I can't see model results in R2jags - what is wrong? - r

Question

I'm trying to run this script in R2jags following the instructions provided in "Lahoz-Monfort JJ, Guillera-Arroita G, Tingley R (2015) Statistical approaches to account for false positive errors in environmental DNA
samples. Molecular Ecology Resources, 16, 673–685." and it seems that it worked ok, but I can't figure out the command to see the results... could anyone please help?
cat("model {
# Priors
psi ~ dunif(0,1)
p11 ~ dunif(0,1)
p10 ~ dunif(0,p10_max)
# Likelihood
for (i in 1:S){
z[i] ~ dbern(psi)
p[i] <- z[i]*p11 + (1-z[i])*p10
for (j in 1:K){
Y[i,j] ~ dbern(p[i])
}
}
} ",fill=TRUE)
sink()
Bayesian <- function(psi,p11,p10,S,K,nsims=100,doprint=TRUE,p10_max=0.05,
ni=100000,nt=2,nc=1,nb=50000,myparallel=TRUE) {
psihat<-p11hat<-p10hat<-rep(nsims)
modelSummaries<-list()
for(ii in 1:nsims){
if (doprint) cat("\r", ii, "of", nsims," ")
hh<-genSimData(psi,r11=0,p11,p10,S,K1=0,K2=K)
# fit the model
jags.inits <-function()(list(psi=runif(1,0.05,0.95),p11=runif(1,p10_max,1),p10=runif(1,0,p10_max)))
jags.data <-list(Y=hh,S=S,K=K,p10_max=p10_max)
jags.params<-c("psi","p11","p10")
Thoropa_model<-jags(data = jags.data, inits = jags.inits, parameters.to.save= jags.params,
model.file= "Thoropa.txt", n.thin= nt, n.chains= nc,
n.iter= ni, n.burnin = nb, parallel=myparallel) #, working.directory= getwd()
# extract results (medians of the marginal posteriors)
psihat[ii] <- model$summary["psi","50%"]
p11hat[ii] <- model$summary["p11","50%"]
p10hat[ii] <- model$summary["p10","50%"]
modelSummaries[[ii]]<-model$summary
}
if (doprint){
printsummres(psihat,thename="estimated psi")
printsummres(p11hat,thename="estimated p11")
printsummres(p10hat,thename="estimated p10")
}
return(list(psihat=psihat,p11hat=p11hat,p10hat=p10hat,modelSummaries=modelSummaries))
}
The file "Thoropa.txt" is a presence/absence matrix as follows:
PCR1 PCR2 PCR3 PCR4 PCR5 PCR6 PCR7 PCR8 PCR9 PCR10 PCR11 PCR12
1 0 0 0 0 0 0 0 0 0 0 0
0 0 0 1 0 0 0 1 0 0 0 0
0 0 0 0 0 0 1 0 0 0 0 0
1 1 1 1 1 1 1 1 1 1 1 1
0 0 0 0 0 0 0 0 0 0 0 0
1 0 1 0 1 1 1 1 1 1 1 1
0 0 1 0 0 0 1 0 0 0 0 0
1 0 1 0 0 0 0 0 1 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
1 0 0 0 1 1 0 0 0 1 0 0
1 1 0 1 0 1 0 1 0 0 1 0
1 1 0 0 0 0 0 1 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
1 1 1 1 0 1 1 1 1 0 1 1
1 1 1 1 1 1 1 1 1 1 1 1
0 0 1 0 1 0 0 0 0 0 1 1
1 1 1 1 1 1 1 1 1 1 1 1
Following the comment from Limey (thank you!) I changed the script to:
sink("Thoropa2.txt")
cat("model {
# Priors
psi ~ dunif(0,1)
p11 ~ dunif(0,1)
p10 ~ dunif(0,p10_max)
# Likelihood
for (i in 1:S){
z[i] ~ dbern(psi)
p[i] <- z[i]*p11 + (1-z[i])*p10
for (j in 1:K){
Y[i,j] ~ dbern(p[i])
}
}
} ",fill=TRUE)
sink()
y=Thoropa# the detection/non detection table
S=nrow(y)
K=ncol(y)
psi ~ dunif(0, 1)
p11 ~ dunif(0, 1)
p10 ~ dunif(0, p10_max)
p10_max=0.05
jags.data<-list(y=y, S=S, K=K, p10_max=p10_max)
jags.inits <-function()(list(psi=runif(0,1),p11=runif(0,1),p10=runif(0,p10_max)))
jags.params<-c("psi","p11","p10")
Thoropa_model<-jags.parallel(data = jags.data, inits = jags.inits, parameters.to.save= jags.params, model.file= "Thoropa2.txt", n.chains= 4, n.thin= 10, n.iter = 100000, n.burnin=50000, jags.seed = 333)
and the data file is as before.
Now I am getting the error message:
"Error in checkForRemoteErrors(val) :
4 nodes produced errors; first error: Indexing outside the bounds"
Could anyone help identify the error in my script? I'm no expert and I'm learning by myself, so sorry if it is a stupid question... (maybe there is something wrong with the format of the data...?)
Thank you all!

Answer 1

Your model is not working because some syntax errors in your R script. Note that the R syntax is different of the jags syntax, even if you are running the jags inside de R.
These are the errors:
The symbol "~" is not used for sampling in R. Delete the lines:
psi ~ dunif(0, 1)
p11 ~ dunif(0, 1)
p10 ~ dunif(0, p10_max)
The Y variable in the jags model is capitalized, so you must correct the syntax in jags.data.
jags.data<-list(Y=y, S=S, K=K, p10_max=p10_max)
In jags.inits, a) the body of the function must be inside of curly braces, and not parentheses, and b) the function runif takes 3 arguments: n (number of values you want to sample), min and max. The correct syntax is the following:
jags.inits <-function(){list(psi=runif(1,0,1),p11=runif(1,0,1),p10=runif(1,0,p10_max))}
Fixing those errors, your model should run without errors. After run the model, you can extract the median of the parameters "psi" using one of these two options:
Thoropa_model$BUGSoutput$median$psi
Thoropa_model$BUGSoutput$summary["psi","50%"]