Getting WinBUGS Leuk example to work from R using R2winBUGS

Question

I am trying to learn to use winBUGS from R, I have experience with R. I have managed to successfully run a simple example from R with no problems. I have been trying to run the Leuk: Survival from winBUGS examples Volume 1. I have managed to run this from winBUGS GUI with no problems. My problem is try as I might ( and I have been trying and searching for days) I cannot get it to run using R2winBUGS.I am sure it is something simple.

The error message I get if I try and set inits in the script is

Error in bugs(data = L, inits = inits, 
      parameters.to.save = params, model.file "model.txt",  : 
      Number of initialized chains (length(inits)) != n.chains

I know this means I have not initialised some of the chains, but I am pasting the inits code from winbugs examples manual and all other settings seem to me to be the same as when run on the winBUGS GUI.

If I try inits=NULL I get another error message

    display(log)
check(C:/BUGS/model.txt)
model is syntactically correct
data(C:/BUGS/data.txt)
data loaded
compile(1)
model compiled
gen.inits()
shape parameter (r) of gamma dL0[1] too small -- cannot sample
thin.updater(1)
update(500)
command #Bugs:update cannot be executed (is greyed out)
set(beta)

Which indicates to me I will still have problems after solving the first one!! I am about to give up on using winBUGS, please can someone save me? I know I am probably going to look stupid, but everyone has to learn:-)

I am using winBUGS 1.4.3 on Windows XP 2002 SP3

My R code is below, many thanks for at least reading this far.

   rm(list = ls())

L<-list(N = 42, T = 17, eps = 1.0E-10,
        obs.t = c(1, 1, 2, 2, 3, 4, 4, 5, 5, 8, 8, 8, 8, 11, 11, 12, 12, 15, 17, 22, 23, 6, 
        6, 6, 6, 7, 9, 10, 10, 11, 13, 16, 17, 19, 20, 22, 23, 25, 32, 32, 34, 35),
        fail = c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 0, 1, 0, 1, 0, 0, 1, 1, 0, 0, 0, 1, 1, 0, 0, 0, 0, 0),
        Z = c(0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5, 0.5,
               -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5, -0.5),
        t = c(1, 2, 3, 4, 5, 6, 7, 8, 10, 11, 12, 13, 15, 16, 17, 22, 23, 35))

### 5.4. Analysis using WinBUGS
library(R2WinBUGS)      # Load the R2WinBUGS library CHOOSE to use WinBUGS
    #library(R2OpenBUGS)        # Load the R2OpenBUGS library CHOOSE to use OpenBUGS
setwd("C://BUGS") 

# Save BUGS description of the model to working directory
sink("model.txt")
cat("

model
{
# Set up data
for(i in 1:N) {
for(j in 1:T) {

# risk set = 1 if obs.t >= t
Y[i,j] <- step(obs.t[i] - t[j] + eps)
# counting process jump = 1 if obs.t in [ t[j], t[j+1] )
# i.e. if t[j] <= obs.t < t[j+1]
dN[i, j] <- Y[i, j] * step(t[j + 1] - obs.t[i] - eps) * fail[i]
}
}
# Model
for(j in 1:T) {
for(i in 1:N) {
dN[i, j] ~ dpois(Idt[i, j]) # Likelihood
Idt[i, j] <- Y[i, j] * exp(beta * Z[i]) * dL0[j] # Intensity
}
dL0[j] ~ dgamma(mu[j], c)
mu[j] <- dL0.star[j] * c # prior mean hazard
# Survivor function = exp(-Integral{l0(u)du})^exp(beta*z)
S.treat[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * -0.5));
S.placebo[j] <- pow(exp(-sum(dL0[1 : j])), exp(beta * 0.5));
}
c <- 0.001
r <- 0.1
for (j in 1 : T) {
dL0.star[j] <- r * (t[j + 1] - t[j])
}
beta ~ dnorm(0.0,0.000001)
}


",fill=TRUE)
sink()

params<- c("beta","S.placebo","S.treat")

inits<-list( beta = 0.0, 
     dL0 = c(1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,1.0,
             1.0,1.0,1.0,1.0,1.0,1.0, 1.0,1.0))

# MCMC settings
nc <-1                  # Number of chains
ni <- 1000              # Number of draws from posterior (for each chain)
ns<-1000 #Number of sims (n.sims)
nb <- floor(ni/2)                   # Number of draws to discard as burn-in
nt <- max(1, floor(nc * (ni - nb) / ns))# Thinning rate
Lout<-list()



# Start Gibbs sampler: Run model in WinBUGS and save results in object called out
out <- bugs(data = L, inits =inits, parameters.to.save = params, model.file = "model.txt", 
n.thin = nt, n.chains = nc, n.burnin = nb, n.iter = ni, debug = T, DIC = TRUE,digits=5,
codaPkg=FALSE, working.directory = getwd())

When I set nc<-2 which I thought was just setting the number of MCMC chains per samples node, I get the following

display(log)
check(C:/BUGS/model.txt)
model is syntactically correct
data(C:/BUGS/data.txt)
data loaded
compile(2)
model compiled
inits(1,C:/BUGS/inits1.txt)
this chain contains uninitialized variables
inits(2,C:/BUGS/inits2.txt)
this chain contains uninitialized variables
gen.inits()
shape parameter (r) of gamma dL0[1] too small -- cannot sample
thin.updater(1)
update(500)
command #Bugs:update cannot be executed (is greyed out)

Getting WinBUGS Leuk example to work from R using R2winBUGS

Answers (1)

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