On 2011-06-03 00:56, Eduardo Bañados Torres wrote:
Hi Everyone,
I am currently struggling with rpy2, I hope someone could help me.
I am trying to do a maximum likelihood using the mle() task in the
stats4 R library,
as part of a python script. mle() receives a R function to calculate
the negative log-likelihood,
my problem is that so far I have could not figure out how to give a
numpy vector to the function,
or make the vector understandable for the R environment. Is there a
way to do this?
mle is evaluating the function minuslog in its parent environment (and
no XX can be found that there, as the error message you obtain in return
indicates it).
One way to overcome this is to create a symbol 'XX' in the enclosing
environment of the function:
fx.closureenv()['XX'] = rpy2.robjects.numpy2ri.numpy2ri(XX)
With the following example will be clearer.
This is a short version, trying to use mle() in a normal distribution.
"I need to make the XX vector understandable for rfunction":
======================================================================
import rpy2.robjects as robjects
from rpy2.robjects.packages import importr
import rpy2.robjects.numpy2ri
import numpy as np
r = robjects.r
stats4 = importr("stats4")
#Normal vector to test the script, which I need to give to the R
function ll
XX = np.random.normal(loc=10.0, scale=2.0, size=100)
N = len(XX)
#negative logarithmic likelihood function of a Gaussian distribution
#This function should receive the XX numpy vector someway
rfunction = '''ll <- function(mean,sigma){
n <- %i
x <- XX ##This is the critical point##
-(-0.5*n*log(2*pi)-n*log(sigma)-0.5*sum(((x-mean)/sigma)^2))
}''' % (N)
fx=r(rfunction)
starterd = {'mean':10,'sigma':1}
starter= robjects.DataFrame(starterd)
fit = stats4.mle(minuslog=fx,start=starter)
summary = R.summary(fit)
print summary
==========================================================================
I hope someone can help me with this or point me out a better solution
By the way, I am using:
rpy2 v2.1.9
R v2.11.0
python v2.6
Thank you!
--
Eduardo Bañados Torres
------------------------------------------------------------------------------
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Discover what all the cheering's about.
Get your free trial download today.
http://p.sf.net/sfu/quest-dev2dev2
_______________________________________________
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
------------------------------------------------------------------------------
Simplify data backup and recovery for your virtual environment with vRanger.
Installation's a snap, and flexible recovery options mean your data is safe,
secure and there when you need it. Discover what all the cheering's about.
Get your free trial download today.
http://p.sf.net/sfu/quest-dev2dev2
_______________________________________________
rpy-list mailing list
rpy-list@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rpy-list
