# ==================================================================== # # TITLE: # # AMR: An R Package for Working with Antimicrobial Resistance Data # # # # SOURCE CODE: # # https://github.com/msberends/AMR # # # # PLEASE CITE THIS SOFTWARE AS: # # Berends MS, Luz CF, Friedrich AW, et al. (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://amr-for-r.org # # ==================================================================== # # Run this file to update the package using: # source("data-raw/_pre_commit_checks.R") library(dplyr, warn.conflicts = FALSE) try(detach("package:data.table", unload = TRUE), silent = TRUE) # to prevent like() to precede over AMR::like devtools::load_all(quiet = TRUE) suppressMessages(set_AMR_locale("English")) pre_commit_lst <- list() # Save internal data to R/sysdata.rda ------------------------------------- usethis::ui_info(paste0("Updating internal package data")) # See 'data-raw/interpretive_rules.tsv' for the interpretive rules reference file pre_commit_lst$INTERPRETIVE_RULES_DF <- utils::read.delim( file = "data-raw/interpretive_rules.tsv", skip = 9, sep = "\t", stringsAsFactors = FALSE, header = TRUE, strip.white = TRUE, na = c(NA, "", NULL) ) %>% # take the order of the reference.rule_group column in the original data file mutate( reference.rule_group = factor(reference.rule_group, levels = unique(reference.rule_group), ordered = TRUE ), sorting_rule = ifelse(grepl("^Table", reference.rule, ignore.case = TRUE), 1, 2) ) %>% arrange( reference.rule_group, reference.version, sorting_rule, reference.rule ) %>% mutate(reference.rule_group = as.character(reference.rule_group)) %>% select(-sorting_rule) pre_commit_lst$TRANSLATIONS <- utils::read.delim( file = "data-raw/translations.tsv", sep = "\t", stringsAsFactors = FALSE, header = TRUE, blank.lines.skip = TRUE, fill = TRUE, strip.white = TRUE, encoding = "UTF-8", fileEncoding = "UTF-8", na.strings = c(NA, "", NULL), allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1" quote = "" ) pre_commit_lst$TRANSLATIONS <- pre_commit_lst$TRANSLATIONS[, which(colnames(pre_commit_lst$TRANSLATIONS) != "en"), drop = FALSE] pre_commit_lst$LANGUAGES_SUPPORTED_NAMES <- c( list(en = list(exonym = "English", endonym = "English")), lapply( pre_commit_lst$TRANSLATIONS[, which(nchar(colnames(pre_commit_lst$TRANSLATIONS)) == 2), drop = FALSE], function(x) list(exonym = x[1], endonym = x[2]) ) ) pre_commit_lst$LANGUAGES_SUPPORTED <- names(pre_commit_lst$LANGUAGES_SUPPORTED_NAMES) # vectors of CoNS and CoPS, improves speed in as.mo() create_species_cons_cops <- function(type = c("CoNS", "CoPS")) { # Determination of which staphylococcal species are CoNS/CoPS according to: # - Becker et al. 2014, PMID 25278577 # - Becker et al. 2019, PMID 30872103 # - Becker et al. 2020, PMID 32056452 # this function returns class MO_staph <- microorganisms MO_staph <- MO_staph[which(MO_staph$genus == "Staphylococcus"), , drop = FALSE] if (type == "CoNS") { MO_staph[ which(MO_staph$species %in% c( "coagulase-negative", "argensis", "arlettae", "auricularis", "borealis", "caeli", "capitis", "caprae", "carnosus", "casei", "caseorum", "caseolyticus", "chromogenes", "cohnii", "condimenti", "croceilyticus", "debuckii", "devriesei", "edaphicus", "epidermidis", "equorum", "felis", "fleurettii", "gallinarum", "halotolerans", "haemolyticus", "hominis", "hsinchuensis", "jettensis", "kloosii", "lentus", "lugdunensis", "massiliensis", "microti", "muscae", "nepalensis", "pasteuri", "petrasii", "pettenkoferi", "piscifermentans", "pragensis", "pseudoxylosus", "pulvereri", "rostri", "saccharolyticus", "saprophyticus", "sciuri", "simulans", "stepanovicii", "succinus", "ureilyticus", "vitulinus", "vitulus", "warneri", "xylosus", "caledonicus", "canis", "durrellii", "lloydii", "ratti", "taiwanensis", "veratri", "urealyticus", "americanisciuri", "marylandisciuri", "shinii", "brunensis", # Kuhnert et al. 2026 (doi:10.1099/ijsem.0.007230), Baek et al. 2025 (J Microbiol, S. parequorum) and # Belhout et al. 2026 (doi:10.1099/ijsem.0.007253, S. xeri); S. parequorum and S. xeri confirmed by # Matthijs S. Berends "dromedarii", "parequorum", "xeri" ) | # old, now renamed to S. schleiferi (but still as synonym in our data of course): (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))), "mo", drop = TRUE ] } else if (type == "CoPS") { MO_staph[ which(MO_staph$species %in% c( "coagulase-positive", "coagulans", "agnetis", "argenteus", "cornubiensis", "delphini", "lutrae", "hyicus", "intermedius", "pseudintermedius", "pseudointermedius", "schweitzeri", "simiae", "roterodami", "singaporensis", "ursi" ) | # old, now renamed to S. coagulans (but still as synonym in our data of course): (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")), "mo", drop = TRUE ] } } pre_commit_lst$MO_CONS <- create_species_cons_cops("CoNS") pre_commit_lst$MO_COPS <- create_species_cons_cops("CoPS") pre_commit_lst$MO_STREP_ABCG <- microorganisms$mo[which(microorganisms$genus == "Streptococcus" & tolower(microorganisms$species) %in% c( "pyogenes", "agalactiae", "dysgalactiae", "equi", "canis", "group a", "group b", "group c", "group g" ))] pre_commit_lst$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(_|$))")] # a synonym only belongs to these lists if its current name does as well (decision by Matthijs S. Berends, 7 October # 2026), e.g. not Staphylococcus caseolyticus (now Macrococcus caseolyticus) in CoNS, nor Staphylococcus roterodami # (now Staphylococcus aureus) in CoPS for (lst in c("MO_CONS", "MO_COPS", "MO_STREP_ABCG", "MO_LANCEFIELD")) { current <- AMR:::synonym_mo_to_accepted_mo(as.character(pre_commit_lst[[lst]])) pre_commit_lst[[lst]] <- pre_commit_lst[[lst]][is.na(current) | current %in% as.character(pre_commit_lst[[lst]])] } rm(lst, current) pre_commit_lst$MO_WHO_PRIORITY_GENERA <- c( # World Health Organization's (WHO) Priority Pathogen List (some are from the group Enterobacteriaceae) "Acinetobacter", "Aspergillus", "Blastomyces", "Campylobacter", "Candida", "Citrobacter", "Clostridioides", "Coccidioides", "Cryptococcus", "Edwardsiella", "Enterobacter", "Enterococcus", "Escherichia", "Fusarium", "Haemophilus", "Helicobacter", "Histoplasma", "Klebsiella", "Morganella", "Mycobacterium", "Neisseria", "Paracoccidioides", "Pneumocystis", "Proteus", "Providencia", "Pseudomonas", "Salmonella", "Serratia", "Shigella", "Staphylococcus", "Streptococcus", "Yersinia" ) pre_commit_lst$MO_RELEVANT_GENERA <- c( "Absidia", "Acanthamoeba", "Acremonium", "Actinomucor", "Aedes", "Alternaria", "Amoeba", "Ancylostoma", "Angiostrongylus", "Anisakis", "Anopheles", "Apiotrichum", "Apophysomyces", "Arthroderma", "Ascaris", "Aspergillus", "Aureobasidium", "Babesia", "Balamuthia", "Balantidium", # COL name of Balantioides coli (Balantidium coli) "Balantioides", "Basidiobolus", "Beauveria", "Bipolaris", "Blastobotrys", "Blastocystis", "Blastomyces", "Brugia", "Candida", "Candidozyma", "Capillaria", "Chaetomium", "Chilomastix", "Chrysonilia", "Chrysosporium", "Cladophialophora", "Cladosporium", "Clavispora", "Clonorchis", "Coccidioides", "Cokeromyces", "Conidiobolus", "Coniochaeta", "Contracaecum", "Cordylobia", "Cryptococcus", "Cryptosporidium", "Cunninghamella", "Curvularia", "Cutaneotrichosporon", "Cyberlindnera", "Cyclospora", "Cystoisospora", "Debaryomyces", "Debaryozyma", "Demodex", "Dermatobia", "Dientamoeba", "Diphyllobothrium", "Dirofilaria", "Diutina", "Echinococcus", "Echinostoma", "Emergomyces", "Emmonsia", "Encephalitozoon", "Entamoeba", "Enterobius", "Enterocytozoon", "Epidermophyton", "Exidia", "Exophiala", "Exserohilum", "Fasciola", "Fasciolopsis", "Fonsecaea", "Fusarium", "Geotrichum", "Giardia", "Graphium", "Haloarcula", "Halobacterium", "Halococcus", "Hansenula", "Hendersonula", "Heterophyes", "Histomonas", "Histoplasma", "Hortaea", "Hymenolepis", "Hypomyces", "Hysterothylacium", "Isospora", # COL name of Cystoisospora belli (Isospora belli) "Kazachstania", "Kloeckera", "Kluyveromyces", "Kodamaea", "Lacazia", "Leishmania", "Lichtheimia", "Loa", "Lodderomyces", "Lomentospora", "Madurella", "Magnusiomyces", "Malassezia", "Malbranchea", "Mansonella", "Metagonimus", "Meyerozyma", "Microascus", "Microsporidium", "Microsporum", "Millerozyma", "Mortierella", "Mucor", "Mycocentrospora", "Naegleria", "Nakaseomyces", "Nannizzia", "Necator", "Nectria", "Neocosmospora", "Ochroconis", "Oesophagostomum", "Oidiodendron", "Onchocerca", "Opisthorchis", "Paecilomyces", "Paracoccidioides", "Paragonimus", "Pediculus", "Penicillium", "Phaeoacremonium", "Phaeomoniella", "Phialophora", "Phlebotomus", "Phoma", "Pichia", "Piedraia", "Pithomyces", "Pityrosporum", "Plasmodium", "Pneumocystis", "Pseudallescheria", "Pseudoscopulariopsis", "Pseudoterranova", "Pulex", "Purpureocillium", "Quambalaria", "Rasamsonia", "Rhinocladiella", "Rhizomucor", "Rhizopus", "Rhodotorula", "Saccharomyces", "Saksenaea", "Saprochaete", "Sarcocystis", "Sarcoptes", "Scedosporium", "Schistosoma", "Schizophyllum", "Schizosaccharomyces", "Scolecobasidium", "Scopulariopsis", "Scytalidium", "Spirometra", "Sporobolomyces", "Sporopachydermia", "Sporothrix", "Sporotrichum", "Stachybotrys", "Strongyloides", "Syncephalastrum", "Syngamus", "Taenia", "Talaromyces", "Toxocara", "Toxoplasma", "Trichinella", "Trichobilharzia", "Trichoderma", "Trichomonas", "Trichophyton", "Trichosporon", "Trichostrongylus", "Trichuris", "Tritirachium", "Trombicula", "Trypanosoma", "Tunga", "Ulocladium", "Ustilago", "Verticillium", "Wallemia", "Wangiella", "Wickerhamomyces", "Wuchereria", "Yarrowia", "Zygosaccharomyces" ) # antibiotic groups # (these will also be used for interpretive_rules() and understanding data-raw/interpretive_rules.tsv) pre_commit_lst$AB_AMINOGLYCOSIDES <- antimicrobials %>% filter(group %like% "aminoglycoside|paromomycin|spectinomycin") %>% pull(ab) pre_commit_lst$AB_AMINOPENICILLINS <- as.ab(c("AMP", "AMX", "AMC")) pre_commit_lst$AB_AMINOCOUMARINS <- antimicrobials %>% filter(name %like% "novobiocin|clorobiocin") %>% pull(ab) pre_commit_lst$AB_ANTIFUNGALS <- antimicrobials %>% filter(group %like% "antifungal") %>% pull(ab) pre_commit_lst$AB_ANTIMYCOBACTERIALS <- antimicrobials %>% filter(group %like% "antimycobacterial") %>% pull(ab) pre_commit_lst$AB_CARBAPENEMS <- antimicrobials %>% filter(group %like% "carbapenem") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS <- antimicrobials %>% filter(group %like% "cephalosporin") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_1ST <- antimicrobials %>% filter(group %like% "cephalosporin.*1") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_2ND <- antimicrobials %>% filter(group %like% "cephalosporin.*2") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_3RD <- antimicrobials %>% filter(group %like% "cephalosporin.*3") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_4TH <- antimicrobials %>% filter(group %like% "cephalosporin.*4") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_5TH <- antimicrobials %>% filter(group %like% "cephalosporin.*5") %>% pull(ab) pre_commit_lst$AB_CEPHALOSPORINS_EXCEPT_CAZ <- pre_commit_lst$AB_CEPHALOSPORINS[pre_commit_lst$AB_CEPHALOSPORINS != "CAZ"] pre_commit_lst$AB_GLYCOPEPTIDES <- antimicrobials %>% filter(group %like% "glycopeptide") %>% pull(ab) pre_commit_lst$AB_FUSIDANES <- antimicrobials %>% filter(name %like% "fusi") %>% pull(ab) pre_commit_lst$AB_IONOPHORES <- antimicrobials %>% filter(name %like% "alamethicin|beauvericin|calcimycin|chloroquine|clioquinol|diiodohydroxyquinoline|dithiocarbamates|enniatin|epigallocatechin|gramicidin|hinokitiol|ionomycin|laidlomycin|lasalocid|maduramicin|monensin|narasin|nigericin|nonactin|nystatin|pyrazole|pyrithione|quercetin|salinomycin|semduramicin|valinomycin|zincophorin") %>% pull(ab) pre_commit_lst$AB_ISOXAZOLYLPENICILLINS <- antimicrobials %>% filter(name %like% "oxacillin|cloxacillin|dicloxacillin|flucloxacillin|meth?icillin") %>% pull(ab) pre_commit_lst$AB_LIPOGLYCOPEPTIDES <- as.ab(c("DAL", "ORI", "TLV")) # dalba/orita/tela pre_commit_lst$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) pre_commit_lst$AB_MACROLIDES <- antimicrobials %>% filter(atc_group2 %like% "macrolide" | (group %like% "macrolide" & is.na(atc_group2)) | name %like% "^(acetylmidecamycin|acetylspiramycin|gamith?romycin|kitasamycin|meleumycin|nafith?romycin|primycin|solith?romycin|tildipirosin|tilmicosin|tulath?romycin|tylosin|tylvalosin)") %>% pull(ab) pre_commit_lst$AB_MONOBACTAMS <- antimicrobials %>% filter(group %like% "monobactam" | name %like% "aztreonam|carumonam|tigemonam") %>% pull(ab) 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) pre_commit_lst$AB_PENICILLINS <- antimicrobials %>% filter(group %like% "penicillin" & !(name %unlike% "/" & name %like% ".*bactam$")) %>% pull(ab) 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$AB_PHENICOLS <- antimicrobials %>% filter(group %like% "phenicol" | atc_group1 %like% "phenicol" | atc_group2 %like% "phenicol") %>% pull(ab) pre_commit_lst$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 %>% filter(group %like% "polymyxin") %>% pull(ab) pre_commit_lst$AB_QUINOLONES <- antimicrobials %>% filter(group %like% "quinolone" | atc_group1 %like% "quinolone" | atc_group2 %like% "quinolone" | name %like% "ozenoxacin") %>% pull(ab) pre_commit_lst$AB_FLUOROQUINOLONES <- antimicrobials %>% # 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) 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$AB_CARBAPENEMS, pre_commit_lst$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$group[i]))) } } group_map[[i]] <- group_map[[i]][order(nchar(group_map[[i]]))] } # create priority list for ab_group() pre_commit_lst$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) # (long strings as strL, as otherwise the file would exceed the file size limit of GitHub) try(haven::write_dta(mo, "data-raw/datasets/microorganisms.dta", strl_threshold = 255), 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())