DF's with nested effects
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DF's with nested effects

Hi all,

I am having trouble coming up with the right DFs (and apparently labels in
the solution file) for nested effects. For example, I have 8 years of data
and a treatment (2 levels) has been applied in year 7 only. I have tried
fitting this as:

trait ~ mu year at(year,7).(treat)

which gives me 7DF for year and still 2DF for treatment. The problem seems
to arise due to missing values for treatment - even though these only occur
in the years where this effect is not fit, and there are no missing values
in the year where this factor is fit. I can (apparently?) fix it by making
sure the factor levels are zero rather than missing. Well, at least the DF
for the treatment become 1 which is what I expected. Previously defining
the treatment seems to have no impact. It is not an option to delete the
records with missing treatments unless I want to throw out an entire years
data (which I don't).

However, I am not sure that making factor levels not missing (but all
zeros) is actually the correct solution. For both the above cases in the
solution file the label seems to show that treatment is fit within year 1
(which can't be right as all factors in year 1=0).

 at(myear,7).csupp        1.0001             0.000       0.000
 at(myear,7).csupp        1.0002             7.248       4.146

As the data is ordered from 1 to 8, I don't think the confusion is arising
for year. Why does the label not state that the appropriate year is 7?

What am I missing here?



Kim Bunter (M.Rur.Sc)
PhD Student
Animal Genetics and Breeding Unit
University of New England
Armidale, NSW, 2351

Ph:  (02) 6773 3788
Fax: (02) 6773 3266
email: kbunter@metz.une.edu.au
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