Where do I start with rJava?
I am not a Java programmer. I program R and C++. I have some java code that I want to include in an R package. The basics of the program are this:
- Read data from standard input.
- Run a MCMC chain.
- output to a file.
I want to convert this to R where I can run the program from R. I am familiar with Rcpp package and am used to some of the conveniences of it. Where do I start with the rJava package to learn to use this code.
Specifically i ha开发者_运维技巧ve the following questions.
- How to I transfer data to java from R, e.g. numeric vector, factor, etc.
- How do I run methods of a class?
- How do I include java code in a package?
The rJava documentation is not very helpful. Does anyone have a tutorial on this?
There's a "simple" way to do this and a somewhat harder way to do this. I'm a simple man so I lean toward the simple solution:
myCommand <- paste("/path/to/java", argument1, argument2, sep=" ")
system(shQuote(myCommand))
Then read in the output file using whatever R function makes sense.
The somewhat harder solution is to edit your Java code so it doesn't read from stdin, but gets passed a vector, or other Java object. I can't really generalize about how to alter your Java code, but if the Java function ultimately needs to be fed a vector, you'd do it something like this:
.jinit()
v <- .jnew("java/util/Vector")
rVector <- as.character(1:10)
addToV <- function( item ){
v$add( item )
}
sapply(rVector, addToV)
I always find dealing with types in rJava to be a considerable pain, as you can see above.
One tip that will save you considerable time is this: When you have a Java object created in rJava you can figure out its methods by typing the name, a dollar sign, and then hit tab. So using the v object created above type "v$" and you should get this:
1> v$
v$add( v$hashCode() v$contains( v$size() v$elementAt( v$capacity() v$containsAll( v$firstElement() v$removeElement( v$iterator() v$wait()
v$get( v$clone() v$isEmpty() v$toArray() v$remove( v$ensureCapacity( v$removeAll( v$insertElementAt( v$removeElementAt( v$listIterator() v$getClass()
v$equals( v$indexOf( v$lastIndexOf( v$toArray( v$elements() v$trimToSize() v$retainAll( v$lastElement() v$setElementAt( v$listIterator( v$notify()
v$toString() v$clear() v$addAll( v$addElement( v$set( v$subList( v$copyInto( v$removeAllElements() v$setSize( v$wait( v$notifyAll()
1> v$
Good luck, and be sure and yell if you have specific snags.
This is covered in the Deducer plug-in development document. While it is geared towards packages extending Deducer, some sections are general.
Running java methods in R: http://www.deducer.org/pmwiki/pmwiki.php?n=Main.Development#wwjoir
Bringing R objects into java and creating a package with java code: http://www.deducer.org/pmwiki/pmwiki.php?n=Main.Development#suaptijc
Full disclosure: Deducer is my project.
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