mirror of
https://github.com/msberends/AMR.git
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dr. M.S. (Matthijs) BerendsandClaude Opus 5.5
83a4853936
- taxonomy build: released taxa (since v2.0.0) that are missing are restored from their last release with their old code and last known status, and are exempt from later removals (decision by Matthijs S. Berends) - exceptions are retired on purpose in data-raw/microorganisms_files/mo_code_retirements.csv with a reason: other organisms with the same genus name (e.g. the Graphium butterflies, wrongly in the Fungi until v3.0.1) and taxa whose genus is now only known in another domain; as.mo() translates these codes to NA with that reason - synonyms without a current name are linked to an accepted name in the same genus that only differs by a Latin gender ending (e.g. Candida glabratus -> Nakaseomyces glabratus) - placeholders such as "(unknown class)" never become records; codes of manually added records are matched by domain and name - integrity rule released_taxon_missing; known defects of the data on main updated Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
906 lines
36 KiB
R
906 lines
36 KiB
R
# ==================================================================== #
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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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# Run this file to update the package using:
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# source("data-raw/_pre_commit_checks.R")
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library(dplyr, warn.conflicts = FALSE)
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try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like
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devtools::load_all(quiet = TRUE)
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suppressMessages(set_AMR_locale("English"))
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pre_commit_lst <- list()
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# Save internal data to R/sysdata.rda -------------------------------------
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usethis::ui_info(paste0("Updating internal package data"))
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# See 'data-raw/interpretive_rules.tsv' for the interpretive rules reference file
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pre_commit_lst$INTERPRETIVE_RULES_DF <- utils::read.delim(
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file = "data-raw/interpretive_rules.tsv",
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skip = 9,
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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strip.white = TRUE,
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na = c(NA, "", NULL)
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) %>%
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# take the order of the reference.rule_group column in the original data file
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mutate(
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reference.rule_group = factor(reference.rule_group,
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levels = unique(reference.rule_group),
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ordered = TRUE
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),
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sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2)
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) %>%
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arrange(
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reference.rule_group,
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reference.version,
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sorting_rule,
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reference.rule
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) %>%
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mutate(reference.rule_group = as.character(reference.rule_group)) %>%
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select(-sorting_rule)
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pre_commit_lst$TRANSLATIONS <- utils::read.delim(
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file = "data-raw/translations.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL),
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allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
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quote = ""
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)
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pre_commit_lst$TRANSLATIONS <- pre_commit_lst$TRANSLATIONS[, which(colnames(pre_commit_lst$TRANSLATIONS) != "en"), drop = FALSE]
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pre_commit_lst$LANGUAGES_SUPPORTED_NAMES <- c(
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list(en = list(exonym = "English", endonym = "English")),
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lapply(
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pre_commit_lst$TRANSLATIONS[, which(nchar(colnames(pre_commit_lst$TRANSLATIONS)) == 2), drop = FALSE],
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function(x) list(exonym = x[1], endonym = x[2])
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)
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)
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pre_commit_lst$LANGUAGES_SUPPORTED <- names(pre_commit_lst$LANGUAGES_SUPPORTED_NAMES)
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# vectors of CoNS and CoPS, improves speed in as.mo()
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create_species_cons_cops <- function(type = c("CoNS", "CoPS")) {
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# Determination of which staphylococcal species are CoNS/CoPS according to:
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# - Becker et al. 2014, PMID 25278577
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# - Becker et al. 2019, PMID 30872103
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# - Becker et al. 2020, PMID 32056452
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# this function returns class <mo>
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MO_staph <- microorganisms
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MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE]
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if (type == "CoNS") {
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MO_staph[
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which(MO_staph$species %in% c(
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"coagulase-negative", "argensis", "arlettae",
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"auricularis", "borealis", "caeli", "capitis", "caprae",
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"carnosus", "casei", "caseorum", "caseolyticus", "chromogenes", "cohnii", "condimenti",
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"croceilyticus",
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"debuckii", "devriesei", "edaphicus", "epidermidis",
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"equorum", "felis", "fleurettii", "gallinarum", "halotolerans",
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"haemolyticus", "hominis", "hsinchuensis", "jettensis", "kloosii",
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"lentus", "lugdunensis", "massiliensis", "microti",
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"muscae", "nepalensis", "pasteuri", "petrasii",
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"pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus",
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"pulvereri", "rostri", "saccharolyticus", "saprophyticus",
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"sciuri", "simulans", "stepanovicii", "succinus",
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"ureilyticus",
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"vitulinus", "vitulus", "warneri", "xylosus",
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"caledonicus", "canis",
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"durrellii", "lloydii",
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"ratti", "taiwanensis", "veratri", "urealyticus",
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"americanisciuri", "marylandisciuri", "shinii", "brunensis"
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) |
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# old, now renamed to S. schleiferi (but still as synonym in our data of course):
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(MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
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"mo",
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drop = TRUE
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]
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} else if (type == "CoPS") {
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MO_staph[
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which(MO_staph$species %in% c(
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"coagulase-positive", "coagulans",
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"agnetis", "argenteus",
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"cornubiensis",
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"delphini", "lutrae",
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"hyicus", "intermedius",
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"pseudintermedius", "pseudointermedius",
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"schweitzeri", "simiae",
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"roterodami",
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"singaporensis",
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"ursi"
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) |
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# old, now renamed to S. coagulans (but still as synonym in our data of course):
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(MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
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"mo",
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drop = TRUE
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]
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}
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}
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pre_commit_lst$MO_CONS <- create_species_cons_cops("CoNS")
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pre_commit_lst$MO_COPS <- create_species_cons_cops("CoPS")
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pre_commit_lst$MO_STREP_ABCG <- microorganisms$mo[which(microorganisms$genus == "Streptococcus" &
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tolower(microorganisms$species) %in% c(
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"pyogenes", "agalactiae", "dysgalactiae", "equi", "canis",
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"group a", "group b", "group c", "group g"
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))]
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pre_commit_lst$MO_LANCEFIELD <- microorganisms$mo[which(microorganisms$mo %like% "^(B_STRPT_PYGN(_|$)|B_STRPT_AGLC(_|$)|B_STRPT_(DYSG|EQUI)(_|$)|B_STRPT_ANGN(_|$)|B_STRPT_(DYSG|CANS)(_|$)|B_STRPT_SNGN(_|$)|B_STRPT_SLVR(_|$))")]
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pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c(
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# World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae)
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"Acinetobacter",
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"Aspergillus",
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"Blastomyces",
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"Campylobacter",
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"Candida",
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"Citrobacter",
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"Clostridioides",
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"Coccidioides",
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"Cryptococcus",
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"Edwardsiella",
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"Enterobacter",
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"Enterococcus",
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"Escherichia",
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"Fusarium",
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"Haemophilus",
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"Helicobacter",
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"Histoplasma",
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"Klebsiella",
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"Morganella",
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"Mycobacterium",
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"Neisseria",
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"Paracoccidioides",
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"Pneumocystis",
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"Proteus",
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"Providencia",
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"Pseudomonas",
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"Salmonella",
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"Serratia",
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"Shigella",
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"Staphylococcus",
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"Streptococcus",
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"Yersinia"
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)
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pre_commit_lst$MO_RELEVANT_GENERA <- c(
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"Absidia",
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"Acanthamoeba",
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"Acremonium",
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"Actinomucor",
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"Aedes",
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"Alternaria",
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"Amoeba",
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"Ancylostoma",
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"Angiostrongylus",
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"Anisakis",
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"Anopheles",
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"Apiotrichum",
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"Apophysomyces",
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"Arthroderma",
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"Ascaris",
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"Aspergillus",
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"Aureobasidium",
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"Babesia",
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"Balamuthia",
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"Balantioides",
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"Basidiobolus",
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"Beauveria",
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"Bipolaris",
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"Blastobotrys",
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"Blastocystis",
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"Blastomyces",
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"Brugia",
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"Candida",
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"Candidozyma",
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"Capillaria",
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"Chaetomium",
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"Chilomastix",
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"Chrysonilia",
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"Chrysosporium",
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"Cladophialophora",
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"Cladosporium",
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"Clavispora",
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"Clonorchis",
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"Coccidioides",
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"Cokeromyces",
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"Conidiobolus",
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"Coniochaeta",
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"Contracaecum",
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"Cordylobia",
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"Cryptococcus",
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"Cryptosporidium",
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"Cunninghamella",
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"Curvularia",
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"Cutaneotrichosporon",
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"Cyberlindnera",
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"Cyclospora",
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"Cystoisospora",
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"Debaryozyma",
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"Demodex",
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"Dermatobia",
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"Dientamoeba",
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"Diphyllobothrium",
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"Dirofilaria",
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"Diutina",
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"Echinococcus",
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"Echinostoma",
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"Emergomyces",
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"Emmonsia",
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"Encephalitozoon",
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"Entamoeba",
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"Enterobius",
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"Enterocytozoon",
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"Epidermophyton",
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"Exidia",
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"Exophiala",
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"Exserohilum",
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"Fasciola",
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"Fasciolopsis",
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"Fonsecaea",
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"Fusarium",
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"Geotrichum",
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"Giardia",
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"Graphium",
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"Haloarcula",
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"Halobacterium",
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"Halococcus",
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"Hansenula",
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"Hendersonula",
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"Heterophyes",
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"Histomonas",
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"Histoplasma",
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"Hortaea",
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"Hymenolepis",
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"Hypomyces",
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"Hysterothylacium",
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"Kazachstania",
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"Kloeckera",
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"Kluyveromyces",
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"Kodamaea",
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"Lacazia",
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"Leishmania",
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"Lichtheimia",
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"Loa",
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"Lodderomyces",
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"Lomentospora",
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"Madurella",
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"Magnusiomyces",
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"Malassezia",
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"Malbranchea",
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"Mansonella",
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"Metagonimus",
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"Meyerozyma",
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"Microascus",
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"Microsporidium",
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"Microsporum",
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"Millerozyma",
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"Mortierella",
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"Mucor",
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"Mycocentrospora",
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"Naegleria",
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"Nakaseomyces",
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"Nannizzia",
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"Necator",
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"Nectria",
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"Neocosmospora",
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"Ochroconis",
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"Oesophagostomum",
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"Oidiodendron",
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"Onchocerca",
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"Opisthorchis",
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"Paecilomyces",
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"Paracoccidioides",
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"Paragonimus",
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"Pediculus",
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"Penicillium",
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"Phaeoacremonium",
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"Phaeomoniella",
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"Phialophora",
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"Phlebotomus",
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"Phoma",
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"Pichia",
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"Piedraia",
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"Pithomyces",
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"Pityrosporum",
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"Plasmodium",
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"Pneumocystis",
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"Pseudallescheria",
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"Pseudoscopulariopsis",
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"Pseudoterranova",
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"Pulex",
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"Purpureocillium",
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"Quambalaria",
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"Rasamsonia",
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"Rhinocladiella",
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"Rhizomucor",
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"Rhizopus",
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"Rhodotorula",
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"Saccharomyces",
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"Saksenaea",
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"Saprochaete",
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"Sarcocystis",
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"Sarcoptes",
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"Scedosporium",
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"Schistosoma",
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"Schizophyllum",
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"Schizosaccharomyces",
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"Scolecobasidium",
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"Scopulariopsis",
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"Scytalidium",
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"Spirometra",
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"Sporobolomyces",
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"Sporopachydermia",
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"Sporothrix",
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"Sporotrichum",
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"Stachybotrys",
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"Strongyloides",
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"Syncephalastrum",
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"Syngamus",
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"Taenia",
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"Talaromyces",
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"Teleomorph",
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"Toxocara",
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"Toxoplasma",
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"Trichinella",
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"Trichobilharzia",
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"Trichoderma",
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"Trichomonas",
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"Trichophyton",
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"Trichosporon",
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"Trichostrongylus",
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"Trichuris",
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"Tritirachium",
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"Trombicula",
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"Trypanosoma",
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"Tunga",
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"Ulocladium",
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"Ustilago",
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"Verticillium",
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"Wallemia",
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"Wangiella",
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"Wickerhamomyces",
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"Wuchereria",
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"Yarrowia",
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"Zygosaccharomyces"
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)
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# antibiotic groups
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# (these will also be used for interpretive_rules() and understanding data-raw/interpretive_rules.tsv)
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pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>%
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filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>%
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pull(ab)
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pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC"))
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pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>%
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filter(name %like% "novobiocin|clorobiocin") %>%
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pull(ab)
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pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>%
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filter(group %like% "antifungal") %>%
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pull(ab)
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pre_commit_lst$AB_ANTIMYCOBACTERIALS <- antimicrobials %>%
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filter(group %like% "antimycobacterial") %>%
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pull(ab)
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pre_commit_lst$AB_CARBAPENEMS <- antimicrobials %>%
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filter(group %like% "carbapenem") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS <- antimicrobials %>%
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filter(group %like% "cephalosporin") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_1ST <- antimicrobials %>%
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filter(group %like% "cephalosporin.*1") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_2ND <- antimicrobials %>%
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filter(group %like% "cephalosporin.*2") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_3RD <- antimicrobials %>%
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filter(group %like% "cephalosporin.*3") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_4TH <- antimicrobials %>%
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filter(group %like% "cephalosporin.*4") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>%
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filter(group %like% "cephalosporin.*5") %>%
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pull(ab)
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pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"]
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pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>%
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filter(group %like% "glycopeptide") %>%
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pull(ab)
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pre_commit_lst$AB_FUSIDANES <- antimicrobials %>%
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filter(name %like% "fusi") %>%
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pull(ab)
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pre_commit_lst$AB_IONOPHORES <- antimicrobials %>%
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filter(name %like% "alamethicin|beauvericin|calcimycin|chloroquine|clioquinol|diiodohydroxyquinoline|dithiocarbamates|enniatin|epigallocatechin|gramicidin|hinokitiol|ionomycin|laidlomycin|lasalocid|maduramicin|monensin|narasin|nigericin|nonactin|nystatin|pyrazole|pyrithione|quercetin|salinomycin|semduramicin|valinomycin|zincophorin") %>%
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pull(ab)
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pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antimicrobials %>%
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filter(name %like% "oxacillin|cloxacillin|dicloxacillin|flucloxacillin|meth?icillin") %>%
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pull(ab)
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pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela
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pre_commit_lst$AB_GLYCOPEPTIDES_EXCEPT_LIPO <- pre_commit_lst$AB_GLYCOPEPTIDES[!pre_commit_lst$AB_GLYCOPEPTIDES %in% pre_commit_lst$AB_LIPOGLYCOPEPTIDES]
|
|
pre_commit_lst$AB_LINCOSAMIDES <- antimicrobials %>%
|
|
filter(atc_group2 %like% "lincosamide" | (group %like% "lincosamide" & is.na(atc_group2) & name %like% "^(pirlimycin|clinda)")) %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_MACROLIDES <- antimicrobials %>%
|
|
filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2)) | name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|primycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_MONOBACTAMS <- antimicrobials %>%
|
|
filter(group %like% "monobactam" | name %like% "aztreonam|carumonam|tigemonam") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_NITROFURANS <- antimicrobials %>%
|
|
filter(name %like% "^furaz|nitrofura" | atc_group2 %like% "nitrofuran") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_OXAZOLIDINONES <- antimicrobials %>%
|
|
filter(group %like% "oxazolidinone") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_PENICILLINS <- antimicrobials %>%
|
|
filter(group %like% "penicillin" & !(name %unlike% "/" & name %like% ".*bactam$")) %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_PEPTIDES <- antimicrobials %>%
|
|
filter(ab %in% pre_commit_lst$AB_GLYCOPEPTIDES | name %like% "thiostrepton|actinomycin|bacitracin|daptomycin|vancomycin|teixobactin|tyrocidine|gramicidin|zwittermicin|epothilone|fabclavine|bleomycin|ciclosporin|cyclosporine|siderophores|pyoverdine|enterobactin|myxochelin") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_PHENICOLS <- antimicrobials %>%
|
|
filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_PHOSPHONICS <- antimicrobials %>%
|
|
filter(group %like% "phosphonic" | name %like% "fosfo") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_PLEUROMUTILINS <- antimicrobials %>%
|
|
filter(name %like% "retapamulin|tiamulin|pleuromutilin") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_POLYMYXINS <- antimicrobials %>%
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|
filter(group %like% "polymyxin") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_QUINOLONES <- antimicrobials %>%
|
|
filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone" | name %like% "ozenoxacin") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>%
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|
# see DOI 10.23937/2378-3656/1410369, more specifically this table: https://www.clinmedjournals.org/articles/cmrcr/cmrcr-8-369-table1.html
|
|
filter(ab %in% pre_commit_lst$AB_QUINOLONES & name %unlike% " acid|nalidixic|cinoxacin|flumequine|oxolinic|ozenoxacin|piromidic|pipemidic|rosoxacin") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_RIFAMYCINS <- antimicrobials %>%
|
|
filter(name %like% "Rifampi|Rifabutin|Rifapentine|rifamy") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_SPIROPYRIMIDINETRIONES <- antimicrobials %>%
|
|
filter(name %like% "zoliflodacin") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_STREPTOGRAMINS <- antimicrobials %>%
|
|
filter(atc_group2 %like% "streptogramin" | name %like% "streptogramin|virginiamycin|ostreogrycin") %>%
|
|
pull(ab)
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|
pre_commit_lst$AB_TETRACYCLINES <- antimicrobials %>%
|
|
filter(atc_group1 %like% "tetracycline" | atc_group2 %like% "tetracycline" | name %like% "chlortetracycline|cetocycline|demeclocycline|doxycycline|eravacycline|lymecycline|meclocycline|meth?acycline|minocycline|omadacycline|oxytetracycline|rolitetracycline|sarecycline|tetracycline|tigecycline") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_TETRACYCLINES_EXCEPT_TGC <- pre_commit_lst$AB_TETRACYCLINES[pre_commit_lst$AB_TETRACYCLINES != "TGC"]
|
|
pre_commit_lst$AB_TRIMETHOPRIMS <- antimicrobials %>%
|
|
filter(atc_group1 %like% "trimethoprim" | atc_group2 %like% "trimethoprim" | name %like% "trimethoprim|ormetroprim|iclaprim") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_SULFONAMIDES <- antimicrobials %>%
|
|
filter(name %like% "(^|/)sulf[oai]") %>%
|
|
pull(ab)
|
|
pre_commit_lst$AB_UREIDOPENICILLINS <- as.ab(c("PIP", "TZP", "AZL", "MEZ"))
|
|
pre_commit_lst$AB_BETALACTAMS <- sort(c(
|
|
pre_commit_lst$AB_PENICILLINS,
|
|
pre_commit_lst$AB_CEPHALOSPORINS,
|
|
pre_commit_lst$AB_CARBAPENEMS,
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|
pre_commit_lst$AB_MONOBACTAMS
|
|
))
|
|
pre_commit_lst$AB_BETALACTAMASE_INHIBITORS <- antimicrobials %>%
|
|
filter(atc_group2 %like% "Beta-lactamase inhibitors" | name %like% "bactam") %>%
|
|
pull(ab)
|
|
# for EUCAST:
|
|
pre_commit_lst$AB_BETALACTAMS_WITH_INHIBITOR <- antimicrobials %>%
|
|
filter(ab %in% pre_commit_lst$AB_BETALACTAMS & name %like% "/" & name %unlike% "EDTA") %>%
|
|
pull(ab)
|
|
# this will be used for documentation:
|
|
pre_commit_lst$DEFINED_AB_GROUPS <- sort(names(pre_commit_lst)[names(pre_commit_lst) %like% "^AB_" & names(pre_commit_lst) != "AB_LOOKUP"])
|
|
|
|
# Check that all AB_* groups with >= 4 members have a corresponding function
|
|
for (grp in pre_commit_lst$DEFINED_AB_GROUPS[pre_commit_lst$DEFINED_AB_GROUPS %unlike% "BETALACTAMASE_INHIBITORS|EXCEPT"]) {
|
|
if (length(pre_commit_lst[[grp]]) >= 4) {
|
|
fn_name <- tolower(gsub("^AB_", "", grp))
|
|
if (!fn_name %in% ls(envir = asNamespace("AMR"))) {
|
|
stop("Group '", grp, "' has ", length(pre_commit_lst[[grp]]),
|
|
" members (", toString(ab_name(pre_commit_lst[[grp]], tolower = T)), ") but no corresponding function '", fn_name, "()' exists in the AMR namespace.",
|
|
call. = FALSE
|
|
)
|
|
}
|
|
}
|
|
}
|
|
|
|
# Update the antimicrobials$group column
|
|
usethis::ui_info("Updating 'group' column in antimicrobials data set from AB_* vectors")
|
|
prettify_group_name <- function(name) {
|
|
raw <- gsub("^AB_", "", name)
|
|
pretty <- tools::toTitleCase(gsub("_", " ", tolower(raw)))
|
|
pretty[pretty %like% " (except|with) "] <- ""
|
|
pretty <- gsub(" (1st|2nd|3rd|4th|5th|6th)", " (\\1 gen.)", pretty)
|
|
pretty <- gsub("([Bb])eta[-]?", "\\1eta-", pretty)
|
|
pretty <- gsub(" Inhibitor", " inhibitor", pretty)
|
|
pretty <- pretty[pretty != ""]
|
|
return(pretty)
|
|
}
|
|
group_map <- vector("list", length = nrow(antimicrobials))
|
|
names(group_map) <- antimicrobials$ab
|
|
for (group_name in pre_commit_lst$DEFINED_AB_GROUPS) {
|
|
ab_vector <- pre_commit_lst[[group_name]]
|
|
pretty_name <- prettify_group_name(group_name)
|
|
for (ab in ab_vector) {
|
|
ab_chr <- as.character(ab)
|
|
group_map[[ab_chr]] <- sort(unique(c(group_map[[ab_chr]], pretty_name)))
|
|
}
|
|
}
|
|
for (i in seq_along(group_map)) {
|
|
if (is.null(group_map[[i]])) {
|
|
group_map[[i]] <- "Other"
|
|
if (antimicrobials$group[i] %unlike% "other") {
|
|
usethis::ui_warn(paste0("AB had a group but not anymore: ", antimicrobials$name[i], " (", antimicrobials$ab[i], "), was ", toString(antimicrobials$group[i])))
|
|
}
|
|
}
|
|
group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))]
|
|
}
|
|
|
|
# create priority list for ab_group()
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|
pre_commit_lst$ABX_PRIORITY_LIST <- c(
|
|
"Aminopenicillins",
|
|
"Isoxazolylpenicillins",
|
|
"Ureidopenicillins",
|
|
"Oxazolidinones",
|
|
"Carbapenems",
|
|
"Cephalosporins (1st gen.)",
|
|
"Cephalosporins (2nd gen.)",
|
|
"Cephalosporins (3rd gen.)",
|
|
"Cephalosporins (4th gen.)",
|
|
"Cephalosporins (5th gen.)",
|
|
"Cephalosporins",
|
|
"Penicillins",
|
|
"Monobactams",
|
|
"Aminoglycosides",
|
|
"Lipoglycopeptides",
|
|
"Glycopeptides",
|
|
"Peptides",
|
|
"Lincosamides",
|
|
"Streptogramins",
|
|
"Macrolides",
|
|
"Nitrofurans",
|
|
"Phenicols",
|
|
"Phosphonics",
|
|
"Polymyxins",
|
|
"Fluoroquinolones",
|
|
"Quinolones",
|
|
"Rifamycins",
|
|
"Spiropyrimidinetriones",
|
|
"Trimethoprims",
|
|
"Sulfonamides",
|
|
"Tetracyclines",
|
|
"Ionophores",
|
|
"Antifungals",
|
|
"Antimycobacterials",
|
|
"Fusidanes",
|
|
"Beta-lactams",
|
|
"Beta-lactamase inhibitors",
|
|
"Pleuromutilins",
|
|
"Aminocoumarins",
|
|
"Other"
|
|
)
|
|
if (!all(unlist(antimicrobials$group) %in% pre_commit_lst$ABX_PRIORITY_LIST)) {
|
|
stop("Missing group(s) in priority list: ", paste(setdiff(unlist(antimicrobials$group), pre_commit_lst$ABX_PRIORITY_LIST), collapse = ", "))
|
|
}
|
|
for (i in seq_along(group_map)) {
|
|
group_map[[i]] <- intersect(pre_commit_lst$ABX_PRIORITY_LIST, group_map[[i]])
|
|
}
|
|
antimicrobials$group <- unname(group_map)
|
|
usethis::use_data(antimicrobials, overwrite = TRUE, version = 2, compress = "xz")
|
|
|
|
pre_commit_lst$AB_LOOKUP <- create_AB_AV_lookup(antimicrobials)
|
|
pre_commit_lst$AV_LOOKUP <- create_AB_AV_lookup(antivirals)
|
|
|
|
# MO codes of earlier releases that are not in the current data set anymore, with the current code of the same
|
|
# taxon (see data-raw/microorganisms_files/README.md). as.mo() uses this to translate them, instead of guessing.
|
|
source("tests/testthat/helper-microorganisms.R")
|
|
mo_registry <- read_mo_registry(".")
|
|
mo_renames <- read_mo_renames(".")
|
|
retired <- mo_registry[!mo_registry$mo %in% as.character(microorganisms$mo), c("mo", "fullname", "rank"), drop = FALSE]
|
|
renamed <- match(retired$mo, mo_renames$mo)
|
|
retired$fullname[!is.na(renamed)] <- mo_renames$new_name[renamed[!is.na(renamed)]]
|
|
# the same name, or else the same name without a rank suffix (such as "Kapabacteria {class}") and the same rank
|
|
current_mo <- as.character(microorganisms$mo)[match(retired$fullname, microorganisms$fullname)]
|
|
by_rank <- as.character(microorganisms$mo)[match(
|
|
paste(mo_name_without_suffix(retired$fullname), retired$rank),
|
|
paste(mo_name_without_suffix(microorganisms$fullname), microorganisms$rank)
|
|
)]
|
|
mo_retirements <- read_mo_retirements(".")
|
|
pre_commit_lst$MO_RETIRED_CODES <- data.frame(
|
|
old_mo = retired$mo,
|
|
mo = ifelse(is.na(current_mo), by_rank, current_mo),
|
|
fullname = retired$fullname,
|
|
# codes retired on purpose, because their taxon was another organism, never lead to a taxon
|
|
reason = mo_retirements$reason[match(retired$mo, mo_retirements$mo)],
|
|
stringsAsFactors = FALSE
|
|
)
|
|
pre_commit_lst$MO_RETIRED_CODES$mo[!is.na(pre_commit_lst$MO_RETIRED_CODES$reason)] <- NA_character_
|
|
rm(mo_registry, mo_renames, mo_retirements, retired, renamed, current_mo, by_rank)
|
|
|
|
# Export to package as internal data ----
|
|
# usethis::use_data() must receive unquoted object names, which is not flexible at all.
|
|
# we'll use good old base::save() instead
|
|
save(
|
|
list = names(pre_commit_lst),
|
|
file = "R/sysdata.rda",
|
|
envir = as.environment(pre_commit_lst),
|
|
compress = "xz",
|
|
version = 2,
|
|
ascii = FALSE
|
|
)
|
|
usethis::ui_done("Saved to {usethis::ui_value('R/sysdata.rda')}")
|
|
|
|
|
|
# Export data sets to the repository in different formats -----------------
|
|
|
|
for (pkg in c("haven", "openxlsx2", "arrow")) {
|
|
if (!pkg %in% rownames(utils::installed.packages())) {
|
|
message("NOTE: package '", pkg, "' not installed! Ignoring export where this package is required.")
|
|
}
|
|
}
|
|
if ("digest" %in% rownames(utils::installed.packages())) {
|
|
md5 <- function(object) digest::digest(object, "md5")
|
|
} else {
|
|
# will write all files anyway, since MD5 hash cannot be determined
|
|
md5 <- function(object) "unknown-md5-hash"
|
|
}
|
|
|
|
write_md5 <- function(object) {
|
|
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
|
|
writeLines(md5(object), conn)
|
|
close(conn)
|
|
}
|
|
changed_md5 <- function(object) {
|
|
path <- paste0("data-raw/", deparse(substitute(object)), ".md5")
|
|
if (!file.exists(path)) {
|
|
return(TRUE)
|
|
}
|
|
tryCatch(
|
|
{
|
|
conn <- file(path)
|
|
compared <- md5(object) != readLines(con = conn)
|
|
close(conn)
|
|
compared
|
|
},
|
|
error = function(e) TRUE
|
|
)
|
|
}
|
|
|
|
# give official names to ABs and MOs
|
|
clin_break <- clinical_breakpoints %>%
|
|
mutate(mo_name = microorganisms$fullname[match(mo, microorganisms$mo)], .after = mo) %>%
|
|
mutate(ab_name = antimicrobials$name[match(ab, antimicrobials$ab)], .after = ab)
|
|
if (changed_md5(clin_break)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('clinical_breakpoints')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(clin_break)
|
|
try(saveRDS(clin_break, "data-raw/datasets/clinical_breakpoints.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(clinical_breakpoints, "data-raw/datasets/clinical_breakpoints.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(clin_break, "data-raw/datasets/clinical_breakpoints.sav"), silent = TRUE)
|
|
# long notes as strL, otherwise Stata's fixed-width strings make the file exceed 100 MB; a missing string is "" in Stata
|
|
try(haven::write_dta(clin_break %>% mutate(note = if_else(is.na(note), "", note)), "data-raw/datasets/clinical_breakpoints.dta", strl_threshold = 255), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(clin_break, "data-raw/datasets/clinical_breakpoints.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(clin_break, "data-raw/datasets/clinical_breakpoints.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(clin_break, "data-raw/datasets/clinical_breakpoints.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(microorganisms)
|
|
try(saveRDS(microorganisms, "data-raw/datasets/microorganisms.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
max_50_snomed <- sapply(microorganisms$snomed, function(x) paste(x[seq_len(min(50, length(x), na.rm = TRUE))], collapse = " "))
|
|
mo <- microorganisms
|
|
mo$snomed <- max_50_snomed
|
|
mo <- dplyr::mutate_if(mo, ~ !is.numeric(.), as.character)
|
|
try(haven::write_sav(mo, "data-raw/datasets/microorganisms.sav"), silent = TRUE)
|
|
try(haven::write_dta(mo, "data-raw/datasets/microorganisms.dta"), silent = TRUE)
|
|
mo_all_snomed <- microorganisms %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(mo_all_snomed, "data-raw/datasets/microorganisms.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(mo_all_snomed, "data-raw/datasets/microorganisms.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms, "data-raw/datasets/microorganisms.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms, "data-raw/datasets/microorganisms.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms.codes)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.codes')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(microorganisms.codes)
|
|
try(saveRDS(microorganisms.codes, "data-raw/datasets/microorganisms.codes.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(microorganisms.codes, "data-raw/datasets/microorganisms.codes.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(microorganisms.codes, "data-raw/datasets/microorganisms.codes.sav"), silent = TRUE)
|
|
try(haven::write_dta(microorganisms.codes, "data-raw/datasets/microorganisms.codes.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(microorganisms.codes, "data-raw/datasets/microorganisms.codes.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms.codes, "data-raw/datasets/microorganisms.codes.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms.codes, "data-raw/datasets/microorganisms.codes.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(microorganisms.groups)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('microorganisms.groups')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(microorganisms.groups)
|
|
try(saveRDS(microorganisms.groups, "data-raw/datasets/microorganisms.groups.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(microorganisms.groups, "data-raw/datasets/microorganisms.groups.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(microorganisms.groups, "data-raw/datasets/microorganisms.groups.sav"), silent = TRUE)
|
|
try(haven::write_dta(microorganisms.groups, "data-raw/datasets/microorganisms.groups.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(microorganisms.groups, "data-raw/datasets/microorganisms.groups.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(microorganisms.groups, "data-raw/datasets/microorganisms.groups.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(microorganisms.groups, "data-raw/datasets/microorganisms.groups.parquet"), silent = TRUE)
|
|
}
|
|
|
|
ab <- dplyr::mutate_if(antimicrobials, ~ !is.numeric(.), as.character)
|
|
if (changed_md5(ab)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('antimicrobials')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(ab)
|
|
try(saveRDS(antimicrobials, "data-raw/datasets/antimicrobials.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(haven::write_sav(ab, "data-raw/datasets/antimicrobials.sav"), silent = TRUE)
|
|
try(haven::write_dta(ab, "data-raw/datasets/antimicrobials.dta"), silent = TRUE)
|
|
ab_lists <- antimicrobials %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(ab_lists, "data-raw/datasets/antimicrobials.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(ab_lists, "data-raw/datasets/antimicrobials.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(antimicrobials, "data-raw/datasets/antimicrobials.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(antimicrobials, "data-raw/datasets/antimicrobials.parquet"), silent = TRUE)
|
|
}
|
|
|
|
av <- dplyr::mutate_if(antivirals, ~ !is.numeric(.), as.character)
|
|
if (changed_md5(av)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('antivirals')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(av)
|
|
try(saveRDS(antivirals, "data-raw/datasets/antivirals.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(haven::write_sav(av, "data-raw/datasets/antivirals.sav"), silent = TRUE)
|
|
try(haven::write_dta(av, "data-raw/datasets/antivirals.dta"), silent = TRUE)
|
|
av_lists <- antivirals %>% mutate_if(is.list, function(x) sapply(x, paste, collapse = ","))
|
|
try(write.table(av_lists, "data-raw/datasets/antivirals.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(av_lists, "data-raw/datasets/antivirals.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(antivirals, "data-raw/datasets/antivirals.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(antivirals, "data-raw/datasets/antivirals.parquet"), silent = TRUE)
|
|
}
|
|
|
|
# give official names to ABs and MOs
|
|
intrinsicR <- data.frame(
|
|
microorganism = mo_name(intrinsic_resistant$mo, language = NULL, keep_synonyms = TRUE, info = FALSE),
|
|
antibiotic = ab_name(intrinsic_resistant$ab, language = NULL),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
if (changed_md5(intrinsicR)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('intrinsic_resistant')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(intrinsicR)
|
|
try(saveRDS(intrinsicR, "data-raw/datasets/intrinsic_resistant.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(intrinsicR, "data-raw/datasets/intrinsic_resistant.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(intrinsicR, "data-raw/datasets/intrinsic_resistant.sav"), silent = TRUE)
|
|
try(haven::write_dta(intrinsicR, "data-raw/datasets/intrinsic_resistant.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(intrinsicR, "data-raw/datasets/intrinsic_resistant.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(intrinsicR, "data-raw/datasets/intrinsic_resistant.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(intrinsicR, "data-raw/datasets/intrinsic_resistant.parquet"), silent = TRUE)
|
|
}
|
|
|
|
if (changed_md5(dosage)) {
|
|
usethis::ui_info(paste0("Saving {usethis::ui_value('dosage')} to {usethis::ui_value('data-raw/datasets/')}"))
|
|
write_md5(dosage)
|
|
try(saveRDS(dosage, "data-raw/datasets/dosage.rds", version = 2, compress = "xz"), silent = TRUE)
|
|
try(write.table(dosage, "data-raw/datasets/dosage.txt", sep = "\t", na = "", row.names = FALSE), silent = TRUE)
|
|
try(haven::write_sav(dosage, "data-raw/datasets/dosage.sav"), silent = TRUE)
|
|
try(haven::write_dta(dosage, "data-raw/datasets/dosage.dta"), silent = TRUE)
|
|
try(openxlsx2::write_xlsx(dosage, "data-raw/datasets/dosage.xlsx"), silent = TRUE)
|
|
try(arrow::write_feather(dosage, "data-raw/datasets/dosage.feather"), silent = TRUE)
|
|
try(arrow::write_parquet(dosage, "data-raw/datasets/dosage.parquet"), silent = TRUE)
|
|
}
|
|
|
|
# Set `antibiotics` as a deprecated data set
|
|
antibiotics <- structure(antimicrobials, class = c("deprecated_amr_dataset", class(antimicrobials)))
|
|
usethis::use_data(antibiotics, internal = FALSE, overwrite = TRUE, compress = "xz", version = 2)
|
|
rm(antibiotics)
|
|
|
|
suppressMessages(reset_AMR_locale())
|
|
|
|
devtools::load_all(quiet = TRUE)
|
|
suppressMessages(set_AMR_locale("English"))
|
|
|
|
files_changed <- function(paths = "^(R|data)/") {
|
|
tryCatch(
|
|
{
|
|
changed_files <- system("git status", intern = TRUE)
|
|
changed_files <- unlist(strsplit(changed_files, " "))
|
|
any(changed_files %like% paths[paths != "R/sysdata.rda"])
|
|
},
|
|
error = function(e) TRUE
|
|
)
|
|
}
|
|
|
|
# Update URLs -------------------------------------------------------------
|
|
if (files_changed()) {
|
|
usethis::ui_info("Checking URLs for redirects")
|
|
# Step 1: Get sources from tools (excluding man/)
|
|
sources <- tools:::url_db_from_package_sources(".")
|
|
sources <- sources[!grepl("^man/", sources$Parent), ]
|
|
# Step 2: Get URLs from .R files in R/
|
|
r_files <- list.files("R", pattern = "\\.R$", full.names = TRUE)
|
|
# Function to extract URLs from a file
|
|
extract_urls_from_file <- function(file_path) {
|
|
lines <- readLines(file_path, warn = FALSE)
|
|
urls <- stringr::str_extract_all(lines, "https?://[^\\s)\"'>]+")
|
|
urls <- unlist(urls)
|
|
if (length(urls) == 0) {
|
|
return(NULL)
|
|
}
|
|
# Remove trailing punctuation (e.g., .,), etc.)
|
|
urls <- stringr::str_replace(urls, "[\\.,;)]+$", "")
|
|
data.frame(
|
|
URL = urls,
|
|
Parent = gsub("^\\./", "", file_path),
|
|
stringsAsFactors = FALSE
|
|
)
|
|
}
|
|
r_file_urls <- do.call(rbind, lapply(r_files, extract_urls_from_file))
|
|
# Step 3: Combine the two sources
|
|
total <- rbind(sources, r_file_urls)
|
|
# Step 4: Check URLs and update
|
|
results <- urlchecker::url_check(db = total)
|
|
invisible(urlchecker::url_update(results = results))
|
|
}
|
|
|
|
# Style pkg ---------------------------------------------------------------
|
|
if (files_changed(paths = "^(R|tests)/")) {
|
|
usethis::ui_info("Styling package")
|
|
styler::style_pkg(
|
|
include_roxygen_examples = FALSE,
|
|
exclude_dirs = list.dirs(full.names = FALSE, recursive = FALSE)[!list.dirs(full.names = FALSE, recursive = FALSE) %in% c("R", "tests")]
|
|
)
|
|
}
|
|
|
|
# Document pkg ------------------------------------------------------------
|
|
if (files_changed()) {
|
|
usethis::ui_info("Documenting package")
|
|
suppressMessages(devtools::document(quiet = TRUE))
|
|
}
|
|
|
|
# Update index.md and README.md -------------------------------------------
|
|
if (files_changed("README.Rmd") ||
|
|
files_changed("index.Rmd") ||
|
|
files_changed("man/microorganisms.Rd") ||
|
|
files_changed("man/antimicrobials.Rd") ||
|
|
files_changed("man/clinical_breakpoints.Rd") ||
|
|
files_changed("man/antibiogram.Rd") ||
|
|
files_changed("R/antibiogram.R") ||
|
|
files_changed("data-raw/translations.tsv")) {
|
|
usethis::ui_info("Rendering {usethis::ui_field('index.md')} and {usethis::ui_field('README.md')}")
|
|
suppressWarnings(rmarkdown::render("index.Rmd", quiet = TRUE))
|
|
suppressWarnings(rmarkdown::render("README.Rmd", quiet = TRUE))
|
|
unlink("index.html") # remove previews from folder
|
|
unlink("README.html")
|
|
}
|
|
|
|
# Finished ----------------------------------------------------------------
|
|
rm(antimicrobials)
|
|
usethis::ui_done("All done")
|
|
suppressMessages(reset_AMR_locale())
|