mirror of
https://github.com/msberends/AMR.git
synced 2025-07-08 23:21:56 +02:00
(v1.5.0.9008) Internal data sets to pkg, speed for auto col determination
This commit is contained in:
Binary file not shown.
BIN
data-raw/AMR_1.5.0.9008.tar.gz
Normal file
BIN
data-raw/AMR_1.5.0.9008.tar.gz
Normal file
Binary file not shown.
@ -23,12 +23,108 @@
|
||||
# how to conduct AMR analysis: https://msberends.github.io/AMR/ #
|
||||
# ==================================================================== #
|
||||
|
||||
# Run this file to update the package using: -------------------------------
|
||||
# Run this file to update the package using:
|
||||
# source("data-raw/internals.R")
|
||||
# --------------------------------------------------------------------------
|
||||
|
||||
library(dplyr, warn.conflicts = FALSE)
|
||||
devtools::load_all(quiet = TRUE)
|
||||
|
||||
old_globalenv <- ls(envir = globalenv())
|
||||
|
||||
# Helper functions --------------------------------------------------------
|
||||
|
||||
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>
|
||||
MO_staph <- AMR::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", "caeli", "capitis", "caprae",
|
||||
"carnosus", "chromogenes", "cohnii", "condimenti",
|
||||
"debuckii", "devriesei", "edaphicus", "epidermidis",
|
||||
"equorum", "felis", "fleurettii", "gallinarum",
|
||||
"haemolyticus", "hominis", "jettensis", "kloosii",
|
||||
"lentus", "lugdunensis", "massiliensis", "microti",
|
||||
"muscae", "nepalensis", "pasteuri", "petrasii",
|
||||
"pettenkoferi", "piscifermentans", "pseudoxylosus",
|
||||
"rostri", "saccharolyticus", "saprophyticus",
|
||||
"sciuri", "simulans", "stepanovicii", "succinus",
|
||||
"vitulinus", "warneri", "xylosus")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies %in% c("schleiferi", ""))),
|
||||
"mo", drop = TRUE]
|
||||
} else if (type == "CoPS") {
|
||||
MO_staph[which(MO_staph$species %in% c("coagulase-positive",
|
||||
"simiae", "agnetis",
|
||||
"delphini", "lutrae",
|
||||
"hyicus", "intermedius",
|
||||
"pseudintermedius", "pseudointermedius",
|
||||
"schweitzeri", "argenteus")
|
||||
| (MO_staph$species == "schleiferi" & MO_staph$subspecies == "coagulans")),
|
||||
"mo", drop = TRUE]
|
||||
}
|
||||
}
|
||||
|
||||
create_AB_lookup <- function() {
|
||||
AB_lookup <- AMR::antibiotics
|
||||
AB_lookup$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$loinc, generalise_antibiotic_name)
|
||||
AB_lookup
|
||||
}
|
||||
|
||||
create_MO_lookup <- function() {
|
||||
MO_lookup <- AMR::microorganisms
|
||||
|
||||
MO_lookup$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)
|
||||
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$fullname_lower), ]
|
||||
}
|
||||
|
||||
create_intr_resistance <- function() {
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
paste(AMR::microorganisms[match(AMR::intrinsic_resistant$microorganism, AMR::microorganisms$fullname), "mo", drop = TRUE],
|
||||
AMR::antibiotics[match(AMR::intrinsic_resistant$antibiotic, AMR::antibiotics$name), "ab", drop = TRUE])
|
||||
}
|
||||
|
||||
|
||||
|
||||
# Save internal data sets to R/sysdata.rda --------------------------------
|
||||
|
||||
# See 'data-raw/eucast_rules.tsv' for the EUCAST reference file
|
||||
library(dplyr, warn.conflicts = FALSE)
|
||||
eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
skip = 10,
|
||||
sep = "\t",
|
||||
@ -48,7 +144,7 @@ eucast_rules_file <- utils::read.delim(file = "data-raw/eucast_rules.tsv",
|
||||
mutate(reference.rule_group = as.character(reference.rule_group)) %>%
|
||||
select(-sorting_rule)
|
||||
|
||||
# Translations ----
|
||||
# Translations
|
||||
translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
sep = "\t",
|
||||
stringsAsFactors = FALSE,
|
||||
@ -62,23 +158,42 @@ translations_file <- utils::read.delim(file = "data-raw/translations.tsv",
|
||||
allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
|
||||
quote = "")
|
||||
|
||||
# Old microorganism codes -------------------------------------------------
|
||||
|
||||
# Old microorganism codes
|
||||
microorganisms.translation <- readRDS("data-raw/microorganisms.translation.rds")
|
||||
|
||||
# for mo_is_intrinsic_resistant() - saves a lot of time when executed on this vector
|
||||
INTRINSIC_R <- create_intr_resistance()
|
||||
|
||||
# for checking input in `language` argument in e.g. mo_*() and ab_*() functions
|
||||
LANGUAGES_SUPPORTED <- sort(c("en", unique(translations_file$lang)))
|
||||
|
||||
# vectors of CoNS and CoPS, improves speed in as.mo()
|
||||
MO_CONS <- create_species_cons_cops("CoNS")
|
||||
MO_COPS <- create_species_cons_cops("CoPS")
|
||||
|
||||
# reference data - they have additional columns compared to `antibiotics` and `microorganisms` to improve speed
|
||||
AB_lookup <- create_AB_lookup()
|
||||
MO_lookup <- create_MO_lookup()
|
||||
MO.old_lookup <- create_MO.old_lookup()
|
||||
|
||||
# Export to package as internal data ----
|
||||
usethis::use_data(eucast_rules_file, translations_file, microorganisms.translation,
|
||||
usethis::use_data(eucast_rules_file,
|
||||
translations_file,
|
||||
microorganisms.translation,
|
||||
INTRINSIC_R,
|
||||
LANGUAGES_SUPPORTED,
|
||||
MO_CONS,
|
||||
MO_COPS,
|
||||
AB_lookup,
|
||||
MO_lookup,
|
||||
MO.old_lookup,
|
||||
internal = TRUE,
|
||||
overwrite = TRUE,
|
||||
version = 2,
|
||||
compress = "xz")
|
||||
|
||||
# Remove from global environment ----
|
||||
rm(eucast_rules_file)
|
||||
rm(translations_file)
|
||||
rm(microorganisms.translation)
|
||||
# Export data sets to the repository in different formats -----------------
|
||||
|
||||
# Save to raw data to repository ----
|
||||
write_md5 <- function(object) {
|
||||
conn <- file(paste0("data-raw/", deparse(substitute(object)), ".md5"))
|
||||
writeLines(digest::digest(object, "md5"), conn)
|
||||
@ -93,7 +208,7 @@ changed_md5 <- function(object) {
|
||||
}, error = function(e) TRUE)
|
||||
}
|
||||
usethis::ui_done(paste0("Saving raw data to {usethis::ui_value('/data-raw/')}"))
|
||||
devtools::load_all(quiet = TRUE)
|
||||
|
||||
# give official names to ABs and MOs
|
||||
rsi <- dplyr::mutate(rsi_translation, ab = ab_name(ab), mo = mo_name(mo))
|
||||
if (changed_md5(rsi)) {
|
||||
@ -169,5 +284,7 @@ if (changed_md5(dosage)) {
|
||||
try(openxlsx::write.xlsx(dosage, "data-raw/dosage.xlsx"), silent = TRUE)
|
||||
}
|
||||
|
||||
rm(write_md5)
|
||||
rm(changed_md5)
|
||||
# remove leftovers from global env
|
||||
current_globalenv <- ls(envir = globalenv())
|
||||
rm(list = current_globalenv[!current_globalenv %in% old_globalenv])
|
||||
rm(current_globalenv)
|
||||
|
||||
Reference in New Issue
Block a user