

Dear all

I have phenotypic data for trees of several populations
grown in a common garden and wish to account for phylogenetic non-independence
between populations. The covariance between populations (based on geographic
distance) is contained in a square matrix “M”. I think that the population non-independence
can be incorporated in MCMCglmm, following the code provided by
Jarrod Hadfield in Stone et al (2011):


Msvd<-svd(M)

Msvd<-Msvd$v%*%(t(Msvd$u)*sqrt(Msvd$d))

testdata$Msvd<-Msvd

M1<-MCMCglmm(x~1,
random=~idv(Msvd),data=testdata) 

 

Is
there a way of doing this for an lmer model?

 

Many
thanks

 

Frazer
Sinclair

 

 



 

Stone, G. N., S. Nee, and J.
Felsenstein. 2011. Controlling for non-independance in comparative analysis of
patterns across populations within species. Philosophical
Transactions of the Royal Society B-Biological Sciences 366:1410-1424.


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