Bugs item #2224978, was opened at 2008-11-05 11:21
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Category: None
Group: rpy
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Conor (kailandifki)
Assigned to: Nobody/Anonymous (nobody)
Summary: Deleting RPy objects
Initial Comment:
Hello, two related problems. First of all, why do I have to delete the object
r.histlist at the end of the loop in the first snippet of code below? If I do
not, then the r.assign function is ignored, and I get the same results over and
over.
Second, why do I have to "do something" with the r.histlist object before I
delete it in the second, larger code snippet below? If I delete the useless
lines :
r.histlist[0]+=1
r.histlist[0]-=1
I get an error message saying that the object r.histlist does not exist (and
therefore cannot be deleted).
Regards,
CONOR.
~~~~~~~~~~~~~~~~~~
from rpy import r
testlist=[3,4,7,2,5,7]
r.library("stats")
for j in testlist:
r.assign('histlist',j)
print r.histlist
r("""
freq<-c(histlist[0:256]/sum(histlist))
intlist<-c(0:255)""")
del r.histlist
~~~~~~~~~~~~~~~~~
listlist=[
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 3, 6, 45, 399, 2559, 11687, 39182,
96319, 177624, 262638, 327388, 376083, 413259, 425285, 404497, 366078, 322999,
280807, 237411, 197816, 163411, 133730, 107215, 83775, 65599, 51165, 41665,
34917, 30284, 26483, 23573, 20757, 18518, 16851, 15058, 13556, 11928, 10893,
9569, 8568, 7508, 6665, 5914, 5182, 4657, 4101, 3679, 3172, 2785, 2428, 2228,
1858, 1583, 1401, 1123, 1049, 868, 754, 608, 538, 392, 290, 289, 229, 171, 148,
134, 82, 80, 57, 38, 44, 32, 20, 17, 12, 15, 9, 7, 6, 7, 3, 6, 7, 2, 3, 2, 0,
0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0],
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 2, 2, 9, 33, 295, 1969, 9613, 34331,
87052, 162771, 239822, 299785, 352484, 402385, 430364, 417884, 378933, 330030,
285064, 247048, 212240, 180614, 147156, 116074, 89835, 69079, 53932, 42736,
35412, 29243, 25666, 22831, 20392, 18323, 16483, 14447, 12690, 11445, 10149,
9017, 7968, 7240, 6679, 5916, 5285, 4748, 4184, 3892, 3413, 3033, 2835, 2462,
2317, 2054, 1770, 1297, 1174, 1005, 872, 687, 593, 517, 396, 355, 242, 227,
182, 150, 123, 101, 75, 73, 59, 54, 38, 35, 22, 25, 9, 16, 9, 4, 7, 11, 2, 2,
2, 1, 2, 2, 0, 0, 1, 1, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0],
]
# Let's import all the functions in R
from rpy import r
# We will need the nonlinear least-squares R package
r.library("stats")
for j in listlist:
# Here we tell R that intense and freq will be used to make the data frame
r.assign('histlist',j)
r("""
freq<-c(histlist[0:256]/sum(histlist))
intlist<-c(0:255)
LogL<-function(p){
alpha<-p[1]
mu1<-p[2]
mu2<-p[3]
sigma1<-p[4]
sigma2<-p[5]
sum(-1*histlist*log(0.00000001+1/((1+alpha)*sigma1*sqrt(2*pi))*exp(-1*(intlist-mu1)^2/(2*sigma1^2))+alpha/((1+alpha)*sigma2*sqrt(2*pi))*exp(-1*(intlist-mu2)^2/(2*sigma2^2))))
}
alpha.start<-0.1
mu1.start<-20
mu2.start<-130
sigma1.start<-7
sigma2.start<-7
out<-optim(
c(alpha.start,mu1.start,mu2.start,sigma1.start,sigma2.start),
LogL,
method="L-BFGS-B",
lower=list(0.05,10,10,4.5,4.5),
upper=list(0.9,200,200,200,200)
)
reslist<-out$par
""")
r.histlist[0]+=1
r.histlist[0]-=1
del r.histlist
print r.reslist
del r.reslist
~~~~~~~~~~~~~~~~~~~
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