<fabio.ufla@yahoo.com.br>

Here is a somewhat crude fix; it adds an additional parameter
(checklevels) to the lmer_finalize and glmer_finalize functions in
lme4 that turns off the unwanted sanity check.  The default is
checklevels=TRUE, which maintains the previous behavior.  The
pedigreemm function is then changed to set checklevels=FALSE before
calling the appropriate finalizing function.  I'm running these
changes locally and they seem to work fine.

Comments or suggestions are welcome, as is consideration of this
change or some variant on it for inclusion in the pedigreemm and lme4
packages.

----- in lmer.R in the lme4 package -----
lmer_finalize <- function(fr, FL, start, REML, verbose, checklevels=TRUE)
{
...
### This checks that the number of levels in a grouping factor < n
### Only need to check the first factor because it is the one with
### the most levels.
    if (checklevels & !(length(levels(dm$flist[[1]])) < length(Y)))
...

glmer_finalize <- function(fr, FL, glmFit, start, nAGQ, verbose,
checklevels=TRUE)
{
...
### This checks that the number of levels in a grouping factor < n
### Only need to check the first factor because it is the one with
### the most levels.
    if (checklevels & !(length(levels(dm$flist[[1]])) < ncol(dm$Zt)))
...

----- in pedigree.R in the pedigreemm package -----
pedigreemm <-
    function(formula, data, family = NULL, REML = TRUE, pedigree = list(),
...
    lmf$checklevels <- FALSE;
    ans <- do.call(if (!is.null(lmf$glmFit)) lme4:::glmer_finalize
else lme4:::lmer_finalize, lmf)
...