ctt {phytools}

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