Re: heterogeneous error structure

Hi Mekonnen HaileMariam,

Could you send me the pedigree and data files of Gilmour's RRM examples?.

sdf01a.ped
sdfwfml.csv

Thanks in advance,

Gustavo
> Hi ASreml users,
>
> I sent this message to Dr Arthur Gilmour a few days ago. He is out can not
> respond before Aug. 21. I have two questions
> 1. How to fit error variance as a quadratic or other polynomial
function, etc?
> 2. After fitting c spline to DIM how to get the var-covariance on daily
basis. I guess I
> have to use the Z matrix in *.res file.
> When I fit polynomials I use the coefficients (Q) from the *.res file and
> pre and post multiple the variance-covariance (G).
> Ie Q'GQ.
>
> Mekonnen
> ----- Forwarded by Mekonnen HaileMariam/NRE on 08/08/2006 04:13 PM -----
>
>
> Mekonnen HaileMariam
> 07/08/2006 11:23 AM
>
>
> To: arthur.gilmour_at_AGRIC.NSW.GOV.AU
> cc:
> Subject: Re: heterogeneous error structure
>
> Dear Arthur Gilmour,
>
> Dear Arthur Gilmour,
> This is a response you sent to the question that was raised about fitting
> heterogeneous error structure.
> I am trying to analyse test day milk yield data recorded over 18 to 24
> months of period so there are about 18 to 24 independent error variances.
> Instead of fitting 18 or 20 error variance I want to fit the residual
> variance (e.g. as a quadratic or other polynomial function), such that Vr
> is a continuous function of days in milk.
>
> When I try to run the as file examples that you sent to the list I am
> getting error with G or R header lines.
> I could run the situation with homogenous error variance.
>
> My *.as file as below
>
> Random regession analysis of milk yield
> cow 10000 !I
> sire !P
> ys 13 !I
> herdTD 31083 !I
> ageAtTest
> milkY !M0 !*0.1
> DIM
> TestNum
> sirePed
> TestDATA !MAXIT 20 !ASUV
> milkY ~ mu pol(DIM,-6) pol(ageAtTest,-3) !r pol(DIM,5).cow !r
> pol(DIM,4).sire ,
> !f herdTD mv
> 1 2 2 !STEP .01
> 10000 !S2==1
> 18 0 DIAG 5.96 !GP +17
> 5.90
> 5.96
> 5.96
> 5.96
> 5.90
> 5.96
> 5.96
> 5.96
> 5.90
> 5.96
> 5.96
> 5.96
> 5.90
> 4.96
> 4.96
> 4.96
> 4.90
> pol(DIM,1).cow 2
> pol(DIM,1) 0 US 8.974 !+2 !GP
> 4.012 14.87
> 2.033 5.662 9.557
> -0.2175 0.1828 3.151 7.860
> 0.02175 0.01828 0.3151 0.7860 2.1
> 0.002175 0.001828 0.03151 0.07860 0.21 0.11
> cow
>
> pol(DIM,4).sire 2
> pol(DIM,4) 0 US 2.974 !+14 !GP
> 1.012 4.87
> 1.033 1.662 2.557
> 0.02175 0.1828 1.151 2.860
> 0.002175 0.01828 0.01151 0.2860 0.25
> sire
>
> After this I want to try splines instead of pol.
>
> Thanks for your help
> Mekonnen Haile-Mariam
>
>
> ----- Forwarded by Mekonnen HaileMariam/NRE on 07/08/2006 09:57 AM -----
>
>
> arthur.gilmour_at_AGRIC.NSW.GOV.AU
> Sent by: ASREML-L_at_AGRIC.NSW.GOV.AU
> 09/03/2005 12:26 PM
> Please respond to ASREML-L
>
>
> To: ASREML-L_at_AGRIC.NSW.GOV.AU
> cc:
> Subject: Re: heterogeneous error structure
>
>
> Dear Alistair,
>
> I enclose a random regression example for your consideration.
>
>
>
> Following is an amended version of your job.
>
>
> TRAIT ~ mu SEX AGEF !r pol(sAGE,2).ANIMAL pol(sAGE,2).ide(ANIMAL) MOTHER
> !f mv
> 0 0 2
> #1 1 3
>
> #0 0 ID 3 # single homogeneous error variance
>
> pol(sAGE,2).ANIMAL 2
> pol(sAGE,2) 0 US !GP
> 1.64
> 0.96 7.801
> 0.01 0.01 0.01
> ANIMAL 0 AINV
>
> pol(sAGE,2).ide(ANIMAL) 2
> pol(sAGE,2) 0 US !GP
> 1.64
> 0.96 7.801
> 0.01 0.01 0.01
> ide(ANIMAL) 0 ID
>
> #MOTHER 1
> #MOTHER 0 IDV 0.226
>
>
> This assumes an animal model with repeat observations in time
> for the animals. This has a common independent residual variance plus
> the animal level random regression covariance structure at the residual
> and the genetic level.
>
> You could extend it to have a random regression for the maternal
> component.
>
> It is sometimes difficult to get solutions for the US variance structures
> as it is difficult to identify the good starting values. !GP should
> help.
>
>
> Best wishes in the Name of Jesus Christ, my Saviour.
> Check out http://members.dodo.net.au/~cargovale
>
> Arthur Gilmour PhD
> Principal Research Scientist (Biometrics)
> NSW Department of Primary Industries
> Orange Agricultural Institute, Forest Rd, ORANGE, 2800, AUSTRALIA
>
> mailto:Arthur.Gilmour_at_agric.nsw.gov.au
> fax: 02 6391 3899; 02 6391 3922 Australia +61
> telephone work: 02 6391 3815; home: 02 6364 3288;
>
> http://www.agric.nsw.gov.au/reader/17263
> http://www.asreml.co.uk/
> The ASReml discussion group ASREML-L_at_agric.nsw.gov.au
> has reactivated. To join, mailto:arthur.gilmour_at_agric.nsw.gov.au
> Cookbook: http://uncronopio.org/luis/asreml_cookbook.html
>
> Ellen is doing well after her Hip replacement on 24 Feb but
> she will need crutches for a while yet.
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>

Gustavo A. Gutierrez
Graduate student
Animal Breeding and Genetics
Iowa State University
227 Kildee Hall, Ames
phone office:515-2942712
IA 50011-3150
http://www.ans.iastate.edu/stud/grad/directory/?id=ggr03
Received on Tue Aug 10 2006 - 14:56:34 EST