geiger (version 1.0-91)

sim.char: Simulate character evolution

Description

Simulates evolution of discrete or continuous characters on a phylogenetic tree

Usage

sim.char(phy, model.matrix, nsims = 1, model = "brownian", root.state = 1)

Arguments

phy

Phylogenetic tree

model.matrix

Matrix describing model: either vcv matrix or q matrix

nsims

Number of simulations to run

model

"brownian", "speciational", or "discrete"

root.state

Starting state at root, only needed for discrete model.

Value

• Array of simulated data, either two or three-dimensional. The first dimension is the number of taxa, the second the number of characters, and the third the number of simulated data sets.

Details

This function simulates either discrete or continuous data on a phylogenetic tree. The model variable determines the type of simulation to be run. There are three options: "discrete," which evolves characters under a continuous time Markov model, and two continuous models, "brownian" and "speciational." Brownian is a constant rate Brownian motion model, while speciational is a Brownian model on a tree where all branches have the same length. The model.matrix parameter gives the structure of the model, and should be either a transition matrix, Q, for model = "discrete," or a trait variance-covariance matrix for model = "brownian" or "speciational." For discrete models, one character at a time is simulated, and the size of the model.matrix gives the number of character states; for continuous models, multivariate characters can be simulated, with their evolution goverened by a covariance matrix specified in the model.matrix. "root.state" is only needed for the discrete model.

Examples

data(geospiza)
attach(geospiza) 


s<-ic.sigma(geospiza.tree, geospiza.data)
sims<-sim.char(geospiza.tree, s, 100)

# Discrete character evolution
q<-list(rbind(c(-.5, .5), c(.5, -.5)))
sims<-sim.char(geospiza.tree, q, model="discrete", n=100)