Nothing
coda.create <- function(object,file.name,write.index=TRUE,par.list=list("mupsi1.chain","e.chain","x.chain","b.chain","y.chain","alpha.chain"),niter=101000,nthin=10) {
p.list.insert <- function(mcmc.list){
pchain = mcmc.list[[c("p.chain")]]
lengthm = length(mcmc.list)
for(i in 1:nrow(pchain)) {
mcmc.list[[length(mcmc.list)+1]] = pchain[i,]
names(mcmc.list)[length(mcmc.list)] = paste('p.',i,sep='')
}
mcmc.list
}
if(nthin!=1) message(paste('NOTE: This function assumes nthin=', nthin, ' has already been applied',sep=''))
if("p.chain"%in%par.list){
nyear = nrow(object$p.chain)
object = p.list.insert(object)
nvars = length(names(object))
par.list = c(par.list,names(object)[(nvars-nyear+1):nvars])
}
iter.num.short=seq(1,niter,by=nthin)
value=NULL
par.list = par.list[par.list!="p.chain"]
iter.num=rep(iter.num.short,length(par.list))
for(i in 1:length(par.list)){
value=c(value,object[[names(object)[names(object)==par.list[i]]]])
}
temp=data.frame(iter.num,value)
write.table(temp,paste(file.name,".txt",sep=""),col.names=FALSE,row.names=FALSE,sep="\t")
if(write.index==TRUE) {
row.num=seq(1,length(iter.num),by=length(iter.num.short))
row.num2=c((row.num[2:length(row.num)]-1),length(iter.num))
write.table(data.frame(as.character(par.list),row.num,row.num2),file=paste(file.name,"_Index",".txt",sep=""),col.names=FALSE,row.names=FALSE,sep="\t") }
}
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