Calling Custom functions from Python using rpy2

Question

Is there a way to call functions defined in a file say myfunc.r

---------------myfunc.r --------------
myfunc = function(){
  return(c(1,2,3,4,5,6,7,8,9,10)         


        

Answer 1

I'd suggest to use what user3282437 suggested here:

import rpy2.robjects as robjects
r_source = robjects.r['source']
r_source('/path_to_file/myfunc.R')
r_getname = robjects.globalenv['getname']

I'm not sure that it's a global issue, but on my Windows machine direct call like agstudy advised:

import rpy2.robjects as robjects
robjects.r('source("some_file.R")')

leads to python crash.

Answer 2

There are features in rpy2 that should help making this cleaner than dumping objects into the global workspace.

from rpy2.robjects.packages import STAP
# if rpy2 < 2.6.1 do:
# from rpy2.robjects.packages import SignatureTranslatedAnonymousPackage
# STAP = SignatureTranslatedAnonymousPackage
with open('myfunc.r', 'r') as f:
    string = f.read()
myfunc = STAP(string, "myfunc")

The objects in the R file can now be accessed with myfunc.myfunc and myfunc.getname.

Check the documention about importing arbitrary R code as a package (older doc here).

Answer 3

You can do something like this ( python code here)

import rpy2.robjects as robjects
robjects.r('''
       source('myfunc.r')
''')

 r_getname = robjects.globalenv['getname']

then you call it

r_getname()