Q_reducedbichrom: Calculates a Q matrix for reduced BiChroM model
In fmichonneau/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. By default the two parameters assumed equal are "rho0"="rho1" but user can specify which two parameters are the same

fmichonneau/chromploid documentation built on May 16, 2019, 1:43 p.m.