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. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

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 June 22, 2024, 10:39 a.m.