we have been over the DF question before, but I have another result I am
The problem: only a subsection of the full data has a particular effect
recorded. We wish to estimate this effect without subsetting the data,
given that other effects of significance are estimated from the complete
data, and these estimates behave poorly in the subset. So, we wish to
analyse a data set where factor levels are missing for all animals without
Previously, Arthur indicated that missing factor levels are treated as a
zero level. In our case we have four factor levels (+ the one that is
missing). The DF reported are 4 instead of three, and all levels have a
non-zero solution reported. No equations are generated for level zero,
which probably explains why there is no zero solution for level zero.
How are these results to be interpreted? Are the solutions meaningful, and
what exactly do they represent a deviation from for the effect of interest?
I can't really see that we should have four degrees of freedom for
starters, or that you can generate a legitimate DF by having missing
records. There is no equation fitting a dummy effect for all animals where
the level is missing (unless this became one of the singularities
reported?). We get identical solutions when we specify the effect is only
to be fit for animals with records (eg using at(yesrecord,1).effect).
Any comments much appreciated.
Animal Genetics and Breeding Unit
University of New England
Armidale, NSW, 2351
Ph (ISD): -61-2-67733788
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