Advanced User Guide

This website is designed to provide an interactive environment for learning and using basic statistics integrated with statistical software package R. It introduces a variety of statistical methods in scientific disciplines, and helps to develop the foundation of statistical data analysis via interactive approach. It should work immediately with Microsoft IE or Mozilla if you have Jave; it is available freely at http://www.java.com. If you are seeing a java applet properly below then you have it!

R is a language and environment for statistical computing and graphics, and is available as Free Software under the terms of the Free Software Foundation's GNU General Public License. CRAN R project has the most recent software packages for Unix, Linux, Windows, and Mac. If the java applet is successfully communicating with R remotely or locally, it should display the version of R running (R system variable R.version.string). Otherwise, it displays null, or other message, or nothing, and R is not currently available.

By default all the resources are set up remotely, and it is not necessary for you to have R on your local machine. It means, however, that you are entirely dependent on the service performed by the remote server. Alternatively, you can set it up locally as explained in the following:

Local configuration for off-line users. If you do not have R yet, the very first step is to download and install R into your own machine, which is usually done in a quick and easy single step. Once R is ready, you just need to make a few changes at your home directory to run R locally. Whether R will be communicated to a remote server or a local machine can be decided by a local configuration file if it exists and is readable at your machine. In Windows XP your home directory is something like ``C:\Documents and Settings\John Doe'', and the working directory is ``C:\Documents and Settings\John Doe\Desktop'', which is simply known as Desktop. The configuration file has to be saved with file name ``ISR-init.txt'' under user's Desktop. Here is an example of ISR-init.txt which requests the local execution of R:

rcmd = "C:/Program Files/R/rw1090/bin/R.exe CMD BATCH"  # Local R command
workdir = "../"                            # Directory for temporary files

Linux users: In Linux operating system home and working directory are the same and at the top of user account which is something like ``/home/john". Here the command ``/usr/bin/R CMD BATCH'' behaves differently from that in Windows. Instead you need a little script, say Rvanilla.sh, to run R locally:

rcmd = "/home/john/Rvanilla.sh"  # Local R command
workdir = "/tmp/"                # Directory for temporary files

Java security permission. It is important to know that the JRE's default security allows no network application to read, write, or execute any file on the client side unless the permission is explicitly granted by the user and written in .java.policy at the client's home directory (that is, at ``C:\Documents and Settings\John Doe'' in Windows XP). Here is an example of .java.policy which allows java applications at http://www.math.tntech.edu/ISR/ to execute (plus read/write) R on the client side:

grant codeBase "http://www.math.tntech.edu/eSTAT/-"
  permission java.security.AllPermission;

Copyright. TTU Department of Mathematics 2005 under the terms of GNU Free Documentation License. This website is designed to provide an experimental LATEX-based open-editing environment which can be generated and edited by anyone; currently editing is restricted. Ask mmachida@tntech.edu for the latest development including the entire collection of LaTeX, HTML, and java source code.

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