Problems with coda

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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