Question

I am trying to run a simple linear regression (using rpy2 from Python) and encountered a strangely worded error when running the script below:

from numpy import array, rec
from numpy.random import normal as nprandom
from rpy2.robjects import numpy2ri, r

foo = array(range(10))
bar = foo + nprandom(0,1,10)

d = rec.fromarrays([foo, bar], names=('foo','bar'))
fit = r.lm('bar ~ foo', data=d)
print fit.rx2('coefficients')

here is the console output:

>>> from numpy import array, rec
>>> from numpy.random import normal as nprandom
>>> from rpy2.robjects import numpy2ri, r
>>> 
>>> foo = array(range(10))
>>> bar = foo + nprandom(0,1,10)
>>> 
>>> d = rec.fromarrays([foo, bar], names=('foo','bar'))
>>> fit = r.lm('bar ~ foo', data=d)
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/usr/local/lib/python2.6/dist-packages/rpy2/robjects/functions.py", line 82, in __call__
    return super(SignatureTranslatedFunction, self).__call__(*args, **kwargs)
  File "/usr/local/lib/python2.6/dist-packages/rpy2/robjects/functions.py", line 33, in __call__
    new_kwargs[k] = conversion.py2ri(v)
  File "/usr/local/lib/python2.6/dist-packages/rpy2/robjects/__init__.py", line 134, in default_py2ri
    raise(ValueError("Nothing can be done for the type %s at the moment." %(type(o))))
ValueError: Nothing can be done for the type <class 'numpy.core.records.recarray'> at the moment.
>>> print fit.rx2('coefficients')

I am running Python 2.6.5 and have numpy version 1.6.1

Does any one know what is causing this error?

Answer 1

You need to add:

rpy2.robjects.activate()

after importing numpy2ri. This SO post references the rpy2 documentation:

That import alone is sufficient to switch an automatic conversion of
numpy objects into rpy2 objects.

Why make this an optional import, while it could have been included in
the function py2ri() (as done in the original patch submitted for that
function) ?

Although both are valid and reasonable options, the design decision
was taken in order to decouple rpy2 from numpy the most, and do not
assume that having numpy installed automatically meant that a
programmer wanted to use it.

Hope this solves your problem.