Never used coplot, but why not try removing the rows with missing variables?
Perhaps with:

dat <- cbind(E2=resid(baea.ancova6, type = "normalized"), year, population)
coplot(E2~year|population, data=dat[apply(dat, 1, function(x) !any(is.na
(x))),])

Regards,
Simon Knapp

On Mon, Jan 18, 2010 at 6:54 AM, LisaB <lisabaril@hotmail.com> wrote:

>
> Hello - I'm trying to construct a coplot to check the residuals conditioned
> on a factor using the following formula, however I keep getting an error
> message.  I've used the same formula for another data set and it worked
> fine
> - the only difference is that now I have missing values for each level (2
> levels) of the factor. Is this the problem and how can I fix it.  Thank
> you.
>
> > E2 <- resid(baea.ancova6, type = "normalized")
> > coplot(E2~year|population)
> Error in bad.lengths() : incompatible variable lengths
>
> --
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>
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