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  ASReml  ~  ASreml-R additve genetic-maternal genetic covariance

craig walling
Posted: Wed Apr 15, 2009 11:23 am Reply with quote
Joined: 10 Apr 2009 Posts: 8
Hi,

I am trying to use ASreml-R to estimate the covariance between additive and maternal genetic variances for birth weight. The model runs fine without trying to specify the covariance, coded as:

model4<-asreml(fixed= wt ~ 1, random = ~ped(animal, var=T) + ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

However, I can't get the model to run linking animal and mother together. I have tried specifying this model as both:

model5<-asreml(fixed= wt ~ 1, random = ~ us(link(ped(animal, var=T))):ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

model6<-asreml(fixed= wt ~ 1, random = ~ us(link(~ped(animal, var=T))):ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

neither of which will run. The first attempt give an error message "Error in switch(mode(x), "NULL" = structure(NULL, class = "formula"), : invalid formula". The second seems to make more of an attempt to run (it takes longer to return an error message), but then fails and gives "Error in data[[obj]] : object is not subsettable".

Has anyone tried to do this before? Am I doing something obviously wrong? Is it possible to fit these covariances in ASreml-R, given that the information in the manual is very limited?

Many thanks for any help you can offer

Craig
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david.butler
Posted: Fri Apr 17, 2009 6:37 am Reply with quote
Joined: 12 Dec 2008 Posts: 24
Craig,

The syntax of link() is limited and virtually restricted to the random regression type case. General covariance structures that parallel the capabilities in asreml standalone are implemented in Release 3 with the "str()" function. Release 3 will be available in the coming weeks as soon as the documentation is updated.

Dave.


From: ASReml users discussion group [mailto:ASREML-L@DPI.NSW.GOV.AU] On Behalf Of craig walling
Sent: Wednesday, 15 April 2009 9:24 PM
To: ASREML-L@DPI.NSW.GOV.AU
Subject: ASreml-R additve genetic-maternal genetic covariance



Hi,

I am trying to use ASreml-R to estimate the covariance between additive and maternal genetic variances for birth weight. The model runs fine without trying to specify the covariance, coded as:

model4<-asreml(fixed= wt ~ 1, random = ~ped(animal, var=T) + ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

However, I can't get the model to run linking animal and mother together. I have tried specifying this model as both:

model5<-asreml(fixed= wt ~ 1, random = ~ us(link(ped(animal, var=T))):ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

model6<-asreml(fixed= wt ~ 1, random = ~ us(link(~ped(animal, var=T))):ped(mother, var=T) + ide(mother, var=T), ginverse=list(animal=Dped, mother=Dped), data=juvtraits)

neither of which will run. The first attempt give an error message "Error in switch(mode(x), "NULL" = structure(NULL, class = "formula"), : invalid formula". The second seems to make more of an attempt to run (it takes longer to return an error message), but then fails and gives "Error in data[[obj]] : object is not subsettable".

Has anyone tried to do this before? Am I doing something obviously wrong? Is it possible to fit these covariances in ASreml-R, given that the information in the manual is very limited?

Many thanks for any help you can offer

Craig








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