ctt: Generates (or simulates) a 'changes through time' plot from a...

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Generates (or simulates) a 'changes through time' plot from a set of stochastic map character histories

Description

Create a 'changes through time' plot from a "multiSimmap" object.

Usage

ctt(trees, segments=20, ...)
sim.ctt(tree, Q, anc=NULL, nmaps=100, ...)
sim.multiCtt(tree, Q, anc=NULL, nmaps=100, nsim=100, ...)

Arguments

trees	an object of class "multiSimmap".
segments	number of segments to break up the history of the tree.
tree	for sim.ctt, an object of class "phylo".
Q	for sim.ctt, a transition matrix to use for simulation.
anc	ancestral state at the root node for simulation.
nmaps	number of stochastic maps per simulation.
nsim	for sim.multiCtt only, the number of simulations to run.
...	optional arguments.

Details

This function generates a 'changes through time' plot in the style of a lineage-through-time (LTT) plot. It shows the mean rate or the mean number of changes per unit time from a set of stochastic character map trees.

Value

An object of class "ctt" or "multiCtt".

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.

See Also

ltt

phytools documentation built on June 22, 2024, 10:39 a.m.