The conversion doesn't work for me with matrices either, but the output is
different on my machine.
This is what I get:
[code START]
>>> import numpy
>>> b = [[1,2,3],[4,5,6]]
>>>bb = numpy.matrix(b)
>>> bb
matrix([[1, 2, 3],
[4, 5, 6]])
>>> import rpy2.robjects as ro
>>> import rpy2.robjects.numpy2ri
>>> bR = ro.conversion.py2ri(bb)
>>> bR
<RArray - Python:0x014E7D00 / R:0x0211AFB0>
>>> print bR
[,1] [,2] [,3]
[1,] NA NA NA
[2,] NA NA NA
[code END]
If you convert the numpy matrix into an array prior to the RPy2-conversion
it works fine.
aa = numpy.array(bb)
cheers
Oliver
"Simone Gabbriellini" <simone.gabbriell...@gmail.com> wrote on 15.01.2009
09:51:30:
> 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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> >> >>>>>>
> >>
> >>
>
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> >>
> >>
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