-----Original Message-----
From: R-sig-meta-analysis <r-sig-meta-analysis-bounces at 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 at r-project.org
Cc: Pengzhen Huang <maiqi1317 at 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