On Wed, May 18, 2011 at 2:16 PM, William Stein <wst...@gmail.com> wrote:
> On Wed, May 18, 2011 at 12:24 PM, kcrisman <kcris...@gmail.com> wrote:
>> On the page you linked to:
>> "This the documentation for what will be soon the older version of
>> rpy2. Do consider the upcoming 2.1.x releases if you are starting a
>> project now."
>>
>> If you look at http://rpy.sourceforge.net/rpy2/doc-2.2/html/changes.html
>> it also seems like in higher-numbered releases there are changes in
>> this functionality. Maybe this is a known bug; can you try
>>
>> from rpy2.robjects.numpy2ri import numpy2ri
>> ro.conversion.py2ri = numpy2ri
>>
>> as on the 2.2 documentation and see if that works.
>
> Nope, not at all.
>
>> That said, I never use it - I always use the Sage pexpect interface to
>> R. But now I will bookmark this worksheet if I get the chance to give
>> another R/Sage talk!
>
> The Sage pexpect is slow and brittle if the size of data you need to
> move into or out of R is large. The rpy2 interface is much more
> robust in this regard.
> But rpy2 is also somewhat weird and wacky, as I learned today.
And, surprisingly, it is not very fast for evaluating basic
expression. It's really *shockingly* slow for a C library interface.
I don't know how it can be so bad:
sage: import rpy2.robjects as robjects
sage: R = robjects.r
sage: print R('2 + 3') # the rpy2 cython interface (note the import!)
[1] 5
sage: timeit("r('2+3')")
5 loops, best of 3: 1.46 ms per loop
sage: timeit("R('2+3')")
625 loops, best of 3: 686 µs per loop
sage: timeit("pari('2+3')")
625 loops, best of 3: 5.64 µs per loop
Seriously? 686 microseconds to do 2+3? Our PARI C library
interface does that in 5.64 microseconds.
-- William
>
>
> Maybe we need to upgrade the rpy2 in Sage...
>
> William
>
>
>>
>> On May 18, 2:14 pm, William Stein <wst...@gmail.com> wrote:
>>> Hi,
>>>
>>> I was preparing a lecture [1] on rpy2 [2] in Sage (version 4.6.2) and notice
>>> that the following very important central bit of rpy2 functionality --
>>> namely converting a numpy array to R -- seems to be horribly broken:
>>>
>>> sage: import rpy2.robjects as robjects # standard
>>> sage: import rpy2.robjects.numpy2ri # enable automatic
>>> conversion from numpy to R
>>> sage: import numpy # make numpy available
>>> sage: print robjects.r(numpy.array([1,2,3], dtype=float)) # try
>>> it out; sad result.
>>> [1] 3
>>>
>>> The output *should* be a vector with 3 entries, I think.
>>> There are similar problems with numpy arrays.
>>>
>>> The same problem happens with 4.7.rc1.
>>>
>>> I've never used rpy2 seriously before now, so if I'm just confused,
>>> can somebody who knows rpy2 better let me know.
>>>
>>> -- William
>>>
>>> [1] http://flask.sagenb.org/home/pub/57/
>>> [2]http://rpy.sourceforge.net/rpy2/doc-2.0/html/numpy.html
>>>
>>> --
>>> William Stein
>>> Professor of Mathematics
>>> University of Washingtonhttp://wstein.org
>>
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>
>
>
> --
> William Stein
> Professor of Mathematics
> University of Washington
> http://wstein.org
>
--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
--
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