On 15.10.2010 20:40, Sally Luo wrote:
Hi R users,
I am trying to call openbugs from R. And I got the following error message:
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
model is syntactically correct
expected the collection operator c error pos 8 (error on line 1)
Well, something is wrong, but hard to say without the data.
I'd suggest to try the whole thing in OpenBUGS at first and see if it
runs there. Afterwards go into R where it should work as well.
If you still fail to find the error, you may send the stuff to my
address privately and I may find some time to take a look. But please
try yourself at first.
Best wishes,
Uwe Ligges
variable ww is not defined in model or in data set
[1] "C:\\DOCUME~1\\maomao\\LOCALS~1\\Temp\\RtmpqJk9R3/inits1.txt"
Initializing chain 1: model must be compiled before initial values loaded
model must be initialized before updating
model must be initialized before DIC an be monitored
Error in samplesSet(parametersToSave) :
model must be initialized before monitors used
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
I did define variable "ww" in my data and model (they are listed below). I
am not sure if this is due to some errors in my code (please see below) or
because openbugs cannot handle the model I am using. In my model, y[i] also
depends on all other y[j]s. Could you help me figure out the problem and
hopefully get the code to work?
Many thanks for your help. --- Maomao
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
data<-list("y","cap2","pol2","cap1","pol1","g","wo","wd","ww","mu","tau")
inits<-function() {list(beta=beta0, rho_o=rho_o_0, rho_d=rho_d_0,
rho_w=rho_w_0)}
parameters<-c("beta", "rho_o", "rho_d", "rho_w")
probit.sim<-BRugsFit(data,inits,parameters,modelFile="spatial.openbugs.txt",numChains=1,nIter=2000)
# my model
model {
for (i in 1:676) {
y[i] ~ dbern(p[i])
wwy[i]<- inprod(ww[i, 1:676] , y[])
woy[i]<- inprod(wo[i, 1:676] , y[])
wdy[i]<- inprod(wd[i, 1:676] , y[])
probit(p[i])<- rho_o * woy[i] + rho_d * wdy[i] + rho_w * wwy[i] + beta[1] +
beta[2] * cap2[i] + beta[3] * pol2[i] + beta[4] * cap1[i] + beta[5] *
pol1[i] + beta[6] * g[i]+ e[i]
}
# Priors
for (j in 1:6) {
beta[1:6] ~ dmnorm(mu[1:6], tau[1:6, 1:6])
}
rho_o ~ dunif(-1,1)
rho_d ~ dunif(-1,1)
rho_w ~ dunif(-1,1)
for (i in 1:676) {
e[i] ~ dnorm(0, 1)
}
}
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and provide commented, minimal, self-contained, reproducible code.
