locate.yeti {phytools}R Documentation

Locate a cryptic, recently extinct, or missing taxon on a tree

Description

This function uses ML (or REML) to place a recently extinct, cryptic, or missing taxon on an ultrametric (i.e., time-calibrated) phylogeny.

Usage

locate.yeti(tree, X, ...)

Arguments

tree

an object of class "phylo".

X

a matrix with continuous character data.

...

optional arguments including: method ("ML" or "REML", defaults to "ML"); search ("heuristic" or "exhaustive", defaults to "heuristic"); constraint, a vector containing the daughter node numbers from tree$edge for each edge to try; plot a logical argument specifying whether or not to plot the likelihood profile on edges (defaults to FALSE); rotate a logical indicating whether or not to rotate the data based on the input tree; and quiet, which is logical and has an obvious interpretation.

Value

Optimized tree as an object of class "phylo".

Author(s)

Liam Revell liam.revell@umb.edu

References

Felsenstein, J. (1981) Maximum likelihood estimation of evolutionary trees from continuous characters. American Journal of Human Genetics, 25, 471-492.

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

Revell, L. J., D. L. Mahler, R. G. Reynolds, and G. J. Slater. (In press) Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous character data: A case study with the lizard Anolis roosevelti. Evolution.

[Package phytools version 0.4-60 Index]