Re: residual covariance (repeated measures)

From: Craig Hardner <c.hardner_at_UQ.EDU.AU>
Date: Wed, 23 Sep 2009 16:47:39 +1000

Dear Brian


I have been working through this issue a number of ways. You will
recall I was working with a trait measured on 2 different years.


I have just created a data set that has balanced records (i.e missing
values for those individuals that were assessed in one year but not
assessed in the other year).


I have tried this model:


ind.02<- asreml(avfruitwt~1+Year+Plant_year+Year:Plant_year,

                random =~us(Year):ped(Ind),

                ginverse =list(Ind=Ainv),

                rcov =~us(Year):Ind,

                na.method.X ='include',

                data =ofulladata,

                maxiter =50)


but get a R!variance component=1 in the variance component estimates
(included below), which I do believe I want as I would have thought the
residual variance should be contained in the us(Year) estimates . This
however appears to be the same structure of variance components as for
the multivariate analysis for example 8.8 in the ASReml-R manual. Am I
missing something? Is there a way to indicate not to include a variance
component for R!variance?


                                       gamma component std.error
z.ratio constraint

Year:ped(Ind)!Year.2000-01:2000-01 27620.966 27620.966 10164.303
2.7174482 Unconstrained

Year:ped(Ind)!Year.2001-02:2000-01 26057.113 26057.113 9509.155
2.7402133 Unconstrained

Year:ped(Ind)!Year.2001-02:2001-02 27838.093 27838.093 10468.244
2.6592898 Unconstrained

R!variance 1.000 1.000 NA
NA Fixed

R!Year.2000-01:2000-01 7509.581 7509.581 5346.690
1.4045290 Unconstrained

R!Year.2001-02:2000-01 4130.145 4130.145 5030.054
0.8210937 Unconstrained

R!Year.2001-02:2001-02 12003.223 12003.223 5526.508
2.1719361 Unconstrained


Thanks again


Dr Craig Hardner

Research Fellow

School of Land, Crop and Food Sciences

University of Queensland

St Lucia 4072 Queensland, Australia

ph: +61 7 3346 9465

email: <>


From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of brian.cullis_at_INDUSTRY.NSW.GOV.AU
Sent: Wednesday, 23 September 2009 11:20 AM
Subject: Re: residual covariance (repeated measures)


Dear craig
yes this is correct. I hope this works ok

warm regards

Brian Cullis|Research Leader, Biometrics &
Senior Principal Research Scientist |
Industry & Investment NSW | Wagga Wagga Agricultural Institute | Pine
Gully Road | Wagga Wagga NSW 2650 |
PMB | Wagga Wagga NSW 2650
T: 02 6938 1855 | M: 0439 448 591 | F: 02 6938 1809 | E:,au
W: |

Visiting Professorial Fellow
School of Mathematics and Applied Statistics
Faculty of Informatics
University of Wollongong

Faculty of Agriculture, Food & Natural Resources
The University of Sydney

Adjunct Professor
School of Computing and Mathematics
Charles Sturt University

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Received on Thu Sep 23 2009 - 16:47:39 EST

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