rateshift {phytools}

Find the temporal position of one or more rate shifts

Description

Fits a model with one or more temporal rate shifts for a continuous trait on the tree.

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.

Details

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.

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 [e-mail]

References

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.

See Also

brownie.lite