Fits a model with one or more temporal rate shifts for a continuous trait on the tree.
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, ...)A fitted object of class "rateshift", or, in the case of likSurface.rateshift, a likelihood surface for the shift points.
object of class "phylo".
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".
number of rates.
number of iterations of optimization routine to ensure convergence.
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.
for likSurface.rateshift.
for likSurface.rateshift.
logical argument for likSurface.rateshift. If plot=FALSE then the surface is returned.
Liam Revell liam.revell@umb.edu
rateshift attempts to find the location of one or more rate shifts. This model is quite easy to compute the likelihood for, but quite difficult to optimize as the likelihood surface is often rugged.
likSurface.rateshift plots the likelihood surface.
Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.
Revell, L. J. and L. J. Harmon (2022) Phylogenetic Comparative Methods in R. Princeton University Press.
brownie.lite