Interoperability with pandas — rpy2 3.5.13 documentation (original) (raw)

This section of the documentation is focused on the practical use of the conversion helper for pandas. The conversion from and to pandas.DataFramecan 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.

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 nameDataFrame 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 pandas to R¶

Pandas data frame:

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

pd_df

R data frame converted from a pandas data frame:

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

r_from_pd_df

R/rpy2 DataFrame (3 x 2)

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

base = importr('base')

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

int_values str_values Min. :1.0 Length:3 1st Qu.:1.5 Class :character Median :2.0 Mode :character Mean :2.0 3rd Qu.:2.5 Max. :3.0

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)

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

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

pd_from_r_df

Date and time objects¶

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

pd_df

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

r_from_pd_df

R/rpy2 DataFrame (10 x 1)

The timezone used for conversion is the system’s default timezone unlessrpy2.robjects.vectors.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 (ro.default_converter + pandas2ri.converter).context(): r_from_pd_tz_df = ro.conversion.py2rpy(pd_tz_df)

r_from_pd_tz_df

R/rpy2 DataFrame (10 x 1)