rpy2 / R interface¶
Warning
Up to pandas 0.19, a pandas.rpy
module existed with functionality to
convert between pandas and rpy2
objects. This functionality now lives in
the rpy2 project itself.
See the updating section
of the previous documentation for a guide to port your code from the
removed pandas.rpy
to rpy2
functions.
rpy2 is an interface to R running embedded in a Python process, and also includes functionality to deal with pandas DataFrames.
Converting data frames back and forth between rpy2 and pandas should be largely
automated (no need to convert explicitly, it will be done on the fly in most
rpy2 functions).
To convert explicitly, the functions are pandas2ri.py2ri()
and
pandas2ri.ri2py()
.
See also the documentation of the rpy2 project: https://rpy2.readthedocs.io.
In the remainder of this page, a few examples of explicit conversion is given. The pandas conversion of rpy2 needs first to be activated:
In [1]: from rpy2.robjects import r, pandas2ri
In [2]: pandas2ri.activate()
Transferring R data sets into Python¶
Once the pandas conversion is activated (pandas2ri.activate()
), many conversions
of R to pandas objects will be done automatically. For example, to obtain the ‘iris’ dataset as a pandas DataFrame:
In [3]: r.data('iris')
Out[3]:
R object with classes: ('character',) mapped to:
<StrVector - Python:0x1c38693688 / R:0x7fb961f93ee8>
['iris']
In [4]: r['iris'].head()