Thank you very much for your reply. I finally managed to get some time to
get back to this. I tried to parse and evaluate the expression from R the
problem is I cannot do this in multiple lines. Is there anyway to do this?
Because of that I went for the second option but now I get an error. My
code is: from rpy2.robjects.packages import importr import rpy2.rinterface
as rinterface rinterface.initr() IntSexpVector = rinterface.IntSexpVector
log = rinterface.globalenv.get("log") lfactorial =
rinterface.globalenv.get("lfactorial") lgamma =
rinterface.globalenv.get("lgamma") stats = importr('stats') sum =
rinterface.globalenv.get("sum")
def rp(rp,k):
print rp
r = rinterface.FloatSexpVector(rp[0])
p = rinterface.FloatSexpVector(rp[1])
return
sum(lgamma(k+r))-sum(lfactorial(k))-len(k)*lgamma(r)+len(k)*r*log(1-p)+sum(k)*log(p)
cost_fr = [rinterface.rternalize(rp)] start_params =
rinterface.FloatSexpVector([-1.2, 1]) res = stats.optim(start_params,
cost_fr)
and I get rpy2.rinterface.RRuntimeError: Error in function (par) : could
not find function "fn". What am I doing wrong?
2011/6/16 Laurent Gautier <[email protected]>:
> On 2011-06-16 17:20, B. Santos wrote:
>>
>> Hello everyone,
>>
>> I am trying to use rpy2 to estimate the parameters of a specified
>> function. But I am failing miserable to understand how I can do this
>> using rpy2. I have the following R code:
>> alphabeta<-function(alphabeta,x,dicerAcc) { alpha<-alphabeta[1]
>> beta<-alphabeta[2] if (any(alphabeta<0)) return(NA)
>> sum((alpha*log(beta) + lgamma(alpha + x) + x * log(dicerAcc) -
>> lgamma(alpha) - (alpha + x) * log(beta+dicerAcc) -
>> lfactorial(x))[dicerAcc
>>>
>>> noiseT]) ab<- optim(c(1,100), alphabeta, control=list(fnscale=-1), x =
>>
>> x, dicerAcc = dicerAcc)$par
>>
>> Is there anyway to do this. I would imagine the easy way would be to
>> import
>> the function from R but I imagine that means I would have to create a
>> package just for the function which is less than ideal.
>>
>
> You can just parse and evaluate a string as R code as an anonymous R
> function.
> http://rpy.sourceforge.net/rpy2/doc-2.2/html/rinterface.html#parsing-and-evaluating-r-code
>
> and then use base.eval().
>
> You can also consider writing your cost function in Python:
> http://rpy.sourceforge.net/rpy2/doc-2.2/html/rinterface.html#calling-python-functions-from-r
>
>
> HTH,
>
>
> L.
>>
>> Looking forward to your suggestion. Thank you very much in advance,
>> Bruno Santos
>>
>>
>>
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