Q_reducedbichrom: Calculates a Q matrix for reduced BiChroM model
In roszenil/chromploid: Chromosome Number and Ploidy Evolution Models

Calculates a Q matrix for reduced BiChroM model

1 2	Q_reducedbichrom(log.pars, size, equal.param = c("rho0", "rho1"), location.par = 5)

`log.pars`	a vector of size 9 with ln values of parameters (lambda0, lambda1, mu0, mu1, rho, q01, 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)
`equal.param`	by default "rho0"="rho1" but user can specify the parameters forced to be equal
`location`	position in log.pars where the value of the equal.param is located, by default location=5

This function assumes that two parameter values are equal. This is useful for calculating likelihood ratio tests in BiChrom. For now the only test that can be performed is when chromosome doubling parameters are assumed as "rho0"="rho1" (very soon for any two comparisons)

roszenil/chromploid documentation built on May 27, 2019, 11:42 p.m.