Wednesday, December 5, 2012

Hypothesis testing using fitDiversityModel

A user had this question about using the function fitDiversityModel (which implements an ML version of the method in Mahler et al. (2010) to test hypotheses about phenotypic diversification:

I have one short question. In the paper by L. Mahler & al. they also tested the model with a single evolutionary rate. I’m asking me if it is “enough” to write it like that: Constant.time.results <- fitDiversityModel(tree,x,d=NULL)

The answer is "no" - but it is very easy to conduct the desired test. If fitDiversity(...,d=NULL), then the function estimates lineage density at each node as if the radiation is occurring within a single region (and there is no extinction or missing taxa - but that is a matter for another day); and then fits a model in which the rate of evolution varies as a function of lineage density. This will generally not be our null model. For that, we should specify d to be a vector of zeroes. We can then use a likelihood ratio test (for example) to test the null hypothesis that the pace of evolution has declined with increasing lineage density.

Here's a worked example, simulated so that the null is correct:
> require(phytools)
> # simulate tree & data under the null
> tree<-pbtree(n=100)
> x<-fastBM(tree)
> # fit the lineage-density model assuming a single region
> # (i.e., all contemporary ancestors were competitors)
> fitLD<-fitDiversityModel(tree,x)
no values for lineage density provided; computing assuming single biogeographic region
> fitLD
$logL
[1] -126.7954
$sig0
[1] 1.171704
$psi [1] -0.004116475
$vcv
            sig0           psi
sig0  0.121592376 -1.833989e-03
psi  -0.001833989  3.240988e-05

> # now fit the null hypothesis of constant rate
> d<-rep(0,tree$Nnode); names(d)<-1:tree$Nnode+length(tree$tip)
> fitNull<-fitDiversityModel(tree,x,d)
psi not estimable because diversity is constant through time.
> fitNull
$logL
[1] -127.0581
$sig0
[1] 0.9602251
$vcv
            sig0
sig0 0.01844064

> # now test using LR
> LR<-2*(fitLD$logL-fitNull$logL)
> P<-pchisq(LR,df=1,lower.tail=F)
> P
[1] 0.4685722

The null model is just pure Brownian motion; and we would obtain the same parameter estimate and likelihood using, say, fitContinuous in the geiger package:
> fitContinuous(tree,x)
Fitting BM model:
$Trait1
$Trait1$lnl
[1] -127.0581
$Trait1$beta
[1] 0.9602253
$Trait1$aic
[1] 258.1161
$Trait1$aicc
[1] 258.2411
$Trait1$k
[1] 2

That's it.

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