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 rateshift
plot(x, ...)
likSurface.rateshift(tree, x, nrates=2, shift.range=NULL,
   density=20, plot=TRUE, ...)

Value

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

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.

Author

Liam Revell liam.revell@umb.edu

References