Thanks Laurent,
I've decided to change to rpy2 instead and use that framework:
A few questions I have :
I am able to create a model using nls or lm
say
model = robjects.r.nls("y~a*x^3 + b*x^2 + c*x + d",start =
robjects.r.list(a = 0, b = 0, c = 0, d = 0))
it succesfully creates the model .
Now, in rpy I would extract the $coefficients , $fitted from nls
by
pointing to the model as a dictionary
list(r.print_(model['m']['fitted'])())
would return a list of the fitted points
now in rpy2 i successfully get to point to 'm'
by returning model.r['m']
which returns a vector
however, i am having difficulty getting to $fitted under $m and
printing the results.
any ideas would be appreciated.
thanks,
manuel
On Aug 5, 2009, at 12:12 PM, Laurent Gautier wrote:
Are you using rpy2-2.1dev ?
If so, there were issues and you will want a (very) fresh update of
the code on the bitbucket repository.
L.
Manuel A. Rivas wrote:
Thanks Laurent,
Were you able to succesfully create the lm ?
I get the following error with NO_CONVERSION:
>>> rpy.r.lm(rpy.r("y ~ x"), data = rpy.r.data_frame(x=my_x, y=my_y))
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
265, in __call__
return self.eval(self.parse(text=s))
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
199, in __call__
a = a.getSexp()
AttributeError: 'Robj' object has no attribute 'getSexp'
thanks,
manuel
On Aug 5, 2009, at 11:17 AM, Laurent Gautier wrote:
Manuel A. Rivas wrote:
Hello , I am trying to use the r.nls function from rpy2 in the
same fashion as rpy by importing rpy_classic. In R: the syntax y
~ x would tell the lm function that y depends on x as its model.
In python using rpy I would use rpy's "evaluate a string"
functionality. i.e.
>>> from rpy import r
>>> my_x = [5.05, 6.75, 3.21, 2.66]
>>> my_y = [1.65, 26.5, -5.93, 7.96]
>>> print r.lm(r("y ~ x"), data = r.data_frame(x=my_x, y=my_y))
['coefficients']
as described in the man pages: However, if I do the same with rpy2
>>> from rpy2.rpy_classic import r
>>> my_x = [5.05, 6.75, 3.21, 2.66]
>>> my_y = [1.65, 26.5, -5.93, 7.96]
>>> r.lm(r("y ~ x"), data = r.data_frame(x=my_x, y=my_y))
I get the following error: Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
265, in __call__
return self.eval(self.parse(text=s))
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
215, in __call__
res = rpy2py(res)
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
174, in rpy2py
res = rpy2py_basic(obj)
File "/home/radon00/rivas/lib/python/rpy2/rpy_classic.py", line
160, in rpy2py_basic
raise ValueError("Invalid type for 'obj'.")
ValueError: Invalid type for 'obj'.
any ideas how to do the same operation in rpy2 with rpy_classic?
Try adding this to the beginning:
import rpy2.rpy_classic as rpy
rpy.set_default_mode(rpy.NO_CONVERSION)
(rpy_classic is way behind the rest of rpy2 because of limited
time on my end, and seemingly limited interest/contributions from
users in having it improved to a full compatibility).
L.
thanks,
Manuel Rivas
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