Description Usage Arguments Details Value

View source: R/Q_bichromlinear.R

Calculates Q-matrix for BiChroM model

1 | ```
Q_bichromlinear(log.theta, size)
``` |

`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) |

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

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

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