Use rpy2 with pandas dataframe

Question

I want to aplly some R function to a pandas dataframe

df = pd.DataFrame( np.random.randn(5,2), # 5 rows, 2 columns
               columns = ["A","B"], # name of columns
               index = ["Max", "Nathy", "Tom", "Joe", "Kathy"] )

How can I apply for example the summary dunction from R?

I have the following code:

import numpy as np
import pandas as pd

import rpy2
# print(rpy2.__version__) ## 2.9.4

from rpy2.rinterface import R_VERSION_BUILD
# print(R_VERSION_BUILD) ## ('3', '5.1', '', 74947)

from rpy2.robjects.packages import importr
# import R's "base" package
base = importr('base')

Answer 1

You are almost there. In order to run R functions, you need to convert the pandas Dataframe to R Dataframe. Once we have the R object we can call the functions as shown below.

import rpy2
from rpy2.robjects.packages import importr # import R's "base" package
base = importr('base')

from rpy2.robjects import pandas2ri # install any dependency package if you get error like "module not found"
pandas2ri.activate()

# Create pandas df
df = pd.DataFrame( np.random.randn(5,2), # 5 rows, 2 columns
               columns = ["A","B"], # name of columns
               index = ["Max", "Nathy", "Tom", "Joe", "Kathy"] )

# Convert pandas to r
r_df = pandas2ri.py2ri(df)
type(r_df)

#calling function under base package
print(base.summary(r_df))