Q_bichromlinear: Calculates Q-matrix for BiChroM model

In roszenil/chromploid: Chromosome Number and Ploidy Evolution Models

Description

Calculates Q-matrix for BiChroM model

Usage

Q_bichromlinear(log.theta, size)

Arguments

log.theta	vector of size 12 indicating parameters in ln scale for BiChoM the order of the parameters is (lambda0, lambda1, mu0, mu1, rho0, rho1, kappa0, q01, kappa1, q10, e0, e1)
size	Maximum number of chromosomes in the sample (recommended no more than 50, states larger than that should be coded as 51)

Details

Q_bichromlinear determines the Q-matrix for a model of chromosome number change associated with a binary state with traits coded as 0 or 1. It is linear because binary trait change rate is a linear function of chromosome number.

Note: This is a beta version, the linear function for binary trait change rate from state 0 to 1 is kappa0+ (chromosome number)*q01

Value

Q a sparse matrix of size 2*(size+1)

roszenil/chromploid documentation built on March 19, 2018, 4:42 p.m.