Q_bichromlinear: Calculates Q-matrix for BiChroM model

Description Usage Arguments Details Value

View source: R/Q_bichromlinear.R

Description

Calculates Q-matrix for BiChroM model

Usage

1
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.