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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