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New mo algorithm, prepare for 2.0
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R/zzz.R
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R/zzz.R
@ -1,12 +1,16 @@
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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# AMR: An R Package for Working with Antimicrobial Resistance Data #
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# #
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# SOURCE #
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# https://github.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2018-2022 Berends MS, Luz CF et al. #
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# CITE AS #
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# Berends MS, Luz CF, Friedrich AW, Sinha BNM, Albers CJ, Glasner C #
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# (2022). AMR: An R Package for Working with Antimicrobial Resistance #
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# Data. Journal of Statistical Software, 104(3), 1-31. #
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# doi:10.18637/jss.v104.i03 #
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# #
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# Developed at the University of Groningen, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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@ -24,16 +28,24 @@
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# ==================================================================== #
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# set up package environment, used by numerous AMR functions
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pkg_env <- new.env(hash = FALSE)
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pkg_env$mo_failed <- character(0)
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pkg_env$mo_field_abbreviations <- c(
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"AIEC", "ATEC", "BORSA", "CRSM", "DAEC", "EAEC",
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"EHEC", "EIEC", "EPEC", "ETEC", "GISA", "MRPA",
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"MRSA", "MRSE", "MSSA", "MSSE", "NMEC", "PISP",
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"PRSP", "STEC", "UPEC", "VISA", "VISP", "VRE",
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"VRSA", "VRSP"
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AMR_env <- new.env(hash = FALSE)
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AMR_env$mo_uncertainties <- data.frame(
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original_input = character(0),
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input = character(0),
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fullname = character(0),
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mo = character(0),
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candidates = character(0),
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minimum_matching_score = integer(0),
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keep_synonyms = logical(0),
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stringsAsFactors = FALSE
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)
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pkg_env$rsi_interpretation_history <- data.frame(
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AMR_env$mo_renamed <- list()
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AMR_env$mo_previously_coerced <- data.frame(
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x = character(0),
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mo = character(0),
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stringsAsFactors = FALSE
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)
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AMR_env$rsi_interpretation_history <- data.frame(
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datetime = Sys.time()[0],
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index = integer(0),
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ab_input = character(0),
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@ -49,6 +61,7 @@ pkg_env$rsi_interpretation_history <- data.frame(
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interpretation = character(0),
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stringsAsFactors = FALSE
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)
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AMR_env$has_data.table <- pkg_is_available("data.table", also_load = FALSE)
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# determine info icon for messages
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utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
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@ -57,12 +70,12 @@ is_latex <- tryCatch(import_fn("is_latex_output", "knitr", error_on_fail = FALSE
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)
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if (utf8_supported && !is_latex) {
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# \u2139 is a symbol officially named 'information source'
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pkg_env$info_icon <- "\u2139"
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AMR_env$info_icon <- "\u2139"
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} else {
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pkg_env$info_icon <- "i"
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AMR_env$info_icon <- "i"
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}
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.onLoad <- function(...) {
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.onLoad <- function(lib, pkg) {
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# Support for tibble headers (type_sum) and tibble columns content (pillar_shaft)
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# without the need to depend on other packages. This was suggested by the
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# developers of the vctrs package:
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@ -117,14 +130,9 @@ if (utf8_supported && !is_latex) {
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s3_register("vctrs::vec_math", "mic")
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# if mo source exists, fire it up (see mo_source())
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try(
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{
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if (file.exists(getOption("AMR_mo_source", "~/mo_source.rds"))) {
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invisible(get_mo_source())
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}
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},
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silent = TRUE
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)
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if (tryCatch(file.exists(getOption("AMR_mo_source", "~/mo_source.rds")), error = function(e) FALSE)) {
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invisible(get_mo_source())
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}
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# be sure to print tibbles as tibbles
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if (pkg_is_available("tibble", also_load = FALSE)) {
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@ -135,7 +143,6 @@ if (utf8_supported && !is_latex) {
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# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
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assign(x = "AB_lookup", value = create_AB_lookup(), envir = asNamespace("AMR"))
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assign(x = "MO_lookup", value = create_MO_lookup(), envir = asNamespace("AMR"))
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assign(x = "MO.old_lookup", value = create_MO.old_lookup(), envir = asNamespace("AMR"))
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# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
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assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
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}
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@ -157,30 +164,34 @@ create_MO_lookup <- function() {
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# all the rest
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MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
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MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
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} else {
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MO_lookup$fullname_lower <- ""
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warning("MO table updated - Run: source(\"data-raw/_pre_commit_hook.R\")", call. = FALSE)
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}
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# # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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# if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
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# MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
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# } else {
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# MO_lookup$fullname_lower <- ""
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# warning("MO table updated - Run: source(\"data-raw/_pre_commit_hook.R\")", call. = FALSE)
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# }
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# add a column with only "e coli" like combinations
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MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower, perl = TRUE)
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MO_lookup$fullname_lower <- create_MO_fullname_lower()
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MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
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MO_lookup$species_first <- substr(MO_lookup$species, 1, 1)
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# so arrange data on prevalence first, then kingdom, then full name
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MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
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}
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create_MO.old_lookup <- function() {
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MO.old_lookup <- AMR::microorganisms.old
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MO.old_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", tolower(trimws(MO.old_lookup$fullname))))
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# add a column with only "e coli"-like combinations
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MO.old_lookup$g_species <- trimws(gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO.old_lookup$fullname_lower))
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# so arrange data on prevalence first, then full name
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MO.old_lookup[order(MO.old_lookup$prevalence, MO.old_lookup$fullname_lower), , drop = FALSE]
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create_MO_fullname_lower <- function() {
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MO_lookup <- AMR::microorganisms
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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MO_lookup$fullname_lower <- tolower(trimws(paste(
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MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies
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)))
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ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
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MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
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MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
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MO_lookup$fullname_lower
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}
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create_intr_resistance <- function() {
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