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  ASReml  ~  ASREML-R Changing residual variance

Sixburgh58
Posted: Thu Oct 10, 2019 1:46 pm Reply with quote
Joined: 28 Jun 2019 Posts: 1
Hello everyone,

I am using a paternal half-sib, maternal full-sib breeding design to estimate the heritability of sex ratio in a laboratory population of snapping turtles. Each female is mated to 3-4 males. I want to estimate the relative contribution of sire and dam(nested within sire) to sex ratio variation. I have coded sex as a binary trait with females = 0 and males = 1. Here is the model I am running in ASREML-R:

model.1 <- asreml(fixed = sex ~ 1, random = ~sire + sire/dam, data=phenotypeA, family = asr_binomial(link=logit))

With this model, residual variance is fixed at 1 by default. However, I want to set the residual variance to a different value.

I attempted to change the residual variance following the instructions in the ASREML-R reference manual version 4 under section 3.7.1.1 Replacing elements in an internal object. Here is the code I used to change the initial value of residual variance from 1 to 3.2899:

model.2 <- asreml(fixed = sex ~ 1, random = ~sire + sire/dam, data=phenotypeA, family = asr_binomial(link=logit), start.values=TRUE)

model.2$vparameters.table[1, 2] = 3.2899

model.3 <- asreml(fixed = sex ~ 1, random = ~sire + sire/dam, data=phenotypeA, family = asr_binomial(link=logit), G.param = model.2)

After running model.3, and calculating heritability, the estimate remains the same. I checked the variance components table for model.3 and the residual variance remains fixed at 1.

My question is, how can I change the residual variance value from the default?

Thank you very much for your help!
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