When plotting runjags output, how does one plot a single specific variable, when many other variables have similar names? Providing a quoted variable name with the varsargument doesn't seem to do it (it still provides all partial matches).
Here is a simple reproducible example.
N <- 200
nobs <- 3
psi <- 0.35
p <- 0.45
z <- rbinom(n=N, size=1,prob=psi)
y <- rbinom(n=N, size=nobs,prob=p*z)
sink("model.txt")
cat("
model {
for (i in 1:N){
z[i] ~ dbern(psi)
pz[i] <- z[i]*p
y[i] ~ dbin(pz[i],nobs)
} #i
psi ~ dunif(0,1)
p ~ dunif(0,1)
}
",fill = TRUE)
sink()
m <-list(y=y,N=N,nobs=nobs)
inits <- function(){list(psi=runif(1),p=runif(1),z=as.numeric(y>0))}
parameters <- c("p","psi")
ni <- 1000
nt <- 1
nb <- 200
nc <- 3
ad <- 100
library(runjags)
out <- run.jags(model="model.txt",monitor=parameters,data=m,n.chains=nc,inits=inits,burnin=nb,
sample=ni,adapt=ad,thin=nt,modules=c("glm","dic"),method="parallel")
windows(9,4)
plot(out,plot.type=c("trace","histogram"),vars="p",layout=c(1,2),new.window=FALSE)
It should be possible to double quote variables to get an exact match, but this seems to be broken. It should also be possible to specify a logical vector to vars but this seems to be broken for the plot method ... how embarrassing. The following does work though:
# Generate a logical vector to use with matching variable names:
variables <- extract(out, 'stochastic')
variables['psi'] <- FALSE
# Add summary statistics only for the specified variables and pre-draw plots:
out2 <- add.summary(out, vars=variables, plots=TRUE)
plot(out2, plot.type=c("trace","histogram"))
I will fix the other issues for the next release.
Matt