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

[Viechtbauer, Wolfgang (NP)]

Dear Pengzhen,

You missed one of the main message of the paper. As shown in the simulation study, it is absolutely essential to include both the random species effect with phylogeny and the random species effect without phylogeny in the model.

As for your questions:

1) If your model includes moderators, then I would include those also when computing lambda.

2) Impossible to say without a reproducible example.

Best,
Wolfgang

> -----Original Message-----
> From: R-sig-meta-analysis <r-sig-meta-analysis-bounces using r-project.org> On Behalf
> Of Pengzhen Huang via R-sig-meta-analysis
> Sent: Tuesday, November 28, 2023 19:22
> To: r-sig-meta-analysis using r-project.org
> Cc: Pengzhen Huang <maiqi1317 using 163.com>
> Subject: [R-meta] The phylogenetic signal of a single trait and its significance
>
> 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