This function estimates the evolutionary parameters and ancestral states for Brownian evolution using likelihood. It is also possible (for model="BM") to allow for missing data for some tip taxa.
anc.ML(tree, x, maxit=2000, model=c("BM","OU","EB"), ...)an object of class "phylo".
a vector of tip values for species; names(x) should be the species names.
an optional integer value indicating the maximum number of iterations for optimization.
model of continuous character evolution ont he tree. It's possible that only model="BM" & model="EB" work in the present version as model="OU" has not be thoroughly tested & some bugs were reported for an earlier version.
other arguments.
An object of class "anc.ML" with at least the following four elements (if not more, depending on model):
the variance of the BM process.
a vector with the ancestral states.
the log-likelihood.
the value of $convergence returned by optim() (0 is good).
Because this function relies on a high dimensional numerical optimization of the likelihood function, fastAnc should probably be preferred for most purposes. If using anc.ML, users should be cautious to ensure convergence. This has been ameliorated in phytools >= 0.2-48 by seeding the ML optimization with the result from fastAnc. For model="EB" this should also not be a problem as the numerical optimization is performed for only sig2 and r, while the ML values of the ancestral states are obtained during every iteration of the optimization algorithmically using the re-rooting method.
Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.
Schluter, D., Price, T., Mooers, A. O., and Ludwig, D. (1997) Likelihood of ancestor states in adaptive radiation. Evolution 51, 1699-1711.
# NOT RUN {
tree<-pbtree(n=50)
x<-fastBM(tree) # simulate using fastBM
anc.ML(tree,x) # fit model & estimate ancestral states
# }
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