pandas

In [1]:

    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`.

In [2]:

    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:

In [3]:

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

    pd_df

Out[3]:

| int_values | str_values
--- | --- | ---
0 | 1 | abc
1 | 2 | def
2 | 3 | ghi

R data frame converted from a `pandas` data frame:

In [4]:

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

    r_from_pd_df

Out[4]:
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`:

In [5]:

    base = importr('base')

    with localconverter(ro.default_converter + pandas2ri.converter):
      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:

In [6]:

    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:

In [7]:

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

    r_df

Out[7]:
R/rpy2 DataFrame (3 x 2)

int_values | str_values
--- | ---
... | ...

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

In [8]:

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

    pd_from_r_df

Out[8]:

| int_values | str_values
--- | --- | ---
1 | 1 | abc
2 | 2 | def
3 | 3 | ghi

## Date and time objects¶

In [9]:

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

    pd_df

Out[9]:

| 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

In [10]:

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

    r_from_pd_df

Out[10]:
R/rpy2 DataFrame (10 x 1)

Timestamp
...

The timezone used for conversion is the system's default timezone unless `rpy2.robjects.vectors.default_timezone` is specified... or unless the time zone is specified in the original time object:

In [11]:

    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

Out[11]:
R/rpy2 DataFrame (10 x 1)

Timestamp
...