aberezin R packages installed

installPackages.R

#These are the packages I use in R

update.packages(ask=FALSE)
install.packages('RPostgreSQL') 
install.packages('RMySQL')
install.packages('RJDBC') #Need JDBC driver, for example Merlia.jar
install.packages('maptools')
install.packages('MBA')
install.packages('sp')
install.packages('ggplot2')
install.packages('spatstat')
install.packages('geosphere')
install.packages('lattice')
install.packages('image2lz') #image cropping for example
install.packages('fields')
install.packages("sqldf", dep = TRUE)
install.packages('scales')
install.packages('knitr')
install.packages('geosphere')  #great for distance and area calculation
install.packages('zipcode')
install.packages('devtools')
install.packages('yaml',type='source') #at the time, the binary was old
install_github('rCharts', 'ramnathv') #at the time, yaml had to be installed separtely from source
install.packages("RJSONIO")
install.packages("RCurl")
install_github("plotly/R-api")  #in beta
install.packages('directlabels')
install.packages('gridExtra')
install.packages('RTextTools')
install.packages("yhatr")	#runs R in the cloud.  Nice alternative to your own Rserver
install.packages('reshape')
install.packages('lubridate') #Improved date manipulation
install.packages('googleVis') #googleVisualization
install.packages('GGally') #generalized pairs plotting. Nice for 1st pass understanding of data.


####################################
#  BELOW THIS LINE ARE NONTRIVIAL INSTALLS. They vary by OS, require complilation, etc.   
####################################


#The following installs rpud based on r-tutor.com on osx-10.9 with an nvidia card and nvidia cuda installed.
install.packages(c(" coda", "SparseM"))
#note however that it wants you to do this
#    R CMD INSTALL rpud_ < version >. tar.gz
# but you need to do this first because osx maverick xtools no longer supports llvm-gcc and only supports clang
# which is incompatible with nvcc which is whaßt the INSTALL script will use
#   sudo port install llvm-gcc42
#   sudo port select --set gcc mp-llvm-gcc42
 

source("http://www.bioconductor.org/biocLite.R")
biocLite("pcaMethods")

install.packages('rgeos') #maptools likes this package installed
#install.packages('gpclib') #polygon clipping is good but restrictive license.

#For tutorial, see http://www.nceas.ucsb.edu/scicomp/usecases/ReadWriteESRIShapeFiles
install.packages('rgdal')  #note for OSX below


# install GDAL 1.9 Complete from http://www.kyngchaos.com/software:frameworks
# download rgdal package src rgdal_0.7-8.tar.gz  from http://cran.r-project.org/web/packages/rgdal/index.html
# make sure the mac developer tools are up to date
# R64 CMD install --configure-args='--with-gdal-config=/Library/Frameworks/GDAL.framework/unix/bin/gdal-config --with-proj-include=/Library/Frameworks/PROJ.framework/unix/include --with-proj-lib=/Library/Frameworks/PROJ.framework/unix/lib' rgdal_0.7-8.tar.gz
# Note: you may also need --no-multiarch for the above install

# Install DIRlib locally. Note below on OSX
# r64 CMD INSTALL --no-multiarch  DIRLib
# You prob dont need the --no-multiarch if you only installed the 64b R
# see also http://www.compmath.com/blog/2010/07/installing-package-on-mac-os-x/

#If you want rgl
#download http://download.r-forge.r-project.org/src/contrib/rgl_0.92.879.tar.gz 
#R64 CMD INSTALL --with-libpng-prefix=/usr/X11/lib/ rgl