phytools (version 1.2-0)

fit.bd: Fits birth-death (speciation/extinction) model to reconstructed phylogeny

Description

The function fit.bd fits a birth-death model to a phylogenetic tree with edge lengths and a (potentially) incomplete sampling fraction.

The function fit.yule fits a pure-birth model with a (potentially) incomplete sampling fraction.

The function lik.bd computes the likelihood of a set of birth & death rates given the set of branching times computed for a tree and a sampling fraction.

Usage

fit.bd(tree, b=NULL, d=NULL, rho=1, ...)
fit.yule(tree, b=NULL, d=NULL, rho=1, ...)
lik.bd(theta, t, rho=1, N=NULL)
# S3 method for fit.bd
print(x, ...)

Value

fit.bd returns an object of class "fit.bd" which can be printed. This object is a list containing the fitted model parameters, likelihood, optimization conditions, a summary of the optimization, and a likelihood function.

fit.yule returns an object of class "fit.yule". This object is a list containing the fitted model parameter, likelihood, optimization conditions, a summary of the optimization, and a likelihood function.

Arguments

tree

object of class "phylo".

b

birth (speciation) rate. Presently doesn't do anything as the rate cannot be fixed.

d

death (extinction) rate. Presently doesn't do anything as the rate cannot be fixed.

rho

sampling fraction.

theta

vector of b and d for likelihood function.

t

branching times for calculation of the likelihood.

N

number of tips in the tree.

x

object of class "fit.bd" for print method.

...

optional arguments.

Author

Liam Revell

References

Nee, S., May, R. M. and Harvey, P. H. (1994) The reconstructed evolutionary process. Philosophical Transactions of the Royal Society of London B, 344, 305-311.

Stadler, T. (2012) How can we improve the accuracy of macroevolutionary rate estimates? Systematic Biology, 62, 321-329.

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

See Also

birthdeath

Examples

data(salamanders)
## compute sampling fraction based on 55 species of Plethodon
sampling.f<-Ntip(salamanders)/55
## fit birth-death model
bd.fit<-fit.bd(salamanders,rho=sampling.f)
print(bd.fit)
## fit Yule model
yule.fit<-fit.yule(salamanders,rho=sampling.f)
print(yule.fit)
## compare b-d and yule models
anova(yule.fit,bd.fit)
## create a likelihood surface for b-d model
ngrid<-100
b<-seq(0.01,0.06,length.out=ngrid)
d<-seq(0.005,0.03,length.out=ngrid)
logL<-sapply(d,function(d,b) sapply(b,function(b,d) 
    bd.fit$lik(c(b,d)),d=d),b=b)
contour(x=b,y=d,logL,nlevels=100,
    xlab=expression(lambda),
    ylab=expression(mu),bty="l")
title(main="Likelihood surface for plethodontid diversification",
    font.main=3)
points(bd.fit$b,bd.fit$d,cex=1.5,pch=4,
    col="blue",lwd=2)
legend("bottomright","ML solution",pch=4,col="blue",
    bg="white",pt.cex=1.5,pt.lwd=2)