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

View source: R/sim.rates.R

sim.ratesR Documentation

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 liam.revell@umb.edu

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


liamrevell/phytools documentation built on March 4, 2024, 3:27 a.m.