R: Ancestral character estimation with a trend

anc.trend {phytools}

R Documentation

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.

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.

Value

A list 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).

Author(s)

Liam Revell liam.revell@umb.edu

References

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

Examples

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

[Package phytools version 0.4-60 Index]