# ==================================================================== # # TITLE # # Antimicrobial Resistance (AMR) Data Analysis for R # # # # SOURCE # # https://github.com/msberends/AMR # # # # LICENCE # # (c) 2018-2022 Berends MS, Luz CF et al. # # Developed at the University of Groningen, the Netherlands, in # # collaboration with non-profit organisations Certe Medical # # Diagnostics & Advice, and University Medical Center Groningen. # # # # This R package is free software; you can freely use and distribute # # it for both personal and commercial purposes under the terms of the # # GNU General Public License version 2.0 (GNU GPL-2), as published by # # the Free Software Foundation. # # We created this package for both routine data analysis and academic # # research and it was publicly released in the hope that it will be # # useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. # # # # Visit our website for the full manual and a complete tutorial about # # how to conduct AMR data analysis: https://msberends.github.io/AMR/ # # ==================================================================== # # set up package environment, used by numerous AMR functions pkg_env <- new.env(hash = FALSE) pkg_env$mo_failed <- character(0) # determine info icon for messages utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`) is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE)(), error = function(e) FALSE) if (utf8_supported && !is_latex) { # \u2139 is a symbol officially named 'information source' pkg_env$info_icon <- "\u2139" } else { pkg_env$info_icon <- "i" } .onLoad <- function(...) { # Support for tibble headers (type_sum) and tibble columns content (pillar_shaft) # without the need to depend on other packages. This was suggested by the # developers of the vctrs package: # https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R s3_register("pillar::pillar_shaft", "ab") s3_register("pillar::pillar_shaft", "mo") s3_register("pillar::pillar_shaft", "rsi") s3_register("pillar::pillar_shaft", "mic") s3_register("pillar::pillar_shaft", "disk") s3_register("tibble::type_sum", "ab") s3_register("tibble::type_sum", "mo") s3_register("tibble::type_sum", "rsi") s3_register("tibble::type_sum", "mic") s3_register("tibble::type_sum", "disk") # Support for frequency tables from the cleaner package s3_register("cleaner::freq", "mo") s3_register("cleaner::freq", "rsi") # Support for skim() from the skimr package if (pkg_is_available("skimr", also_load = FALSE, min_version = "2.0.0")) { s3_register("skimr::get_skimmers", "mo") s3_register("skimr::get_skimmers", "rsi") s3_register("skimr::get_skimmers", "mic") s3_register("skimr::get_skimmers", "disk") } # Support for autoplot() from the ggplot2 package s3_register("ggplot2::autoplot", "rsi") s3_register("ggplot2::autoplot", "mic") s3_register("ggplot2::autoplot", "disk") s3_register("ggplot2::autoplot", "resistance_predict") # Support for fortify from the ggplot2 package s3_register("ggplot2::fortify", "rsi") s3_register("ggplot2::fortify", "mic") s3_register("ggplot2::fortify", "disk") # Support vctrs package for use in e.g. dplyr verbs s3_register("vctrs::vec_ptype2", "ab.character") s3_register("vctrs::vec_ptype2", "character.ab") s3_register("vctrs::vec_cast", "character.ab") s3_register("vctrs::vec_ptype2", "mo.character") s3_register("vctrs::vec_ptype2", "character.mo") s3_register("vctrs::vec_cast", "character.mo") s3_register("vctrs::vec_ptype2", "ab_selector.character") s3_register("vctrs::vec_ptype2", "character.ab_selector") s3_register("vctrs::vec_cast", "character.ab_selector") s3_register("vctrs::vec_ptype2", "disk.integer") s3_register("vctrs::vec_ptype2", "integer.disk") s3_register("vctrs::vec_cast", "integer.disk") # if mo source exists, fire it up (see mo_source()) try({ if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) { invisible(get_mo_source()) } }, silent = TRUE) # reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed # they cannott be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB) assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR")) assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR")) assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR")) # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR")) # for building the website, only print first 5 rows of a data set # if (Sys.getenv("IN_PKGDOWN") != "" && !interactive()) { # ... # } } # Helper functions -------------------------------------------------------- create_AB_lookup <- function() { AB_lookup <- AMR::antibiotics AB_lookup$generalised_name <- generalise_antibiotic_name(AB_lookup$name) AB_lookup$generalised_synonyms <- lapply(AB_lookup$synonyms, generalise_antibiotic_name) AB_lookup$generalised_abbreviations <- lapply(AB_lookup$abbreviations, generalise_antibiotic_name) AB_lookup$generalised_loinc <- lapply(AB_lookup$loinc, generalise_antibiotic_name) AB_lookup$generalised_all <- unname(lapply(as.list(as.data.frame(t(AB_lookup[, c("ab", "atc", "cid", "name", colnames(AB_lookup)[colnames(AB_lookup) %like% "generalised"]), drop = FALSE]), stringsAsFactors = FALSE)), function(x) { x <- generalise_antibiotic_name(unname(unlist(x))) x[x != ""] })) AB_lookup } create_MO_lookup <- function() { MO_lookup <- AMR::microorganisms MO_lookup$kingdom_index <- NA_real_ MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1 MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2 MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3 MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4 # all the rest MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5 # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc. MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus, MO_lookup$species, MO_lookup$subspecies))) ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE) MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname"]) MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE)) # add a column with only "e coli" like combinations MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE) # so arrange data on prevalence first, then kingdom, then full name MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), ] } create_MO.old_lookup <- function() { MO.old_lookup <- AMR::microorganisms.old MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname)))) # add a column with only "e coli"-like combinations MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower)) # so arrange data on prevalence first, then full name MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), ] } create_intr_resistance <- function() { # for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab) }