prunePed in MCMCglmm

Hi all,

I'm having problems using the prunePed function in the MCMCglmm package and
wondered if anyone else had come across a similar issue.

The result is that I end up with a "prunedpedigree" file which contains
5,161 records- one for each phenotyped individual, giving their dam and
sire. However, it does not provide additional records for the parentage of
their parents or other informative relatives.

ISTM prunePed() doesn't work if the individual IDs are factors (numeric 
and character are OK).  With keep=FALSE, prunePed() reduces to this loop:

     nind <- length(ind.keep) + 1
     while (length(ind.keep) != nind) {
         nind <- length(ind.keep)
         ind.keep <- union(na.omit(c(unlist(pedigree[, 2:3][match(ind.keep,
             pedigree[, 1]), ]))), ind.keep)
     }
     pedigree <- pedigree[sort(match(ind.keep, pedigree[, 1])),]

which fails for factor IDs in the union of the parental IDs with the 
existing set of individual IDs. This was a bit confusing in that the
BTped example uses factor IDs.

Cheers, David Duffy.

| David Duffy (MBBS PhD)
| email: David.Duffy at qimrberghofer.edu.au  ph: INT+61+7+3362-0217 fax: -0101
| Genetic Epidemiology, QIMR Berghofer Institute of Medical Research
| 300 Herston Rd, Brisbane, Queensland 4006, Australia  GPG 4D0B994A