mirror of
https://github.com/msberends/AMR.git
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96 lines
3.9 KiB
R
96 lines
3.9 KiB
R
# ==================================================================== #
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# TITLE #
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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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# 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 and the University Medical #
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# Center Groningen in The Netherlands, in collaboration with many #
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# colleagues from around the world, see our website. #
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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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# 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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# #
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# Visit our website for the full manual and a complete tutorial about #
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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# ==================================================================== #
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# Run this file to update the languages used in the packages:
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# source("data-raw/_language_update.R")
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if (!file.exists("DESCRIPTION") || !"Package: AMR" %in% readLines("DESCRIPTION")) {
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stop("Be sure to run this script in the root location of the AMR package folder.\n",
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"Working directory expected to contain the DESCRIPTION file of the AMR package.\n",
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"Current working directory: ", getwd(),
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call. = FALSE
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)
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}
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# save old global env to restore later
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lang_env <- new.env(hash = FALSE)
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# load current internal data into new env
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load("R/sysdata.rda", envir = lang_env)
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# replace language objects with updates
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message("Reading translation file...")
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lang_env$TRANSLATIONS <- utils::read.delim(
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file = "data-raw/translations.tsv",
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sep = "\t",
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stringsAsFactors = FALSE,
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header = TRUE,
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blank.lines.skip = TRUE,
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fill = TRUE,
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strip.white = TRUE,
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encoding = "UTF-8",
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fileEncoding = "UTF-8",
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na.strings = c(NA, "", NULL),
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allowEscapes = TRUE, # else "\\1" will be imported as "\\\\1"
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quote = ""
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)
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lang_env$LANGUAGES_SUPPORTED_NAMES <- c(
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list(en = list(exonym = "English", endonym = "English")),
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lapply(
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lang_env$TRANSLATIONS[, which(nchar(colnames(lang_env$TRANSLATIONS)) == 2), drop = FALSE],
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function(x) list(exonym = x[1], endonym = x[2])
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)
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)
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lang_env$LANGUAGES_SUPPORTED <- names(lang_env$LANGUAGES_SUPPORTED_NAMES)
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# save env to internal package data
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# usethis::use_data() does not allow to save a list :(
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message("Saving to internal data...")
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save(
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list = names(lang_env),
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file = "R/sysdata.rda",
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ascii = FALSE,
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version = 2,
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compress = "xz",
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envir = lang_env
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)
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rm(lang_env)
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if ("roxygen2" %in% utils::installed.packages()) {
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message("Updating package documentation...")
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suppressMessages(roxygen2::roxygenise(package.dir = "."))
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} else {
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message("NOTE: please install the roxygen2 package to update package documentation, and run this script again.")
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}
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message("Done!")
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