Mathematica 9 Linking with R

Question

I would like to run a batch job from within the current Mathematica .m file using "R CMD BATCH &" (the job runs in the background when Mathematica proceeds with the current calculations. How can I do that in Mathematica 9?

Answer 1

Here is a possible RLink - based solution. I will use Windows version, since it is easiest for me right now to test on Windows, but it should work on other platforms as well with a few obvious modifications.

First, here is a sample Mathematica script I used to test:

Needs["RLink`"]
InstallR[]

Pause[10]

REvaluate["{
     testdata <- rnorm(100)
     dim(testdata)<-c(10,10)     
     write.table(testdata,\"C:/Temp/testRdata.dat\")
}"]

Quit

which I stored in C:\\Temp\\script.m. The R code inside models your batch script code. The Pause[10] models some running time for the batch script. Now, here is what you do:

Needs["JLink`"];
InstallJava[];
LoadJavaClass["java.lang.Runtime"]

and then

Runtime`getRuntime[]@
   exec[{
      FileNameJoin[{$InstallationDirectory, "math.exe"}], 
      "-script", 
      "\"C:\\Temp\\script.m\""}
   ]

This launches a separate process, which would execute the Mathematica script in C:\\Temp\\script.m, which, in turn, will load RLink and execute your R batch script.

This code returns immedaitely, so that your main kernel is not blocked, and you can compute with it regardless of whether or not the batch job has completed.

In fact, while I did not do it here, this can be further automated,so that you run your batch script from within Mathematica, first saving it to a temporary file. I may add this automation layer later.