mirror of https://github.com/msberends/AMR.git
57 lines
2.4 KiB
R
57 lines
2.4 KiB
R
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# ==================================================================== #
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# TITLE #
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# Antimicrobial Resistance (AMR) Analysis #
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# #
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# AUTHORS #
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# Berends MS (m.s.berends@umcg.nl), Luz CF (c.f.luz@umcg.nl) #
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# #
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# LICENCE #
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# This package is free software; you can redistribute it and/or modify #
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# it under the terms of the GNU General Public License version 2.0, #
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# as published by the Free Software Foundation. #
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# #
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# This R package is distributed in the hope that it will be useful, #
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# but WITHOUT ANY WARRANTY; without even the implied warranty of #
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# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
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# GNU General Public License version 2.0 for more details. #
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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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# 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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devtools::install_dev_deps(repos = repos, quiet = quiet, upgrade = TRUE)
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cat("\nINSTALLED:\n\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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# which ones are needed now?
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# pkg_needed <-
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# if (length(pkg_needed) > 0) {
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# # install them
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# for (i %in% 1:length(pkg_needed)) {
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# install_if_needed(pkg = pkg_needed[i], repos = repos, quiet = quiet)
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# }
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# }
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}
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