R2WinBUGS - Warning messages

Question

I am trying to use R2WinBUGS using this example:

code

(Please only consider the part: ### 5.4. Analysis using WinBUGS)

I am getting this error message:

Error in file(con, "wb") : cannot open the connection
In addition: Warning messages:
1: In file.create(to[okay]) :
  cannot create file 'c:/Program Files/WinBUGS14//System/Rsrc/Registry_Rsave.odc', reason 'Permission denied'
2: In file(con, "wb") :
  cannot open file 'c:/Program Files/WinBUGS14//System/Rsrc/Registry.odc': Permission denied
Warning message:
running command '"c:/Program Files/WinBUGS14//WinBUGS14.exe" /par "D:/R2WinBUGS/normal/script.txt"' had status 1 
> 

I am not sure whether this is crucial for correct functionality (everything else seems to look ok). Is there a way to get rid of this?

Thanks.

Christian

PS:

This is the R code:

library(R2WinBUGS)
setwd("D:/R2WinBUGS/normal")

y10 <- rnorm(n = 10, mean = 600, sd = 30) # Sample of 10 birds
y1000 <- rnorm(n = 1000, mean = 600, sd = 30) # Sample of 1000 birds

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

# Priors
 population.mean ~ dunif(0,5000)        # Normal parameterized by precision
 precision <- 1 / population.variance   # Precision = 1/variance
 population.variance <- population.sd * population.sd
 population.sd ~ dunif(0,100)

# Likelihood
 for(i in 1:nobs){
    mass[i] ~ dnorm(population.mean, precision)
 }
}
",fill=TRUE)
sink()

# Package all the stuff to be handed over to WinBUGS
# Bundle data
win.data <- list(mass = y1000, nobs = length(y1000))

# Function to generate starting values
inits <- function()
  list (population.mean = rnorm(1,600), population.sd = runif(1, 1, 30))

# Parameters to be monitored (= to estimate)
params <- c("population.mean", "population.sd", "population.variance")

# MCMC settings
nc <- 3                 # Number of chains
ni <- 1000              # Number of draws from posterior (for each chain)
nb <- 1                 # Number of draws to discard as burn-in
nt <- 1                 # Thinning rate

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

ls()

out                 # Produces a summary of the object

names(out)

str(out)

hist(out$summary[,8])           # Rhat values in the eighth column of the summary
which(out$summary[,8] > 1.1)        # None in this case

par(mfrow = c(3,1))
matplot(out$sims.array[1:999,1:3,1], type = "l")
matplot(out$sims.array[,,2] , type = "l")
matplot(out$sims.array[,,3] , type = "l")

par(mfrow = c(3,1))
matplot(out$sims.array[1:20,1:3,1], type = "l")
matplot(out$sims.array[1:20,,2] , type = "l")
matplot(out$sims.array[1:20,,3] , type = "l")

par(mfrow = c(3,1))
hist(out$sims.list$population.mean, col = "grey")
hist(out$sims.list$population.sd, col = "blue")
hist(out$sims.list$population.variance, col = "green")

par(mfrow = c(1,1))
plot(out$sims.list$population.mean, out$sims.list$population.sd)

pairs(cbind(out$sims.list$population.mean, out$sims.list$population.sd, out$sims.list$population.variance))

summary(out$sims.list$population.mean)
summary(out$sims.list$population.sd)
sd(out$sims.list$population.mean)
sd(out$sims.list$population.sd)

summary(lm(y1000 ~ 1))

Answer 1

Probably it is windows UAC fault. By default UAC doesn't allow programms to write in almost anything except the user's folder. You can change that by running R as administrator. But I think that will change the library folder unless it is hardcoded in Renviron.site (inside R\etc folder), but I'm not 100% sure about that.

Answer 2

I was able to fix the problem by defining "bugs.directory".

out <- bugs(data = win.data, inits = inits, parameters.to.save = params, model.file = "model.txt", n.thin = nt, n.chains = nc, n.burnin = nb, n.iter = ni, debug = FALSE, DIC = TRUE, working.directory = getwd(), bugs.directory = 'c:/WinBUGS14')

Answer 3

Your link goes out to a huge file that spans many chapters of a book. In the comments section it says:

# You may have to add a 'working.directory' argument to calls to
# the function bugs().

Have you done that yet? There's also a bunch of user-specific stuff like:

setwd("C:/_Marc Kery/_WinBUGS book/Naked code") # May have to adapt that

Have you appropriately modified those items?