Dear Alex,
I show the coding below for estimating the covariance
between direct and maternal.
First, you have male parent as a pedigree factor, f_gp as a simple factor.
You need to declare both as pedigree factors so the identities
are alligned.
I would rerun the existing model with this change.
The variance components for f_gp will probably change by
a factor of 4 or 16 I guess as they are changed to a tree basis
and this may alter the Error variance which I thnk
had 3/4 or 15/16 ths of the f_gp variance in it before.
I may have the details wrong but fit the model and see.
Then, you can proceed to adding in the covariance.
Covariances are sometimes difficult for ASREML to estimate
if the estimates go outside the parameter space. But lets try.
The method depends on having Tr.m_p and Tr.f_gp together in the model.
With m_p and f_gp having the same size, we can regard this as
6 x N rather than 3 x N + 3 x N
So we change the end of the job to
1 2 1 # was 1 2 2
0 0 0 # unchanged
3 0 US 0.4 0.9 16 0.5 6.5 17 # unchanged
Tr.m_p 2
6 0 US !+21
0.02
0.2 2.2
0.08 0.5 3.7
0.01 0.01 0.01 0.02
0.01 0.01 0.01 0.05 1.6
0.01 0.01 0.01 0.03 0.4 1.3
m_p
Except I would put in the solutions from the reruns as starting values.
I have put 0.01 as initial values of the covariances.
It is important that the intial values
are consistent (i.e. do not generate a non positve definite matrix)
NB ASREML expects the halfstored matrix is lower triangle rowwise =
upper triangle column-wise. Your larout below is upper triangle rowwise.
I hope this gets you going.
Arthur
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> From: Alex.Hulzebosch@alg.vf.wau.nl
> Date: Fri, 12 Mar 1999 10:21:22 +0100
> Subject: multitrait siremgs-model problem
> To: asreml@ram.chiswick.anprod.csiro.au
> MIME-version: 1.0
>
> I am trying to fit a multivariate sire maternal grandsire model. The solutions
> I get seem to be OK. However I would like to estimate the covariance between
> the sire and maternal component of the same trait. Is this possible? I have
> used the following .as file:
>
> calveas 6
> weight
> gest
> race 6
> sexparity 4
> yearseason 100 !I
> m_p 90 !P ===> m_p !P
> f_gp 129 !I ===> f_gp !P
>
> ../pest/mgs.ped !MGS
> ../pest/mgsall.dat !skip 1
> calveas weight gest ~ Trait Tr.race Tr.sexparity !r Tr.m_p Tr.f_gp !f
> Tr.yearseason
> 1 2 2
> 0 0 0
> 3 0 US 0.4 0.9 16 0.5 6.5 17
> Tr.m_p
> 3 0 US 0.02 0.2 2.2 0.08 0.5 3.7
> m_p
> Tr.f_p
> 3 0 US 0.02 0.05 1.6 0.03 0.4 1.3
> f_p
>
> For the covariances I get the following estimates:
> Sire
> Maternal
> Trait 1 (Calveas) 0.015 0.16 0.085
> Trait 2 (Weight) 2.0 0.52
> Trait 3 (Gest) 3.2
> Trait 1 0.019 0.059 0.035
> Trait 2 1.4 0.37
> Trait 3 1.1
>
>
> In fact it might be possible to estimate the (non-symmetric) 3x3 matrix with
> covariances between the maternal and sire components.
> Could anyone help me with this problem?
>
> Alex Hulzebosch
> Department of Animal Breeding and Genetics
> Wageningen, the Netherlands
> --
> Asreml mailinglist archive: http://www.chiswick.anprod.csiro.au/lists/asreml
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Arthur Gilmour PhD mailto:Arthur.Gilmour@agric.nsw.gov.au
Senior Research Scientist (Biometrics) fax: <61> 2 6391 3899
NSW Agriculture <61> 2 6391 3922
Orange Agricultural Institute telephone work: <61> 2 6391 3815
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