Nothing
`setControl` <-
function(model, stem="test",
burn.in=2000, sample=5000, thin=1,
bugs.file=paste(stem,".bug",sep=""),
data.file=paste(stem,"-data.R",sep=""),
inits.file=paste(stem,"-inits.R",sep=""),
monitor.var=model$monitor.var, seed=1)
{
if (class(model) != "modelSegratioMM")
stop("'model' must be of class 'modelSegratioMM'")
if ((length(thin) != 1) & (length(thin) != length(monitor.var)))
stop("Error: 'thin' must be a scalar or vector of thinning for each variable set")
if (length(thin) != 1) { # non-scalar
if (length(names(thin)) == 0) { # set names
names(thin) <- monitor.var
cat("Warning: thin set to\n")
print(thin)
} else { # check that names OK
if (! identical(names(thin), monitor.var)) {# not same in same order
if (identical(sort(names(thin)), sort(monitor.var))) {# OK but reorder
thin <- thin[monitor.var]
} else { # wrong names
stop("incompatible names for 'thin'")
}
}
# names OK
}
}
## superseded now that JAGS Version 1.0 required
##if (.Platform$OS.type == "windows"){# to be fixed after JAGS 0.90 superseded
## jc <- c(paste("seed", seed),
## paste("model in \"",bugs.file,"\"",sep=""))
##} else {
jc <- c(paste("model in \"",bugs.file,"\"",sep=""))
##}
jc <- c(jc, paste("data in \"",data.file,"\"",sep=""),"compile",
paste("inits in \"",inits.file,"\"",sep=""),
"initialize",
paste("update", burn.in))
if (length(thin) == 1 & thin[1] == 1) {
jc <- c(jc, paste("monitor set",monitor.var))
} else {
if (length(thin) == 1) {
thin <- rep(thin,length(monitor.var))
names(thin) <- monitor.var
}
jc <- c(jc, paste("monitor set ",monitor.var,", thin(",thin,")",sep=""))
}
jc <- c(jc, paste("update", sample))
## superseded now that JAGS Version 1.0 required
##if (.Platform$OS.type == "windows"){# to be fixed after JAGS 0.90 superseded
## jc <- c(jc, paste("coda *, stem(\"",stem,"\")",sep=""),"exit")
##} else {
jc <- c(jc, paste("coda *, stem(\"",stem,"CODA\")",sep=""),"exit")
##}
## take model out - waste of space??
res <- list(jags.code=jc, model=model, stem=stem,
burn.in=burn.in, sample=sample, thin=thin, bugs.file=bugs.file,
data.file=data.file, inits.file=inits.file,
monitor.var=monitor.var, call=match.call())
oldClass(res) <- "jagsControl"
return(res)
}
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