locate.yeti {phytools}

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

Description

Uses ML (or REML) to place a recently extinct, cryptic, or missing taxon on an ultrametric (i.e., time-calibrated) phylogeny following Revell et al. (2015).

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 [e-mail]

References

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

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.