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Converting variance ratios using V-predict in ASReml R-4

Functions of variance components and their standard errors can be obtained from the vpredict() function. As the variance parameter names can sometimes be long, the variance parameters are represented in vpredict() by the strings “V1”, “V2”,… in the order they appear in the vparameters component of the asreml object.

By default, for simple models ASReml fits on the ‘gamma’ scale, which means that the returned variance components are variance ratios (for more details please see the ASReml-R Reference Manual, version 4). Therefore, you have to be careful as ASReml-R does not automatically convert variance ratios to variance components or their standard errors. You can fit the model on the component scale if you want to use vpredict() and the standard errors.

Method

ADD : residual = ~idv(units). This will add an additional variance component to the model, that will be fixed to one. For example:

head(harvey)
head(harvey.ped)
harvey.ainv <- ainverse(harvey.ped)

adg0.asr <- asreml(y3 ~ Line,
                   random = ~vm(Calf, harvey.aiv),
                   residual = ~idv(units),
                   data = harvey)

> summary(adg0.asr)$varcomp

                      component std.error   z.ratio bound %ch
vm(Calf, harvey.ainv)  499.5204  500.5139 0.9980149     P   0
units!units            273.1669  410.0206 0.6662273     P   0
units!R                  1.0000        NA        NA     F   0

> # Heritability
> vpredict(adg0.asr, hA ~ V1/(V1 + V2))    
     Estimate        
SEhA 0.6464716 0.5658723
Updated on March 3, 2020

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