2019-01-11 20:37:23 +01:00
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# ==================================================================== #
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# TITLE #
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2021-02-02 23:57:35 +01:00
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# Antimicrobial Resistance (AMR) Data Analysis for R #
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2019-01-11 20:37:23 +01:00
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# #
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# SOURCE #
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2020-07-08 14:48:06 +02:00
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# https://github.com/msberends/AMR #
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2019-01-11 20:37:23 +01:00
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# #
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# LICENCE #
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2020-12-27 00:30:28 +01:00
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# (c) 2018-2021 Berends MS, Luz CF et al. #
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2020-10-08 11:16:03 +02:00
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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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2019-01-11 20:37:23 +01:00
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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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2020-01-05 17:22:09 +01:00
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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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2020-10-08 11:16:03 +02:00
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# #
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# Visit our website for the full manual and a complete tutorial about #
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2021-02-02 23:57:35 +01:00
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# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
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2019-01-11 20:37:23 +01:00
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# ==================================================================== #
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2021-05-15 21:54:56 +02:00
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pkg_suggests <- AMR:::trimws(unlist(strsplit(packageDescription("AMR")$Suggests, ",(\n)?")))
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2019-01-11 20:37:23 +01:00
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2021-05-15 21:36:22 +02:00
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to_install <- pkg_suggests[!pkg_suggests %in% rownames(utils::installed.packages())]
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to_update <- as.data.frame(old.packages(), stringsAsFactors = FALSE)
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2019-01-11 20:37:23 +01:00
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2021-05-15 21:36:22 +02:00
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for (i in seq_len(length(to_install))) {
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cat("Installing package", to_install[i], "\n")
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tryCatch(install.packages(to_install[i], repos = "https://cran.rstudio.com/", dependencies = TRUE, quiet = TRUE),
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2021-05-15 22:35:57 +02:00
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# message = function(m) invisible(),
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2021-05-15 21:36:22 +02:00
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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2019-01-29 00:06:50 +01:00
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2021-05-15 21:36:22 +02:00
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for (i in seq_len(length(to_update))) {
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cat("Updating package", to_install[i], "\n")
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tryCatch(update.packages(to_update[i], repos = "https://cran.rstudio.com/", ask = FALSE),
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2021-05-15 22:35:57 +02:00
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# message = function(m) invisible(),
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2021-05-15 21:36:22 +02:00
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warning = function(w) message(w$message),
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error = function(e) message(e$message))
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}
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2019-06-27 11:57:45 +02:00
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2021-05-15 21:36:22 +02:00
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# saveRDS(to_update, ".github/depends.Rds", version = 2)
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