Calling R script from python using rpy2

问题:

I'm very new to rpy2, as well as R.

I basically have a R script, script.R, which contains functions, such as rfunc(folder). It is located in the same directory as my python script. I want to call it from Python, and then launch one of its functions. I do not need any output from this R function. I know it must be very basic, but I cannot find examples of R script-calling python codes. What I am currently doing, in Python:

import rpy2.robjects as robjects

def pyFunction(folder):
    #do python stuff 
    r=robjects.r
    r[r.source("script.R")]
    r["rfunc(folder)"]
    #do python stuff

pyFunction(folder)

I am getting an error on the line with source:

r[r.source("script.R")] File "/usr/lib/python2.7/dist-packages/rpy2/robjects/__init__.py", line 226, in __getitem__ res = _globalenv.get(item) TypeError: argument 1 must be string, not ListVector

I quite do not understand how the argument I give it is not a string, and I guess the same problem will then happen on the next line, with folder being a python string, and not a R thingie.

So, how can I properly call my script?

回答1:

source is a r function, which runs a r source file. Therefore in rpy2, we have two ways to call it, either:

r['source']("script.R")

or

r.source("script.R")

r[r.source("script.R")] is a wrong way to do it.

Same idea may apply to the next line.

回答2:

Rpy2 can let you turn an R script defining functions and other objects into a Python namespace:

http://rpy.sourceforge.net/rpy2/doc-2.4/html/robjects_rpackages.html#importing-arbitrary-r-code-as-a-package