[R-meta] The phylogenetic signal of a single trait and its significance

[Pengzhen Huang]

Dear list,


I'm building a meta-regression model to test the effect of single trait Y on the effect sizes (ES). Here is the full model I fit:


phy.model <- rma.mv(ES, variance, data=dat, mods = ~ Y + X1 + X2 + X3 + X4, random=list(~1|Species/Group), R=list(Species=A))


in which I include the phylogeny of the species as one of random factors. The variables X1-X4 are other potential factors that may influence the relationship between the trait Y and ES. Now I would like to test the phylogenetic signal in the trait Y.


In section 4.2 of the paper (10.1111/2041-210X.13760), the phylogenetic signal lambda can be calculated as the degree of the phylogenetic signal in the overall variance, i.e., (sigma2 of phylogeny)/(overall sigma2). The significance of the lambda can be measured through a likelihood ratio test (LRT): X2 = −2(ll7 −ll9), where ll7 and ll9 are the (restricted) log-likelihoods of the non-phylogenetic model and corresponding phylogenetic model.




I encounter two issues here:
1) If I would like to get the phylogenetic signal in trait Y, should I just use the rma.mv phylogenetic model that contains the variable Y only? I don’t need to include other variables (X1-X4) (like the model above) in the rma.mv phylogenetic model for this, is that so?


2) When testing the significance of the phylogenetic signal using the LRT stated above, the X2 I get is negative and I could not perform a LRT. May I know that why this happens?




Any advice on these issues would be much appreciated!




All the best,
Pengzhen




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