Hi Oliver,
yes this helps very much... anyway, this works with array or also with matrix?
I ask this because I have a matrix 50x50, and if I do:
mymatrixNump = numpy.matrix(mymatrix)
mymatrixR = ro.conversion.py2ri(mymatrixNump)
I have:
---------------------------------------------------------------------------
RuntimeError Traceback (most recent call last)
/Users/ogabbrie/Desktop/NetworkSimulatorTraits/<ipython console> in <module>()
/Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/rpy2/robjects/numpy2ri.pyc
in numpy2ri(o)
33 # Array-of-PyObject is treated like a Python list:
34 elif o.dtype.kind == "O":
---> 35 res = ro.conversion.py2ri(list(o))
36 # Record arrays map onto R data frames:
37 elif o.dtype.kind == "V":
/Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/rpy2/robjects/numpy2ri.pyc
in numpy2ri(o)
47 raise(ValueError("Unknown numpy array type."))
48 else:
---> 49 res = ro.default_py2ri(o)
50 return res
51
/Library/Frameworks/Python.framework/Versions/4.1.30101/lib/python2.5/site-packages/rpy2/robjects/__init__.pyc
in default_py2ri(o)
87 res = rinterface.SexpVector([o, ], rinterface.STRSXP)
88 elif isinstance(o, list):
---> 89 res = r.list(*[conversion.ri2py(conversion.py2ri(x))
for x in o])
90 elif isinstance(o, complex):
91 res = rinterface.SexpVector([o, ], rinterface.CPLXSXP)
RuntimeError: maximum recursion depth exceeded
2009/1/15 Oliver Tomic <oliver.to...@nofima.no>:
> Hi Simone,
>
> maybe this helps:
>
> [code START]
>>>> import numpy
>
>>>> a = [[1,2,3],[4,5,6]]
>
>>>> aa = numpy.array(a)
>
>>>> aa
> array([[1, 2, 3],
> [4, 5, 6]])
>
>>>> import rpy2.robjects as ro
>
>>>> import rpy2.robjects.numpy2ri
>
>>>> aR = ro.conversion.py2ri(aa)
>
>>>> aR
> <RArray - Python:0x014E7D00 / R:0x0211AF98>
>
>>>> print aR
> [,1] [,2] [,3]
>
> [1,] 1 2 3
>
> [2,] 4 5 6
>
> [code END]
>
>
> cheers
> Oliver
>
>
>
> Laurent Gautier <lgaut...@gmail.com> wrote on 14.01.2009 23:11:28:
>
>> Simone Gabbriellini wrote:
>> > I would like to know if there is something like r.assign('ROBJECT',
>> > PYTHONOBJECT) in rpy2...
>>
>> http://rpy.sourceforge.net/rpy2/doc/html/robjects.html?
>> highlight=assign#environments
>>
>> Or "assign" as you write above:
>> r.assign("foo", 123)
>>
>>
>> > I don't want to use R function to evaluate an object IN Python, I want
>> > to assign a matrix made in python to an R object...
>> >
>> > simone
>> >
>> > 2009/1/14 Simone Gabbriellini <simone.gabbriell...@gmail.com>:
>> >> [so sorry but I just answer your mail... I write to the list and you
>> >> answer to ME and to the list in CC... I have to remember to answer to
>> >> ALL to answer to the mailing list too... again, sorry for that, I
>> >> didn't mean to offend you]
>> >>
>> >> and thanks for the help
>> >> simone
>> >>
>> >> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >>> [why getting off the list ???]
>> >>>
>> >>> Simone Gabbriellini wrote:
>> >>>> please do you have an example?
>> >>>>
>> >>>> because when I read "That import alone is sufficient to switch an
>> >>>> automatic conversion of numpy objects into rpy2 objects." I suppose
>> >>>> that every numpy object is seen by R...
>> >>> Automatic conversion of a numpy object:
>> >>>
>> >>> rlen = robjects.r['length']
>> >>> print(rlen(gladj))
>> >>>
>> >>>
>> >>> You are otherwise giving a *string* to be evaluated as R code
>> >>> (and R not looking into the python namespace when trying resolvea
>> >>> symbol).
>> >>> More on evaluating strings here:
>> >>> http://rpy.sourceforge.net/rpy2/doc/html/robjects.html?
>> highlight=r_repr#strings-as-r-code
>> >>>
>> >>>> thank you,
>> >>>> simone
>> >>>>
>> >>>> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >>>>> Simone Gabbriellini wrote:
>> >>>>>> yes, like that...
>> >>>>>>
>> >>>>>> but simply importing:
>> >>>>>>
>> >>>>>> Import rpy2.robjects.numpy2ri
>> >>>>>>
>> >>>>>> when I do:
>> >>>>>>
>> >>>>>> g1adj = numpy.array(g1adj)
>> >>>>>>
>> >>>>>> robjects.r('QAPset[1,,]<-g1adj')
>> >>>>> R has no way to know your Python variable called "gladj" unless you
>> >>>>> indicate
>> >>>>> it.
>> >>>>>
>> >>>>> print(robjects.r('ls()'))
>> >>>>> should confirm that there is no variable 'gladj' in your globalEnv.
>> >>>>>
>> >>>>>
>> >>>>>> it says:
>> >>>>>>
>> >>>>>> Error in eval(expr, envir, enclos) : object "g1adj" not found...
>> >>>>> The error message above is correct, I think.
>> >>>>>
>> >>>>>> while
>> >>>>>> in the docs it says that:
>> >>>>>> "That import alone is sufficient to switch an automatic conversion
>> >>>>>> of
>> >>>>>> numpy objects into rpy2 objects."
>> >>>>>>
>> >>>>>> should I do something else?
>> >>>>>>
>> >>>>>> thank you,
>> >>>>>> simone
>> >>>>>>
>> >>>>>> 2009/1/14 Laurent Gautier <lgaut...@gmail.com>:
>> >>>>>>> Something like this
>> >>>>>>>
>> >>>>>>> http://rpy.sourceforge.net/rpy2/doc/html/numpy.html?highlight=numpy
>> >>>>>>> ?
>> >>>>>>>
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> Simone Gabbriellini wrote:
>> >>>>>>>> dear List,
>> >>>>>>>>
>> >>>>>>>> is it possible to pass a matrix I've built in python to R via
>> >>>>>>>> rpy2?
>> >>>>>>>>
>> >>>>>>>> I'm sure I'm blind, but I cannot find example about how to
>> pass object
>> >>>>>>>> from python to r, while I see how to pass object from r to
>> >>>>>>>> python...
>> >>>>>>>>
>> >>>>>>>> best regards,
>> >>>>>>>> Simone Gabbriellini
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>>
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