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AMR/R/zzz.R

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R
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# ==================================================================== #
# TITLE #
# Antimicrobial Resistance (AMR) Analysis #
# #
# SOURCE #
# https://github.com/msberends/AMR #
# #
# LICENCE #
# (c) 2018-2020 Berends MS, Luz CF et al. #
# #
# 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 more info: https://msberends.github.io/AMR. #
# ==================================================================== #
.onLoad <- function(libname, pkgname) {
assign(x = "MO_lookup",
value = create_MO_lookup(),
envir = asNamespace("AMR"))
assign(x = "MO.old_lookup",
value = create_MO.old_lookup(),
envir = asNamespace("AMR"))
assign(x = "LANGUAGES_SUPPORTED",
value = sort(c("en", unique(translations_file$lang))),
envir = asNamespace("AMR"))
# support for tibble headers (type_sum) and tibble columns content (pillar_shaft) without the need to depend on other packages
# this was suggested by the developers of the vctrs package:
# https://github.com/r-lib/vctrs/blob/05968ce8e669f73213e3e894b5f4424af4f46316/R/register-s3.R
s3_register("pillar::pillar_shaft", "ab")
s3_register("tibble::type_sum", "ab")
s3_register("pillar::pillar_shaft", "mo")
s3_register("tibble::type_sum", "mo")
s3_register("pillar::pillar_shaft", "rsi")
s3_register("tibble::type_sum", "rsi")
s3_register("pillar::pillar_shaft", "mic")
s3_register("tibble::type_sum", "mic")
s3_register("pillar::pillar_shaft", "disk")
s3_register("tibble::type_sum", "disk")
# support for frequency tables
s3_register("cleaner::freq", "mo")
s3_register("cleaner::freq", "rsi")
}
.onAttach <- function(...) {
if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(getOption("AMR_silentstart", FALSE)))) {
return()
}
packageStartupMessage("Thank you for using the AMR package! ",
"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities:",
"\nhttps://msberends.github.io/AMR/survey.html",
"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use options(AMR_silentstart = TRUE) ]")
}
create_MO_lookup <- function() {
MO_lookup <- AMR::microorganisms
MO_lookup$kingdom_index <- 99
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$kingdom == "Archaea"), "kingdom_index"] <- 4
# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
MO_lookup$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$fullname_lower))
# add a column with only "e coli" like combinations
MO_lookup$g_species <- gsub("^([a-z])[a-z]+ ([a-z]+) ?.*", "\\1 \\2", MO_lookup$fullname_lower)
# so arrange data on prevalence first, then kingdom, then full name
MO_lookup[order(MO_lookup$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), ]
}