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.
# 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# }