Interoperability with pandas

This section of the documentation is focused on the practical use of the conversion helper for pandas. The conversion from and to pandas.DataFrame can create nonnegligible overhead as the C level representations for the underlying arrays may differ between Python and R, and this create the need to copy data from one representation to the other. This is the case for arrays of strings for example. The use of a local converter to limit the scope of conversions, as shown here, is recommended.

For more information about the conversion mechanism, check the more general documentation about rpy2.robjects.conversion.

Note

This section is available as a jupyter notebook pandas.ipynb (HTML render: pandas.html)

from functools import partial
from rpy2.ipython import html
html.html_rdataframe=partial(html.html_rdataframe, table_class="docutils")

R and pandas data frames

R data.frame and :class:pandas.DataFrame objects share a lot of conceptual similarities, and :mod:pandas chose to use the class name DataFrame after R objects.

In a nutshell, both are sequences of vectors (or arrays) of consistent length or size for the first dimension (the “number of rows”). if coming from the database world, an other way to look at them is column-oriented data tables, or data table API.

rpy2 is providing an interface between Python and R, and a convenience conversion layer between :class:rpy2.robjects.vectors.DataFrame and :class:pandas.DataFrame objects, implemented in :mod:rpy2.robjects.pandas2ri.

import pandas as pd
import rpy2.robjects as ro
from rpy2.robjects.packages import importr
from rpy2.robjects import pandas2ri

from rpy2.robjects.conversion import localconverter

From pandas to R

Pandas data frame:

pd_df = pd.DataFrame({'int_values': [1,2,3],
                      'str_values': ['abc', 'def', 'ghi']})

pd_df
int_values str_values
0 1 abc
1 2 def
2 3 ghi

R data frame converted from a pandas data frame:

with localconverter(ro.default_converter + pandas2ri.converter):
  r_from_pd_df = ro.conversion.py2rpy(pd_df)

r_from_pd_df
R/rpy2 DataFrame (3 x 2)
int_values str_values
... ...

The conversion is automatically happening when calling R functions. For example, when calling the R function base::summary:

base = importr('base')

with localconverter(ro.default_converter + pandas2ri.converter):
  df_summary = base.summary(pd_df)
print(df_summary)

['Min.   :1.0  ' '1st Qu.:1.5  ' 'Median :2.0  ' 'Mean   :2.0  '
 '3rd Qu.:2.5  ' 'Max.   :3.0  ' 'Length:3          ' 'Class :character  '
 'Mode  :character  ' NA_character_ NA_character_ NA_character_]

Note that a ContextManager is used to limit the scope of the conversion. Without it, rpy2 will not know how to convert a pandas data frame:

try:
  df_summary = base.summary(pd_df)
except NotImplementedError as nie:
  print('NotImplementedError:')
  print(nie)

NotImplementedError:
Conversion 'py2rpy' not defined for objects of type '<class 'pandas.core.frame.DataFrame'>'

From R to pandas

Starting from an R data frame this time:

r_df = ro.DataFrame({'int_values': ro.IntVector([1,2,3]),
                     'str_values': ro.StrVector(['abc', 'def', 'ghi'])})

r_df
R/rpy2 DataFrame (3 x 2)
int_values str_values
... ...

It can be converted to a pandas data frame using the same converter:

with localconverter(ro.default_converter + pandas2ri.converter):
  pd_from_r_df = ro.conversion.rpy2py(r_df)

pd_from_r_df
int_values str_values
1 1 abc
2 2 def
3 3 ghi

Date and time objects

pd_df = pd.DataFrame({
    'Timestamp': pd.date_range('2017-01-01 00:00:00', periods=10, freq='s')
    })

pd_df
Timestamp
0 2017-01-01 00:00:00
1 2017-01-01 00:00:01
2 2017-01-01 00:00:02
3 2017-01-01 00:00:03
4 2017-01-01 00:00:04
5 2017-01-01 00:00:05
6 2017-01-01 00:00:06
7 2017-01-01 00:00:07
8 2017-01-01 00:00:08
9 2017-01-01 00:00:09 
with localconverter(ro.default_converter + pandas2ri.converter):
  r_from_pd_df = ro.conversion.py2rpy(pd_df)

r_from_pd_df
R/rpy2 DataFrame (10 x 1)
Timestamp
...

The timezone used for conversion is the system’s default timezone unless pandas2ri.default_timezone is specified… or unless the time zone is specified in the original time object:

pd_tz_df = pd.DataFrame({
    'Timestamp': pd.date_range('2017-01-01 00:00:00', periods=10, freq='s',
                               tz='UTC')
    })

with localconverter(ro.default_converter + pandas2ri.converter):
  r_from_pd_tz_df = ro.conversion.py2rpy(pd_tz_df)

r_from_pd_tz_df
R/rpy2 DataFrame (10 x 1)
Timestamp
...