anc.trend: Ancestral character estimation with a trend

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Ancestral character estimation with a trend

Description

This function estimates the evolutionary parameters and ancestral states for Brownian evolution with a directional trend.

Usage

anc.trend(tree, x, maxit=2000)

Arguments

tree	an object of class "phylo".
x	a vector of tip values for species; names(x) should be the species names.
maxit	an optional integer value indicating the maximum number of iterations for optimization.

Details

Note that this will generally only work and produce sensible results for a phylogeny with some non-contemporaneous tips (i.e., a tree with some fossil species).

The function uses optim with method= "L-BFGS-B" internally; however, optimization is only constrained for the sig2 which must be > 0.

Value

An object of class "anc.trend" with the following components:

ace	a vector with the ancestral states.
mu	a trend parameter per unit time.
sig2	the variance of the BM process, \sigma^2.
logL	the log-likelihood.
convergence	the value of $convergence returned by optim() (0 is good).

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

ace, anc.Bayes, anc.ML, optim

Examples

## simulate tree & data using fastBM with a trend (m!=0)
tree<-rtree(n=26,tip.label=LETTERS)
x<-fastBM(tree,mu=4,internal=TRUE)
a<-x[as.character(1:tree$Nnode+Ntip(tree))]
x<-x[tree$tip.label]
## fit no trend model
fit.bm<-anc.ML(tree,x,model="BM")
print(fit.bm)
## fit trend model
fit.trend<-anc.trend(tree,x)
print(fit.trend)
## compare trend vs. no-trend models & estimates
AIC(fit.bm,fit.trend)
layout(matrix(c(3,4,1,2,5,6),3,2,byrow=TRUE),
    heights=c(1.5,3,1.5),widths=c(3,3))
xlim<-ylim<-range(c(a,fit.bm$ace,
    fit.trend$ace))
plot(a,fit.bm$ace,pch=19,
    col=make.transparent("blue",0.5),
    xlab="true ancestral states",
    ylab="ML estimates",
    main=paste("Comparison of true and estimated",
    "\nstates under a no-trend model"),font.main=3,
    cex.main=1.2,bty="l",cex=1.5,
    xlim=xlim,ylim=ylim)
lines(xlim,ylim,lty="dotted")
plot(a,fit.trend$ace,pch=19,
    col=make.transparent("blue",0.5),
    xlab="true ancestral states",
    ylab="ML estimates",
    main=paste("Comparison of true and estimated",
    "\nstates under a trend model"),font.main=3,
    cex.main=1.2,bty="l",cex=1.5,
    xlim=xlim,ylim=ylim)
lines(xlim,ylim,lty="dotted")
par(mfrow=c(1,1))

phytools documentation built on June 22, 2024, 10:39 a.m.