mirror of
https://github.com/msberends/AMR.git
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55 lines
2.6 KiB
R
55 lines
2.6 KiB
R
# ==================================================================== #
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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://gitlab.com/msberends/AMR #
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# #
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# LICENCE #
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# (c) 2019 Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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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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# This R package was created for academic research and was publicly #
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# released in the hope that it will be useful, but it comes WITHOUT #
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# ANY WARRANTY OR LIABILITY. #
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# Visit our website for more info: https://msberends.gitlab.io/AMR. #
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# ==================================================================== #
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install_if_needed <- function(pkg, repos, quiet) {
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package_path <- find.package(pkg, quiet = quiet)
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if (length(package_path) == 0) {
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message("NOTE: pkg ", pkg, " missing, installing...")
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install.packages(pkg, repos = repos, quiet = quiet)
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}
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}
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gl_update_pkg_all <- function(repos = "https://cran.rstudio.com",
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quiet = TRUE,
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install_pkgdown = FALSE,
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install_lintr = FALSE) {
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# update existing
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update.packages(ask = FALSE, repos = repos, quiet = quiet)
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install_if_needed(pkg = "devtools", repos = repos, quiet = quiet)
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if (install_pkgdown == TRUE) {
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install_if_needed(pkg = "pkgdown", repos = repos, quiet = quiet)
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}
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if (install_lintr == TRUE) {
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install_if_needed(pkg = "lintr", repos = repos, quiet = quiet)
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}
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install_if_needed(pkg = "cleaner", repos = repos, quiet = quiet)
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devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
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cat("INSTALLED:\n")
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instld <- as.data.frame(installed.packages())
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rownames(instld) <- NULL
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print(instld[, c("Package", "Version")])
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return(invisible(TRUE))
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}
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