The error message is coming from R, and relates to an improper usage for
the function adk_test. In other words, this is a case of RTFM ;-)
adk.adk_test(IntVector([1,2,3]), IntVector([4,5,6]))
or
adk.adk_test(Vector(IntVector([1,2,3]), IntVector([4,5,6])))
Should work.
L.
PS: rpy2-2.2.0-dev is currently the highest version number (and under
development).
On 11/20/10 11:03 PM, Giovanni Luca Ciampaglia wrote:
> Btw, the same happens when using rimport:
>
> from rpy2.robjects.packages import importr
> from rpy2.robjects import Vector
> adk = importr('adk')
> adk.adk_test(Vector([1,2,3]),Vector([4,5,6]))
>
> So far the only way to get a result was to directly pass a list, as in:
> adk.adk_test([1,2,3,4])
>
> but then it treats the four inputs as 4 independent, size 1 samples.
>
> G
>
> On 20/11/2010 22:02, Giovanni Luca Ciampaglia wrote:
>> Hi all,
>> I am trying to wrap adk.test from R package adk using rpy2 2.2.1 but I
>> am running into problems with passing parameters to it. More
>> specifically I get a runtime error in R:
>>
>>> In [1]: %run ad.py
>>> Carico il pacchetto richiesto: adk
>>> Error in sort.list(unique(x)) :
>>> 'x' must be atomic for 'sort.list'
>>> Have you called 'sort' on a list?
>>> ---------------------------------------------------------------------------
>>> RRuntimeError Traceback (most recent call
>>> last)
>>>
>>> /home/giovanni/repos/peers/ad.py in<module>()
>>> 20 if __name__ == '__main__':
>>> 21 r_adk = R_factory()
>>> ---> 22 r_adk(np.random.rand(100),np.random.rand(100))
>>> 23
>>> 24
>>>
>>> /home/giovanni/repos/peers/ad.py in r_adk(*args)
>>> 14 '''
>>> 15 args = map(Vector, map(list, args))
>>> ---> 16 return adk_test(*args)
>>> 17
>>> 18 return r_adk
>>>
>>> /usr/lib/python2.6/dist-packages/rpy2/robjects/functions.pyc in
>>> __call__(self, *args, **kwargs)
>>> 81 v = kwargs.pop(k)
>>> 82 kwargs[r_k] = v
>>> ---> 83 return super(SignatureTranslatedFunction,
>>> self).__call__(*args, **kwargs)
>>> 84
>>> 85
>>>
>>> /usr/lib/python2.6/dist-packages/rpy2/robjects/functions.pyc in
>>> __call__(self, *args, **kwargs)
>>> 33 for k, v in kwargs.iteritems():
>>> 34 new_kwargs[k] = conversion.py2ri(v)
>>> ---> 35 res = super(Function, self).__call__(*new_args,
>>> **new_kwargs)
>>> 36 res = conversion.ri2py(res)
>>> 37 return res
>>>
>>> RRuntimeError: Error in sort.list(unique(x)) :
>>> 'x' must be atomic for 'sort.list'
>>> Have you called 'sort' on a list?
>> What I do in Python is the following:
>>
>>
>> ****************
>>
>> ''' Anderson-Darling k-samples test '''
>>
>> import numpy as np
>>
>> def R_factory():
>> from rpy2.robjects import r, Vector
>> require = r['require']
>> require('adk')
>> adk_test = r['adk.test']
>>
>> def r_adk(*args):
>> '''
>> R version from adk
>> '''
>> args = map(Vector, map(list, args))
>> return adk_test(*args)
>>
>> return r_adk
>>
>> if __name__ == '__main__':
>> r_adk = R_factory()
>> r_adk(np.random.rand(100),np.random.rand(100))
>>
>> *************
>>
>> The actual code of adk.test is:
>>
>>> function (...)
>>> {
>>> if (nargs() == 1& is.list(list(...)[[1]])) {
>>> samples<- list(...)[[1]]
>>> }
>>> else {
>>> samples<- list(...)
>>> }
>>> k<- length(samples)
>>> if (k< 2)
>>> stop("Must have at least two samples.")
>>> ns<- sapply(samples, length)
>>> if (any(ns == 0))
>>> stop("One or more samples have no observations.")
>>> x<- NULL
>>> for (i in 1:k) x<- c(x, samples[[i]])
>>> n<- length(x)
>>> Z.star<- sort(unique(x))
>> I also tried putting the Vectors in an R list and passing that to r_adk
>> or redefining r_adk(a,b) instead of r_adk(*args) but doesn't seem to
>> like both. I am not an R expert so forgive if it's a very silly question.
>>
>> Best
>>
>> G
>>
>>
>>
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>
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experiences on the web. Be a part of the beta today
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