Re: Using the 'onlyuse' parameter in asreml.predict

From: Arthur Gilmour <arthur.gilmour_at_CARGOVALE.COM.AU>
Date: Tue, 28 Apr 2009 13:35:54 +1000

Dear Kiwi,
It seems your variance components are
ped(RowTree) 95.4
Female 28.8
Male 2.1
Family 1.7
Residual 160.0

I assume there are multiple tree plots but the residual plot variance is

The z-ratio supports the proposition that Male and Family components
are negligible.

I assume the pedigree picks up the additive genetic variance.
Female represents then a maternal effect (mother tree effect).

Heritability is not a clear concept to me with respect to this model
but is usually defined as a function of variance components, based on
the additive component.
i.e. 95.4 / 288
but you might have a different expression.

Your question though queries the use of 'onlyuse' in a predict

Predicting RowTree with only='ped(RowTree)'
should just produce the BLUPs for ped(RowTree), the same as a returned
in the
solutions (coeff).

Without 'only=', they will include average effects of fixed terms
in the model. I do not understand why you call this 'heritability'

Now you might also want to add back the Female effects.
It may not be possible in ASReml 2. If possible, it will require
the present option to properly associate the levels.

I hope this helps

On Tue, 2009-04-28 at 00:55 +0100, kiwi wrote:
> I'm trying to understand just when I should use 'only' with predict().
> My variance components look like this:
> Code:
> gamma component std.error z.ratio
> constraint
> ped(RowTree) 5.965357e-01 9.543092e+01 1.293414e+02 0.73782176
> Positive
> Subblock 1.011929e-07 1.618835e-05 6.775276e-06 2.38932739
> Boundary
> Pplot 2.156411e-07 3.449723e-05 1.443805e-05 2.38932739
> Boundary
> Female 1.804322e-01 2.886467e+01 3.754475e+01 0.76880724
> Positive
> Male 1.296493e-02 2.074068e+00 2.238159e+01 0.09266845
> Positive
> FamilyNo 1.113177e-02 1.780807e+00 7.096272e+00 0.25094959
> Positive
> R!variance 1.000000e+00 1.599752e+02 6.695407e+01 2.38932739
> Positive
> We're interested in (among other things) what the relatively large
> number of trees identified by RowTree can tell us about the individual
> parents described in the pedigree. In case it's not obvious, each
> progeny is a member of a FamilyNo which is related to the Male and
> Female columns in a way described in the pedigree.
> If I do a prediction with no 'only' term, I end up with heritability
> for the parents I'm interested in of something like 0.68 (steps not
> shown). If I include a term
> Code:
> only = 'ped(RowTree)'
> , it's about 0.59.
> What I need to know is under what circumstances would it be
> appropriate to use and when should I omit the 'only' argument? If I
> understand correctly, the predict stage will be averaging over the
> other terms. I can't see just when that would make sense. Perhaps it's
> just that it's not doing what I think it does, so I'd be grateful to
> receive any clarification.
> Would it be different if I'm calculating heritability of the progeny?
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May the God and Father of the Lord Jesus Christ guide and bless you.
Arthur Gilmour
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Received on Wed Apr 28 2009 - 13:35:54 EST

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