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

-----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

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

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

logLik(nonphy)-logLik(phy)

anova.rma(nonphy,phy)

-----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: Thursday, November 30, 2023 14:30
To: r-sig-meta-analysis at r-project.org
Cc: Pengzhen Huang <maiqi1317 at 163.com>
Subject: Re: [R-meta] The phylogenetic signal of a single trait and its
significance

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

From these results, the phylogeny in the phylogenetic model has zero variance
and the phylogenetic signal lambda is very low. Do you think this makes sense?

Thank you again for all your replies!

All the best,
Pengzhen

---- Replied Message ----
| From | Viechtbauer, Wolfgang
(NP)<wolfgang.viechtbauer at maastrichtuniversity.nl> |
| Date | 11/29/2023 13:54 |
| To | R Special Interest Group for Meta-Analysis<r-sig-meta-analysis at r-
project.org> |
| Cc | Pengzhen Huang<maiqi1317 at 163.com> |
| Subject | RE: [R-meta] The phylogenetic signal of a single trait and its
significance |
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 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