Message-ID: <14609f6a.14433.18c206c3d66.Coremail.maiqi1317@163.com>
Date: 2023-11-30T13:30:13Z
From: Pengzhen Huang
Subject: [R-meta] The phylogenetic signal of a single trait and its significance
In-Reply-To: <AS8PR08MB9193BE3B4475AF34FC33A1538B83A@AS8PR08MB9193.eurprd08.prod.outlook.com>
Dear Wolfgang,
(Sorry that I'm not familiar with the operations!) Great thanks for the reminder! I set wrong random factors before. Based on the R code provided in OSF of your paper, I corrected my code and reran my models. Here are the codes from building the tree to running the full models (with all moderators):
> primatetree <- compute.brlen(primatetree1)
> A <- vcv(primatetree, corr=TRUE)
> dat$phylo <- dat$Species
> nonphy<-rma.mv(ES,variance,data=dat,mods=~Y+X1+X2+X3+X4,random=list(~1|Species/Group))
> nonphy
Multivariate Meta-Analysis Model (k = 152; method: REML)
Variance Components:
estim sqrt nlvls fixed factor
sigma^2.1 0.0484 0.2201 28 no Species
sigma^2.2 0.0199 0.1412 63 no Species/Group
........
> phy<-rma.mv(ES,variance,data=dat,mods=~Y+X1+X2+X3+X4,random=list(~1|Species/Group,~1|phylo),R=list(phylo=A))
> phy
Multivariate Meta-Analysis Model (k = 152; method: REML)
Variance Components:
estim sqrt nlvls fixed factor R
sigma^2.1 0.0484 0.2201 28 no Species no
sigma^2.2 0.0199 0.1412 63 no Species/Group no
sigma^2.3 0.0000 0.0000 28 no phylo yes
....
> logLik(nonphy)-logLik(phy)
'log Lik.' 7.11124e-09 (df=16)
> anova.rma(nonphy,phy)
df AIC BIC AICc logLik LRT pval QE
Full 17 208.0528 257.8162 213.1528 -87.0264 217.0285
Reduced 16 206.0528 252.8889 210.5487 -87.0264 0.0000 1.0000 217.0285