phytools (version 0.7-20)

anc.trend: Ancestral character estimation with a trend

Description

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

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.

logL

the log-likelihood.

convergence

the value of $convergence returned by optim() (0 is good).

Details

Note that this will generally only work and produce sensible results for a phylogeny with some non-contemporary tips (i.e., a tree with some fossil species). The function uses optim with method= "L-BFGS-B"; however optimization is only constrained for the sig2 which must be >0.

References

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

See Also

ace, anc.Bayes, anc.ML, optim

Examples

# NOT RUN {
tree<-rtree(20)
x<-fastBM(tree,mu=2) # simulate using fastBM with a trend (m!=0)
anc.trend(tree,x) # fit model & estimate ancestral states
# }