phytools: rateshift – R documentation

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rateshift

Find the temporal position of one or more rate shifts

Description

Function finds the location of one or more rate shifts. likSurface.rateshift plots the likelihood surface (which is sometimes quite rugged).

Usage

rateshift(tree, x, nrates=1, niter=10, method="ML", ...)
## S3 method for class 'rateshift'
plot(x, ...)
likSurface.rateshift(tree, x, nrates=2, shift.range=NULL,
   density=20, plot=TRUE, ...)

Arguments

`tree`	object of class `"phylo"`.
`x`	vector of phenotypic trait values for species. `names(x)` should contain the species names and match `tree$tip.label`. For `plot` method, `x` is an object of class `"rateshift"`.
`nrates`	number of rates.
`niter`	number of iterations of optimization routine to ensure convergence.
`method`	optimization method. Can be `"ML"` (maximum likelihood) or `"REML"` (restricted maximum likelihood).
`...`	optional arguments. In the case of the `plot` method, these will be passed to `plotSimmap`. For `rateshift`, optional arguments include: `tol`, tolerance; `plot` & `print`, logical values indicating whether to plot or print the progress of the optimization (default to `FALSE`); `quiet`, logical argument indicating whether to suppress all notifications (defaults to `FALSE`); `minL`, numeric value; and `fixed.shift`, either a vector of fixed shift points, or a logical value.
`shift.range`	for `likSurface.rateshift`.
`density`	for `likSurface.rateshift`.
`plot`	logical argument for `likSurface.rateshift`. If `plot=FALSE` then the surface is returned.

Value

A fitted object of class "rateshift", or, in the case of likSurface.rateshift, a likelihood surface for the shift points.

Author(s)

Liam Revell liam.revell@umb.edu

References

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