#' This script installs all required libraries automatically
#' Please install libraries manually if it was not possible to install an library automatically
#' Missing libraries are listed in missing_packages.txt
#' To install an library please use following two command:
#' install.packages("name of the missing library")
#' library("name of the missing library)

##################################################################################
######             Set parameters in this section manually                  ######
##################################################################################

#' Please set the directory of the present script as the working folder
#' Note: the path is denoted by forward slash "/"
setwd("D:/path/to/Rhea")


######                  NO CHANGES ARE NEEDED BELOW THIS LINE               ######
##################################################################################
######                             Main Script                              ###### 
##################################################################################
###################       Load all required libraries     ########################

# Check if required packages are already installed, and install if missing
packages <-c("ade4","GUniFrac","phangorn","cluster",
             "fpc","compare","plotrix","PerformanceAnalytics","reshape","ggplot2","gridExtra","grid","ggrepel",
             "gtable","Matrix","cowplot", "Hmisc","corrplot","clusterSim","PMCMRplus")

# Function to check whether the package is installed
InsPack <- function(pack)
{
  if ((pack %in% installed.packages()) == FALSE) {
    install.packages(pack,repos = "http://cloud.r-project.org/")
  } 
}



# Applying the installation on the list of packages
lapply(packages, InsPack)

# Make the libraries
lib <- lapply(packages, require, character.only = TRUE)
not_installed <- which(lib==FALSE)
missing_packages <- lapply(not_installed, function(x) print(packages[x]))


# Adding log file in analysis
sink(file = "missing_packages.txt")
cat ("***************************************","\n")
cat ("Please install following packages manually","\n")
cat (as.character(missing_packages))
sink()


#################################################################################
######                           End of Script                             ######
#################################################################################