mirror of https://github.com/msberends/AMR.git
58 lines
3.2 KiB
R
58 lines
3.2 KiB
R
# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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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) 2018-2021 Berends MS, Luz CF et al. #
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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_1.2.4.10.tar.gz")
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install.packages("data-raw/AMR_latest.tar.gz", dependencies = FALSE)
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install.packages("covr")
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pkg_suggests <- gsub("[^a-zA-Z0-9]+", "", unlist(strsplit(packageDescription("AMR", fields = "Suggests"), ", ?")))
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cat("Packages listed in Suggests:", paste(pkg_suggests, collapse = ", "), "\n")
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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], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
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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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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$Package %in% pkg_suggests), "Package", drop = TRUE]
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if (length(to_update) == 0) {
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message("\nNothing to update\n")
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}
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for (i in seq_len(length(to_update))) {
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cat("Updating package", to_update[i], "\n")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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# message = function(m) invisible(),
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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