Re: [Bugs-r-devel] as.mcmc.list

[Uwe L. <li...@st...>]

Gorjanc Gregor wrote:
> Hi,
> 
> Recently as.mcmc.list.bugs has been introduced as contrbuted by Mike Meredith.
> I think there are some flaws. For example. I have an bugs object with the following details:
> 
> 3 chains, each with 1e+05 iterations (first 10000 discarded), n.thin = 10 n.sims = 27000 iterations saved
> 
> i.e.
> 
> List of 24
>  $ n.chains       : num 3
>  $ n.iter         : num 1e+05
>  $ n.burnin       : num 10000
>  $ n.thin         : num 10
>  $ n.keep         : num 9000
>  $ n.sims         : num 27000
> 
> however, when I create an mcmc object I get
> 
> List of 3
>  $ : mcmc [1:9000, 1:59] 12 12.4 12.8 13.1 12.1 ...
>   ..- attr(*, "dimnames")=List of 2
>   .. ..$ : chr [1:9000] "1001" "1002" "1003" "1004" ...
>   .. ..$ : chr [1:59] "alpha" "deviance" "l[10]" "l[11]" ...
>   ..- attr(*, "mcpar")= num [1:3] 1001 10000 1
> ...
> 
> The last line, i.e., the mcpar, is wrong. It should be
> 
>   ..- attr(*, "mcpar")= num [1:3] 10001 100000 10
> 
> I also do not see the point in setting the rownames, since they are not reflecting the reality, i.e.,
> my chains where thinned, but the rownames are 1001, 1002, ...
> 
> Bellow is the diff of the "fixed" function, but before I commit it, I would like to make sure
> there is consensus about this. I could not find Mikes e-mail. Uwe?

Thanks for the fix. I had not tested all possible cases, obviously. I'm 
fine with it, hence just commit unless anybody else objects. CCing Mike.

Best,
Uwe



> Index: as.mcmc.list.bugs.R
> ===================================================================
> --- as.mcmc.list.bugs.R (revision 105)
> +++ as.mcmc.list.bugs.R (working copy)
> @@ -5,14 +5,14 @@
>      if(dim(x$sims.array)[2] != x$n.chains)
>          stop("Inconsistancy in bug object regarding the number of chains.")
>      mclis <- vector("list", x$n.chains)
> -    strt <- x$n.burnin%/%x$n.thin + 1
> -    end <- x$n.iter%/%x$n.thin
> +    strt <- x$n.burnin + 1
> +    end <- x$n.iter
>      ord <- order(dimnames(x$sims.array)[[3]])
> -    if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
> +    ## This is not necedarry, since strt and end match dims of sims.array
> +    ## if(end - strt + 1 < nrow(x$sims.array[,1,ord])) end <- end + 1
>      for(i in 1:x$n.chains) {
>          tmp1 <- x$sims.array[,i,ord]
> -        rownames(tmp1) <- strt:end
> -        mclis[[i]] <- mcmc(tmp1, strt, end, 1)
> +        mclis[[i]] <- mcmc(tmp1, start=strt, end=end, thin=x$n.thin)
> 
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