[R] Problems with coda

[LUK ShunTim]

Geir Olve Storvik wrote:
> 
> I have successfully installed coda in R, and I am also able to read
> output from a Bugs run into
> coda. When I try to plots from CODA Output Analysis Menu, I do however
> _get_ problems:
> CODA Output Analysis Menu
> *************************
> 
> 1:Plots
> 2:Statistics
> 3:List/Change Options
> 4:Return to Main Menu
> Selection: 1
> Error: "missing" illegal use of missing
> 
> Quitting CODA....
> 
> Do you want to save the BUGS output as an R object file(y/n) ?
> 1:
> 
> I tried to use the same data in the Splus version of coda, and that
> worked fine.
> I have also got the same type of problem with coda in R with output from
> a completely different model.
> 

Geir,

I had the same problem and got it fixed by adding an additional argument
"bwf" to the "densplot" function like this: 

"densplot" <-function (x, combine.chains = F, bwf) 
{
        x <- as.mcmc(x)
# *** Argument bwf required        do.densplot <- function(j, i) {
#     Like the next line
         do.densplot <- function(j, i, bwf) {
                #NB Using R scoping rules
                #
                if (missing(i)) 
                        y <- as.vector(x[, j, , drop = T])
                else y <- as.vector(x[, j, i, drop = T])
                y.orig <- y
# *** R complains about the next line, "illegal use of missing"
                if (missing(bwf)) {
                        N <- length(!is.na(y))
                        bw <- 1.06 * min(sd(y), IQR(y)/1.34) * 
                                N^-0.2
                }
                else {
                        bw <- bwf(y)
                        if (bw == 0) 
                                bw <- 0.1
                }
... 

There are a couple of other bugs, too.
I have notified the author/maintainer of the package and according to
him, it may be due to changes in R between 0.62 and 0.63 and he is
trying to look at the problem. 

Regards,

ST
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