mbd_loglik: Calculates the likelihood for a multiple birth-death process
In Giappo/mbd: Multiple Birth Death Diversification

Description Usage Arguments Value Author(s)

mbd_loglik provides the likelihood for a process in which multiple births (from different parents) at the same time are possible, along with usual sympatric speciation and extinction events.

mbd_loglik(
  pars,
  brts,
  n_0 = 2,
  cond = 1,
  missnumspec = 0,
  lx = mbd::default_lx(brts = brts, missnumspec = missnumspec),
  tips_interval = c(n_0 * (cond > 0), Inf),
  q_threshold = 0.001,
  fortran = TRUE
)

`pars`	vector of parameters: pars[1] is lambda, the sympatric speciation rate; pars[2] is mu, the extinction rate; pars[3] is nu, the multiple allopatric speciation trigger rate; pars[4] is q, the single-lineage speciation probability;
`brts`	A set of branching times of a phylogeny.
`n_0`	the number of lineages at time equals zero.
`cond`	sets the conditioning cond = 0: no conditioning; cond = 1: conditioning on stem or crown age and non-extinction of the phylogeny;
`missnumspec`	The number of species that are in the clade, but missing in the phylogeny.
`lx`	it is the number of ODEs considered for the computation.
`tips_interval`	sets tips boundaries constrain on simulated dataset. It works only if cond == 1, otherwise it must be set to c(0, Inf).
`q_threshold`	adds a threshold for the evaluation of q. This is due because you never want `q` to actually be equal to zero or one.
`fortran`	Set it to TRUE if you want to use FORTRAN routine.