library(R2jags)
source("skate_BUGS_funs.R")
library("coda")
SkateSurveyData <- read.table("../DATA/skate_bugs.dat",header=TRUE)
set.seed(23)
set.seed(round(runif(1,1,10000),0))
st1 <- system.time(tfit_jags <- skate_BUGS_fit(SkateSurveyData))

tfit_jags_mcmc <- as.mcmc(tfit_jags)

results<- list(obj=NULL, coef=unlist(tfit_jags$BUGSoutput$mean), confint.mcmc=HPDinterval(tfit_jags_mcmc), time=c(fit=st1,mcmc=st1), terminfo=NULL, convinfo=list(effsize=effectiveSize(tfit_jags_mcmc), geweke=geweke.diag(tfit_jags_mcmc)))

save("results",file="fit.RData")
save("tfit_jags_mcmc",file="tfit_jags.RData")
save.image()


# alternate Coda diagnostic

                                        #gelman.diag((tfit_jags_mcmc))