locate.fossil: Locate a fossil lineage in a tree using continuous characters

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Locate a fossil lineage in a tree using continuous characters

Description

Uses ML to place a fossil lineage into a tree using continuous traits following Revell et al. (2015).

Usage

locate.fossil(tree, X, ...)

Arguments

tree	an object of class "phylo".
X	a matrix with continuous character data.
...	optional arguments including time.constraint which can be a scalar (positive height above the root of the fossil or negative time before present) or a vector (age range of fossil, either positive or negative); edge.constraint, which is equivalent to constraint in locate.yeti; plot, rotate, and quiet, which have the same interpretation (and defaults) as the equivalent arguments in locate.yeti.

Value

Optimized tree as an object of class "phylo".

Author(s)

Liam Revell [e-mail]

References

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

Felsenstein, J. (2002) Quantitative characters, phylogenies, and morphometrics. In: MacLeod, N. and P. Forey (Eds.) Morphology, Shape and Phylogeny (pp. 27-44). Taylor and Francis, London.

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. (2015) Placing cryptic, recently extinct, or hypothesized taxa into an ultrametric phylogeny using continuous, character data: A case study with the lizard Anolis roosevelti. Evolution, 69, 1027-1035.

phytools documentation built on Nov. 10, 2023, 1:08 a.m.