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fix antibiotics error

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This commit is contained in:
dr. M.S. (Matthijs) Berends
2022-10-30 21:05:46 +01:00
parent d40e0ef20b
commit 9444ed6d1d
37 changed files with 86 additions and 97 deletions
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38
R/zzz.R
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@ -66,9 +66,8 @@ AMR_env$rsi_interpretation_history <- data.frame(
interpretation = character(0),
stringsAsFactors = FALSE
)
AMR_env$has_data.table <- pkg_is_available("data.table", also_load = FALSE)
AMR_env$custom_ab_codes <- character(0)
AMR_env$is_dark_theme <- tryCatch(isTRUE(getExportedValue("getThemeInfo", ns = asNamespace("rstudioapi"))()$dark), error = function(e) FALSE)
AMR_env$is_dark_theme <- NULL
# determine info icon for messages
utf8_supported <- isTRUE(base::l10n_info()$`UTF-8`)
@ -150,8 +149,6 @@ if (utf8_supported && !is_latex) {
# they cannot be part of R/sysdata.rda since CRAN thinks it would make the package too large (+3 MB)
AMR_env$AB_lookup <- create_AB_lookup()
AMR_env$MO_lookup <- create_MO_lookup()
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
assign(x = "INTRINSIC_R", value = create_intr_resistance(), envir = asNamespace("AMR"))
}
.onAttach <- function(lib, pkg) {
@ -184,37 +181,16 @@ create_MO_lookup <- function() {
# all the rest
MO_lookup[which(is.na(MO_lookup$kingdom_index)), "kingdom_index"] <- 5
# # use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
# if (length(MO_FULLNAME_LOWER) == nrow(MO_lookup)) {
# MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
# } else {
# MO_lookup$fullname_lower <- ""
# warning("MO table updated - Run: source(\"data-raw/_pre_commit_hook.R\")", call. = FALSE)
# }
MO_lookup$fullname_lower <- create_MO_fullname_lower()
MO_lookup$fullname_lower <- MO_FULLNAME_LOWER
MO_lookup$full_first <- substr(MO_lookup$fullname_lower, 1, 1)
MO_lookup$species_first <- substr(MO_lookup$species, 1, 1)
# so arrange data on prevalence first, then kingdom, then full name
MO_lookup[order(MO_lookup$prevalence, MO_lookup$kingdom_index, MO_lookup$fullname_lower), , drop = FALSE]
MO_lookup
}
create_MO_fullname_lower <- function() {
MO_lookup <- AMR::microorganisms
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$fullname_lower <- tolower(trimws(paste(
MO_lookup$genus,
MO_lookup$species,
MO_lookup$subspecies
)))
ind <- MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname, perl = TRUE)
MO_lookup[ind, "fullname_lower"] <- tolower(MO_lookup[ind, "fullname", drop = TRUE])
MO_lookup$fullname_lower <- trimws(gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower, perl = TRUE))
MO_lookup$fullname_lower
}
create_intr_resistance <- function() {
add_intrinsic_resistance_to_AMR_env <- 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)
if (is.null(AMR_env$intrinsic_resistant)) {
AMR_env$intrinsic_resistant <- paste(AMR::intrinsic_resistant$mo, AMR::intrinsic_resistant$ab)
}
}