.com/msberends/AMR.git
193 lines
6.2 KiB
R
Executable File
193 lines
6.2 KiB
R
Executable File
# ==================================================================== #
|
|
# TITLE #
|
|
# AMR: An R Package for Working with Antimicrobial Resistance Data #
|
|
# #
|
|
# SOURCE #
|
|
# https://github.com/msberends/AMR #
|
|
# #
|
|
# CITE AS #
|
|
# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
|
|
# (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_hook.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(
|
|
accessed_date = as.Date("2022-12-11"),
|
|
citation = "GBIF Secretariat (2022). GBIF Backbone Taxonomy. Checklist dataset \\doi{10.15468/39omei}.",
|
|
url = "https://www.gbif.org"
|
|
),
|
|
LPSN = list(
|
|
accessed_date = as.Date("2022-12-11"),
|
|
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"
|
|
),
|
|
BacDive = list(
|
|
accessed_date = as.Date("2023-05-12"),
|
|
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(
|
|
accessed_date = as.Date("2021-07-01"),
|
|
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).",
|
|
url = "https://phinvads.cdc.gov"
|
|
),
|
|
LOINC = list(
|
|
accessed_date = as.Date("2022-10-30"),
|
|
citation = "Logical Observation Identifiers Names and Codes (LOINC), Version 2.73 (8 August, 2022).",
|
|
url = "https://loinc.org"
|
|
)
|
|
)
|
|
|
|
globalVariables(c(
|
|
".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",
|
|
"input",
|
|
"intrinsic_resistant",
|
|
"isolates",
|
|
"lang",
|
|
"language",
|
|
"lookup",
|
|
"method",
|
|
"mic ",
|
|
"mic",
|
|
"microorganism",
|
|
"microorganisms",
|
|
"microorganisms.codes",
|
|
"mo",
|
|
"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",
|
|
"value",
|
|
"varname",
|
|
"xvar",
|
|
"y",
|
|
"year",
|
|
"yvar"
|
|
))
|