cbare cbare - 9 months ago 95
Python Question

Converting an RPy2 ListVector to a Python dictionary

The natural Python equivalent to a named list in R is a dict, but RPy2 gives you a ListVector object.

import rpy2.robjects as robjects

a = robjects.r('list(foo="barbat", fizz=123)')

At this point, a is a ListVector object.

<ListVector - Python:0x108f92a28 / R:0x7febcba86ff0>
[StrVector, FloatVector]
foo: <class 'rpy2.robjects.vectors.StrVector'>
<StrVector - Python:0x108f92638 / R:0x7febce0ae0d8>
fizz: <class 'rpy2.robjects.vectors.FloatVector'>
<FloatVector - Python:0x10ac38fc8 / R:0x7febce0ae108>

What I'd like to have is something I can treat like a normal Python dictionary. My temporary hack-around is this:

def as_dict(vector):
"""Convert an RPy2 ListVector to a Python dict"""
result = {}
for i, name in enumerate(vector.names):
if isinstance(vector[i], robjects.ListVector):
result[name] = as_dict(vector[i])
elif len(vector[i]) == 1:
result[name] = vector[i][0]
result[name] = vector[i]
return result

{'foo': 'barbat', 'fizz': 123.0}

b = robjects.r('list(foo=list(bar=1, bat=c("one","two")), fizz=c(123,345))')
{'fizz': <FloatVector - Python:0x108f7e950 / R:0x7febcba86b90>
[123.000000, 345.000000],
'foo': {'bar': 1.0, 'bat': <StrVector - Python:0x108f7edd0 / R:0x7febcba86ea0>
[str, str]}}

So, the question is... Is there a better way or something built into RPy2 that I should be using?

Answer Source

I think to get a r vector into a dictionary does not have to be so involving, how about this:

In [290]:

dict(zip(a.names, list(a)))
{'fizz': <FloatVector - Python:0x08AD50A8 / R:0x10A67DE8>
 'foo': <StrVector - Python:0x08AD5030 / R:0x10B72458>
In [291]:

dict(zip(a.names, map(list,list(a))))
{'fizz': [123.0], 'foo': ['barbat']}

And of course, if you don't mind using pandas, it is even easier. The result will have numpy.array instead of list, but that will be OK in most cases:

In [294]:

import pandas.rpy.common as com
{'fizz': [123.0], 'foo': array(['barbat'], dtype=object)}