R script and instructions to install commonly used R packages and instructions for using OpenBLAS on OS X via Homebrew Raw

Install_R.R

##############################################################################
# title         : InstallPackages.R;
# purpose       : install R packages commonly used by Adam H.Sparks when upgrading or installing R;
# producer      : prepared by A. H. Sparks;
# last update   : in Los Baños, Laguna, PHL, May 2015;
# inputs        : none;
# outputs       : none;
# remarks 1     : in order to download any packages, you need to be on-line, of course;
# remarks 2     : for country outlines and the like see http://www.gadm.org/ to download Rdata packages;
##############################################################################

setRepositories() #select amongst repositories that the R installation is aware of OMEGAHAT is necessary for RKML, etc.

install.packages("ctv", dep = TRUE) #CRAN Task Views
library(ctv) #load ctv library

install.views("Spatial") #spatial analysis
install.packages("gpclib", dep = TRUE)
install.views("Graphics") #Graphic Displays & Dynamic Graphics & Graphic Devices & Visualization
install.views("Environmetrics") #analyse ecological and environmental data

#packages necessary for work that are not included in the CTV
install.packages("doMC", dep = TRUE) #multicore support
install.packages("debug", dep = TRUE) #debug package for step through of functions
install.packages("RCurl", dep = TRUE) #RCurl for fetching data remotely
install.packages("R2HTML", dep = TRUE)
install.packages("RKML", dep = TRUE) #high-level facilities to generate KML for display in Googleearth
install.packages("RKMLDevice", dep = TRUE)
install.packages("RODBC", dep = TRUE)
install.packages("dismo", dep = TRUE)
install.packages("tableplot", dep = TRUE)
install.packages("doBy", dep = TRUE)
install.packages("lubridate", dep = TRUE)
install.packages("sqldf", dep = TRUE)

#cropsim packages
install.packages("cropsim") #Enable R-forge repository first

#packages for big dataset handling
install.packages("data.table", dep = TRUE)
install.packages("biglm", dep = TRUE)
install.packages("biganalytics", dep = TRUE)
install.packages("biglars", dep = TRUE)
install.packages("speedglm", dep = TRUE)

#use ttf and other fonts in graphs
install.packages("extrafont", dep = TRUE)
library(extrafont)
font_import()
loadfonts()

#tools for tidying model outputs
install.packages("broom", dep = TRUE)

#tools for visulazation
devtools::install_github("daattali/ggExtra")
install.packages("gridExtra")

# Tools for network analysis
source("http://bioconductor.org/biocLite.R")
biocLite("impute")
install.packages("WGCNA")

# Color palletes
install.packages("wesanderson", dep = TRUE)

# In order to change which BLAS is used, change the libRblas.dylib symlink
# Option 1 for using openBLAS
cd /Library/Frameworks/R.framework/Resources/lib
sudo rm libRblas.dylib
brew tap homebrew/science
brew install openblas
ln -sf /usr/local/Cellar/openblas/0.2.14_1/lib/libopenblas.dylib /Library/Frameworks/R.framework/Resources/lib/libRblas.dylib

#Option 2 - install r with openblas through homebrew
brew tap homebrew/dupes
brew install tcl-tk --with-tk

ln -s /usr/local/Cellar/tcl-tk/8.6.1/lib/libtcl8.6.dylib /usr/local/lib/libtcl8.6.dylib
ln -s /usr/local/Cellar/tcl-tk/8.6.1/lib/libtk8.6.dylib /usr/local/lib/libtk8.6.dylib

brew tap homebrew/science
brew install r --with-openblas

#eos