sim.rates: Brownian or OU simulation with multiple evolutionary regimes

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

Brownian or OU simulation with multiple evolutionary regimes

Description

Simulates multi-rate or multi-regime continuous trait evolution on a phylogeny.

Usage

sim.rates(tree, sig2, anc=0, nsim=1, internal=FALSE, plot=FALSE)
multiOU(tree, alpha, sig2, theta=NULL, a0=NULL, nsim=1, internal=FALSE, ...)

Arguments

tree	is a stochastic map format phylogenetic tree in modified "phylo" format (e.g., see make.simmap).
sig2	a named vector containing the rates for each state; names should be states in mtree.
anc	optional value for the root state.
nsim	number of simulations.
internal	logical value indicating whether to return states at internal nodes.
plot	logical value indicating whether or not to visual the rate heterogeneity (default value is FALSE.
alpha	single value or vector of values of the OU \alpha parameter.
theta	single value or vector of values of the OU \theta parameter.
a0	optional value of the root state. Defaults to zero.
...	optional arguments.

Details

The function sim.rates conducts BM simulation on a tree with multiple rates.

The function multiOU conducts multi-regime OU simulations on the tree under a range of conditions. multiOU uses a difference equation approximation of the OU process.

Value

A vector (for nsim=1) or matrix containing the tip states for the n species in the tree.

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

fastBM, make.simmap, read.simmap, sim.history

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