Using R functions in python

Question

I am an avid python user. I have been programming and performing a lot of my statistics using R. Recently, I tried to go into one of my notebooks to perform some statistical analysis. I have written over 5000 lines of code. Now, I have used R functions scattered everywhere throughout my program. Unfortunately, I am unable to even use any of the functions i have written before.

This is what i have done before:

%load_ext rmagic
import rpy2.robjects as R
import pandas.rpy.common as com
from rpy2.robjects.packages import importr
import scipy.stats as sp
stats=importr('stats')
TSA = importr('TSA')
forecast = importr('forecast')
fUnitRoots = importr('fUnitRoots')
tseries = importr('tseries')
urca = importr('urca')
VARS = importr('vars')
zoo = importr('zoo')
aod = importr('aod')

Now, I can't even run any of this any more as i get an import error "r_magic extension has been moved".

Also, i have called R functions by doing the following:

%R acf(x)

Above statement no longer works.

But if i do....

R.r('acf(x)')

it works. This seems like an annoying change i have to incorporate in my large program. Is there a workaround towards this solution?

Thanks

my ipython notebook has upgraded to jupyter automatically. Ever since the change, nothing seems to work as before. I followed the example online on how to call R functions in python. It seems like the %R command doesn't work anymore in ipython. I have just went ahead with the online example and it works now. But now i have another issue which i am going to raise in the next question — Rajan S.
– Rajan S., Commented Aug 6, 2015 at 16:33
This is the problem i am running into now: df = com.load_data('mtcars') rdf2 = com.convert_to_r_dataframe(df) robj.globalenv[ — Rajan S.
– Rajan S., Commented Aug 6, 2015 at 16:39
This is the problem i am running into now: df = com.load_data('mtcars') rdf2 = com.convert_to_r_dataframe(df) robj.globalenv['rdf2'] = rdf2 robj.r('y=ts(rdf2)') fit_full = fGarch.garchFit('~1+garch(1,1),data=y,trace=F) For some reason, this gives me errors. "missing value where True/False needed — Rajan S.
– Rajan S., Commented Aug 6, 2015 at 18:20

lgautier · Accepted Answer · 2015-08-06 23:01:51Z

1

The rmagic is now in rpy2. Do: %load_ext rpy2.ipython

answered Aug 6, 2015 at 23:01

lgautier

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