Setup file for a fresh R install or new computer

setup.R

libraries <- c(
  "bear",
  "deSolve",
  "devtools",
  "dplyr",
  "formatR",
  "ggplot2",
  "gridExtra",
  "installr",
  "knitr",
  "lattice",
  "lme4",
  "MASS",
  "metafor",
  "metrumrg",
  "microbenchmark",
  "mvtnorm",
  "nlme",
  "nlmeODE",
  "npde",
  "pacman",
  "pander",
  "plyr",
  "psych",
  "reports",
  "reshape2",
  "roxygen2",
  "Rtools",
  "sas7bdat",
  "stargazer",
  "survival",
  "tidyr",
  "xpose4",
  "xtable"
)

install.packages(libraries)




### check.install function ###############################################

#still need to suppress warning message when trying to load package uninstalled
check.install <- function(libraries) {
  #check to see which libraries and depenedencies are installed by loading them
  inst <- lapply(libraries, require, character.only=T)
  if (any(inst != TRUE)) {
    notinst <- which(inst != TRUE)
    cat(c("Libraries: ", "\n", libraries[notinst], "\n", "were not installed correctly"))
    
  }
  else print("Everything installed!")
}




check.install(libraries)


### Detach loaded packages #####################################################
unload.packages <- function() {
pkgs <- names(sessionInfo()$otherPkgs)
unload.pkgs <- paste('package:', pkgs, sep = "")
lapply(unload.pkgs, detach, character.only = TRUE, unload = TRUE, force = TRUE)
}

unload.packages()


### testing check.install function ###

# test <- list(TRUE, FALSE, TRUE, TRUE, TRUE, FALSE)
# test2 <- list(TRUE, TRUE, TRUE, TRUE, TRUE, TRUE)
# testlib <- (letters[1:length(test)])
# 
# notinst <- which(test != TRUE)
# any(test != TRUE)
# print(testlib[notinst])
# cat(c("Libraries: ", "\n", testlib[notinst], "\n", "were not installed correctly"))


### install slidify ############################################################

library(devtools)
install_github('slidify', 'ramnathv')
install_github('slidifyLibraries', 'ramnathv')
install_github("dpastoor/PKPDmisc")
install_github("dpastoor/PKPDdatasets")


### install pandoc  #############################################################
library(installr)
installr()

#select pandoc from selection menu