mirror of https://github.com/msberends/AMR.git
76 lines
4.2 KiB
R
Executable File
76 lines
4.2 KiB
R
Executable File
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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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) 2018-2020 Berends MS, Luz CF et al. #
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# #
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# This R package is free software; you can freely use and distribute #
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# it for both personal and commercial purposes under the terms of the #
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# GNU General Public License version 2.0 (GNU GPL-2), as published by #
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# the Free Software Foundation. #
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# #
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# We created this package for both routine data analysis and academic #
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# research and it was publicly released in the hope that it will be #
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# useful, but it comes WITHOUT ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.github.io/AMR. #
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# ==================================================================== #
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.onLoad <- function(libname, pkgname) {
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assign(x = "MO_lookup",
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value = create_MO_lookup(),
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envir = asNamespace("AMR"))
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assign(x = "MO.old_lookup",
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value = create_MO.old_lookup(),
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envir = asNamespace("AMR"))
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}
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.onAttach <- function(...) {
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if (!interactive() || stats::runif(1) > 0.1 || isTRUE(as.logical(Sys.getenv("AMR_silentstart", FALSE)))) {
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return()
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}
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packageStartupMessage("Thank you for using the AMR package! ",
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"If you have a minute, please anonymously fill in this short questionnaire to improve the package and its functionalities:",
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"\nhttps://msberends.github.io/AMR/survey.html",
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"\n[ prevent his notice with suppressPackageStartupMessages(library(AMR)) or use Sys.setenv(AMR_silentstart = TRUE) ]")
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}
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create_MO_lookup <- function() {
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MO_lookup <- AMR::microorganisms
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MO_lookup$kingdom_index <- 99
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MO_lookup[which(MO_lookup$kingdom == "Bacteria" | MO_lookup$mo == "UNKNOWN"), "kingdom_index"] <- 1
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MO_lookup[which(MO_lookup$kingdom == "Fungi"), "kingdom_index"] <- 2
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MO_lookup[which(MO_lookup$kingdom == "Protozoa"), "kingdom_index"] <- 3
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MO_lookup[which(MO_lookup$kingdom == "Archaea"), "kingdom_index"] <- 4
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# use this paste instead of `fullname` to work with Viridans Group Streptococci, etc.
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MO_lookup$fullname_lower <- tolower(trimws(paste(MO_lookup$genus,
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MO_lookup$species,
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MO_lookup$subspecies)))
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MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname), "fullname_lower"] <- tolower(trimws(MO_lookup[MO_lookup$genus == "" | grepl("^[(]unknown ", MO_lookup$fullname),
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"fullname"]))
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MO_lookup$fullname_lower <- gsub("[^.a-z0-9/ \\-]+", "", MO_lookup$fullname_lower)
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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)
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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$fullname_lower), ]
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}
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create_MO.old_lookup <- function() {
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MO.old_lookup <- AMR::microorganisms.old
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MO.old_lookup$fullname_lower <- 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 <- 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), ]
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}
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