makeSSEchrom: simulates chromosome number data under a binary SSE model

In coleoguy/chromePlus: Analysis of chromosome number evolution and binary traits

simulates chromosome number data under a binary SSE model

Description

Provides a simulation of chromosome number evolution based on a model where an evolving binary trait effects can effect the rate of speciation, extinction, chromosome gain, and chromosome loss.

Usage

makeSSEchrom(h, lambda1, lambda2, mu1, mu2, 
             asc1, asc2, desc1, desc2, trans1, trans2, 
             max.taxa, x0)

Arguments

h	the maximum haploid number for the simulation
lambda1	speciation in binary state 1
lambda2	speciation in binary state 2
mu1	extinction in state 1
mu2	extinction in state 2
asc1	chromosome gain in state 1
asc2	chromosome gain in state 2
desc1	chromosome loss in state 1
desc2	chromosome loss in state 2
trans1	transition from state 1 to state 2
trans2	transition from state 2 to state 1
max.taxa	simulation will run till this many taxa are present
x0	starting haploid number; the binary state is assigned randomly

Details

When using this function you should insure that h is set high enough that it does not act as a hard barrier on chromosme number.

Value

This function returns a list with three elements. The first is the resulting phylogeny of class phylo. The second is a named vector of the binary states of the tips and the third is a named vector of haploid chromosome numbers.

Author(s)

Heath Blackmon

coleoguy/chromePlus documentation built on July 27, 2023, 12:39 p.m.