phytools: locate.yeti – R documentation

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locate.yeti

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. (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

Phylogenetic Tools for Comparative Biology (and Other Things)

v0.7-70

GPL (>= 2)

Authors

Liam J. Revell

Initial release

2020-9-19