Get result to python variable after executing R script

Question

i am executing a r script from python and i want the output to be available in the python variable. how can i do that?

python script:

import subprocess 

def runR(id, lat, long):
    value = subprocess.popen("C:/R/R-3.2.0/bin/Rscript      E:/Personal/python/script.R --args "+id+" "+lat+" "+long , shell=True)
    print value

R script :

a = "Hello";

I want Hello to be availabe on the python variable value.

why not define the value variable by itself so it will be available for the session instead of in the function?> — Vamsi Prabhala
– Vamsi Prabhala, Commented Jul 13, 2015 at 15:02
Cheaters way: Run the program, write data to a local text file, then access that file from Python :P — rassa45
– rassa45, Commented Jul 13, 2015 at 15:38
That's how I once tried transferring info from Python to PHP/JavaScript — rassa45
– rassa45, Commented Jul 13, 2015 at 15:38
This SO post looks like it answers your question: stackoverflow.com/questions/4846891/… — sunny
– sunny, Commented Jul 13, 2015 at 15:48

jfs · Accepted Answer · 2015-07-15 17:55:57Z

4

You could use rpy2:

import rpy2.robjects as robjects

robjects.r('''
a = "Hello";
''')
a = robjects.r['a']

As an alternative, you could rewrite your R script so that it would dump its result to stdout in some well-known format such as json, then run it using subprocess module, and parse the result:

#!/usr/bin/env python
import json
import subprocess

id, lat, long = 1, 40, 74 
out = subprocess.check_output(r"C:\R\R-3.2.0\bin\Rscript.exe "
                              r"E:\path\to\script.R --args "
                               "{id} {lat} {long}".format(**vars()))
data = json.loads(out.decode('utf-8'))

Note: no need to use shell=True on Windows if you use the full path to the executable here.

edited Jul 15, 2015 at 17:55

answered Jul 14, 2015 at 23:18

jfs

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Comments

Sait · Accepted Answer · 2015-07-13 15:06:29Z

-1

You can modify the following example by your need.

a.py:

print 'hello'

b.py:

import subprocess
result = subprocess.check_output(["python", "a.py"])
print result.strip() + 'world'

Output of b.py:

helloworld

answered Jul 13, 2015 at 15:06

Sait

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2 Comments

user2728024 Over a year ago

r script is just an example that i gave. I need to execute the r code and get the answer in python

rassa45 Over a year ago

You could run the program, write all the data to a text file, then access that file from Python

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