createPhyloBiSSE: Create one phylogeny under the BiSSE model

In ilajaait/deephylo: Infer Parameters from Phylogenies with Deep-Learning

Create one phylogeny under the BiSSE model

Description

The BiSSE diversification model has 6 parameters:

• λ_0 speciation rate of state 0

• λ_1 speciation rate of state 1

• μ_0 extinction rate of state 0

• μ_1 extinction rate of state 1

• q_{01} transition rate from state 0 to 1

• q_{10} transition rate from state 1 to 0

Usage

createPhyloBiSSE(n.tips, params)

Arguments

n.tips	number of tips
params	list $lambda0: speciation rate of state 0 $q: transition rate

Details

We assume 4 constraints:

• λ_1 = 2λ_0

• μ_0 = 0

• μ_1 = 0

• q_{10} = q_{01}

Value

phylogeny (ape format)

Examples

n.tips <- 10 # 10 extant species
lambda0 <- 1 # speciation rate
q <- 0.1 # transition rate
createPhyloBiSSE(n.tips, list(lambda0 = lambda0, q = q))

ilajaait/deephylo documentation built on April 10, 2022, 11:03 a.m.