mirror of
https://github.com/msberends/AMR.git
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96 lines
4.5 KiB
R
96 lines
4.5 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, the Netherlands, in #
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# collaboration with non-profit organisations Certe Medical #
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# Diagnostics & Advice, and University Medical Center Groningen. #
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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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# some old R instances have trouble installing tinytest, so we ship it too
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install.packages("data-raw/tinytest_1.3.1.tar.gz", dependencies = c("Depends", "Imports", "LinkingTo"))
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install.packages(getwd(), repos = NULL, type = "source")
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pkg_suggests <- gsub(
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"[^a-zA-Z0-9.]+", "",
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unlist(strsplit(unlist(packageDescription("AMR",
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fields = c("Suggests", "Enhances", "LinkingTo")
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)),
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split = ", ?"
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))
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)
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pkg_suggests <- unname(pkg_suggests[!is.na(pkg_suggests)])
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cat("################################################\n")
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cat("Packages listed in Suggests/Enhances:", paste(pkg_suggests, collapse = ", "), "\n")
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cat("################################################\n")
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if (.Platform$OS.type != "unix") {
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# no compiling on Windows here
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options(install.packages.compile.from.source = FALSE)
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}
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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
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if (length(to_install) == 0) {
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message("\nNothing to install\n")
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}
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i],
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type = "source",
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repos = "https://cran.rstudio.com/",
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dependencies = c("Depends", "Imports", "LinkingTo"),
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quiet = FALSE
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),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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if (.Platform$OS.type != "unix" && !to_install[i] %in% rownames(utils::installed.packages())) {
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tryCatch(install.packages(to_install[i],
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type = "binary",
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repos = "https://cran.rstudio.com/",
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dependencies = c("Depends", "Imports", "LinkingTo"),
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quiet = FALSE
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),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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}
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}
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to_update <- as.data.frame(utils::old.packages(repos = "https://cran.rstudio.com/"), stringsAsFactors = FALSE)
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to_update <- to_update[which(to_update$Package %in% pkg_suggests), "Package", drop = TRUE]
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if (length(to_update) == 0) {
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message("\nNothing to update\n")
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}
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for (i in seq_len(length(to_update))) {
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cat("Updating package '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message)
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)
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cat("Updated to '", to_update[i], "' v", as.character(packageVersion(to_update[i])), "\n", sep = "")
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}
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