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05_install_packages.R
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05_install_packages.R
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# The aim of this code is to install the required packages
# with the version specified
# Package names
packages <- c("data.table",
"ggplot2",
"cowplot",
"readxl",
"knitr",
"stringr",
"here",
"magrittr",
"RColorBrewer",
"git2r",
"getPass",
"devtools",
"flextable",
"bookdown",
"viridis",
"rmarkdown",
"TTR",
"boot",
"VGAM",
"readr",
"writexl",
"Rfast",
"dvmisc",
"fastmatch",
"dplyr",
"plyr",
"openxlsx",
"mice",
"Hmisc",
"nnet",
"ggthemes",
"shiny",
"DT",
"shinythemes",
"ragg")
# Install packages not yet installed
installed_packages <- packages %in% rownames(installed.packages())
if (any(installed_packages == FALSE)) {
#install.packages(packages[!installed_packages], type = "source", INSTALL_opts = "--byte-compile")
install.packages(packages[!installed_packages], lib = project_lib)
#install.packages(packages[!installed_packages])
}
###########################
# STAPM packages
# Your gitlab username
uname <- ""
devtools::install_git(
"https://github.com/stapm/hseclean.git",
ref = "1.11.3",
build_vignettes = FALSE, lib = project_lib, quiet = TRUE)
#
# devtools::install_git(
# "https://gitlab.com/stapm/r-packages/tobalcepi.git",
# credentials = git2r::cred_user_pass(uname, getPass::getPass()),
# ref = "1.6.5",
# build_vignettes = FALSE, quiet = TRUE)
devtools::install_git(
"https://github.com/stapm/tobalcepi.git",
build_vignettes = FALSE, quiet = TRUE)
devtools::install_git(
"https://gitlab.com/stapm/r-packages/stapmr.git",
credentials = git2r::cred_user_pass(uname, getPass::getPass()),
ref = "1.9.3",
build_vignettes = FALSE, quiet = TRUE)