How to import a data frame from R saved as RData into pandas?

Question

I am trying to import a data frame from R saved as RData into the pandas framework. How can i do this? I tried unsuccessfully to use rpy2 as follows:

import pandas as pd
from rpy2.robjects import r
from rpy2.robjects import pandas2ri
pandas2ri.activate()

# I use iris for convenience but I could have done r.load('my_data.RData')
print(r.data('iris'))
print(r['iris'].head())
print(type(r.data('iris')))

print(pandas2ri.ri2py_dataframe(r.data('iris')))
print(pandas2ri.ri2py(r.data('iris')))
print(pd.DataFrame(r.data('iris')))

outputs:

[1] "iris"

   Sepal.Length  Sepal.Width  Petal.Length  Petal.Width Species
1           5.1          3.5           1.4          0.2  setosa
2           4.9          3.0           1.4          0.2  setosa
3           4.7          3.2           1.3          0.2  setosa
4           4.6          3.1           1.5          0.2  setosa
5           5.0          3.6           1.4          0.2  setosa
<class 'rpy2.robjects.vectors.StrVector'>
   0  1  2  3
0  i  r  i  s
['iris']

I am using pandas 0.20.1 + python 3.6 x64 + Windows 7.

Answer 1

Generic data frame conversion is an expensive operation since copying is required for some types of columns. A local conversion rule might be better:

from rpy2.robjects import pandas2ri
from rpy2.robjects import default_converter
from rpy2.robjects.conversion import localconverter

print(r.data('iris'))
with localconverter(default_converter + pandas2ri.converter) as cv:
    pd_iris = r('iris')
# this is a pandas DataFrame
pd_iris

Otherwise, it only works for this purpose (Linux, the default chapter for the rpy2 branch):

import pandas as pd
from rpy2.robjects import r
from rpy2.robjects import pandas2ri
pandas2ri.activate()

pd_iris = r('iris')
pd_iris

, rpy2 Windows ( - rpy2 Windows).