R: Introduction to statistics and R-Studio

This post will describe some of the common operations of the R statistical package.

Assuming you have installed R on your linux machine.

Step 1: Create a work directory.

 $ mkdir R_Work

$ cd R_Work/

Step 2: Let us invoke "R".

$ R

R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-redhat-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> q()


Basically to quit R, you need to type in q()

Step 3:  Install R-Studio for your Operating System

http://www.rstudio.org/

$>rstudio

Step 4:  Install rJava

It is very important that you get the following command right.

Run as Root

 # sudo R CMD javareconf JAVA=/usr/lib/jvm/java-1.6.0-openjdk-1.6.0.0.x86_64/jre/bin/java JAVA_HOME=/usr/java/latest JAVAC=/usr/java/latest/bin/javac JAR=/usr/java/latest/bin/jar JAVAH=/usr/java/latest/bin/javah

In this case, we are trying to tell R where the OpenJDK java executable is.  You also want to point to locations where your javac, javah and jar executables are available.

Now we are ready to install rJava

# R

> install.packages("rJava")
Installing package(s) into ‘/usr/lib64/R/library’
(as ‘lib’ is unspecified)
--- Please select a CRAN mirror for use in this session ---
Loading Tcl/Tk interface ... done
.....

* DONE (rJava)
Making packages.html  ... done

The downloaded source packages are in
    ‘/tmp/RtmpwsCz85/downloaded_packages’
Updating HTML index of packages in '.Library'
Making packages.html  ... done
>

This was very painful for me. Took me about 20mins to get it right.

By the way, there is a thread that may be useful to you: 

http://r.789695.n4.nabble.com/rjava-JDK-not-found-td889163.html

Error I was getting was:

Make sure R is configured with full Java support (including JDK). Run
R CMD javareconf
as root to add Java support to R. 

Reference

http://cran.r-project.org/doc/manuals/R-intro.html

http://svn.r-project.org/R/trunk/src/scripts/javareconf