how to call a function from R in Python?

Question

I have this function in R and I want to call it in python. I am planning to assign the data which has been manipulated in python to the R function to do further analysis on it. I also need to have the data back to python after the function did the analysis. I know about rpy2 and I used this command

robjects.r('''source('mycode.R')''')
r_test_function = robjects.globalenv['myFunction']

I get this error:

/usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: Error in file(filename, "r", encoding = encoding) :
cannot open the connection

warnings.warn(x, RRuntimeWarning) /usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: In addition: warnings.warn(x, RRuntimeWarning) /usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: Warning message:

warnings.warn(x, RRuntimeWarning) /usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: In file(filename, "r", encoding = encoding) :
warnings.warn(x, RRuntimeWarning) /usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning:

warnings.warn(x, RRuntimeWarning) /usr/local/lib/python2.7/dist-packages/rpy2/rinterface/init.py:186: RRuntimeWarning: cannot open file 'mycode.R': No such file or directory

warnings.warn(x, RRuntimeWarning) Info | ____________________________________________________________________________________________________| Error | Termination with exception status| Error

I used the sys.path.append('thePath') for the directory containing the function. Can someone please help me about this? I have searched a lot about the topic but I could not find anything in my case. Also is what I explained above practical with rpy2?

Thank you,

Does the error happen on your first line or your second line? What's in the file you are sourceing? What's bfast.R? Do you get errors doing basic rpy stuff? — Spacedman
– Spacedman, Commented Aug 30, 2017 at 8:18
I edited the error, the bfast.R is the same as mycode.R. There are multiple R functions in the file I am referring to. Yes, I tried other simple functions, still the same error. — K S
– K S, Commented Aug 30, 2017 at 8:37
Does the error happen on your first line or your second line? What folder did Python start from? Where is the R file in your file system? What do you get if you run getwd() from Rpy2? That's R's working directory. What about file.exists('mycode.R')? That tells you if the file exists. — Spacedman
– Spacedman, Commented Aug 30, 2017 at 14:31

Sagar Dawda · Accepted Answer · 2017-08-30 08:02:17Z

0

Is your concern is getting the full directory path? I am currently working on Python 3.6 to browse through all files in directory and list them. Since you want to work with just one specific file, you could try the following:

import os

file = os.path.abspath(''F:\Training.xlsx'') so your file variable witll look like 'F:\Training.xlsx'

You could simply use the variable file instead of entering the whole directory path.

Hope it helps.

answered Aug 30, 2017 at 8:02

Sagar Dawda

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1 Comment

K S Over a year ago

Hey Sagar, thank you for your reply. I am new to python. I tried your suggestion. Still getting the same error.

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