% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/bd_loglik.R
\name{bd_loglik}
\alias{bd_loglik}
\title{Loglikelihood for diversity-independent diversification model}
\usage{
bd_loglik(
  pars1,
  pars2,
  brts,
  missnumspec,
  methode = "odeint::runge_kutta_cash_karp54"
)
}
\arguments{
\item{pars1}{Vector of parameters:
\cr \cr \code{pars1[1]} corresponds to
lambda0 (speciation rate)
\cr \code{pars1[2]} corresponds to mu0 (extinction
rate)
\cr \code{pars1[3]} corresponds to lambda1 (decline parameter in
speciation rate) or K in diversity-dependence-like models
\cr \code{pars1[4]} corresponds to mu1 (decline parameter in extinction rate)}

\item{pars2}{Vector of model settings:
\cr \cr \code{pars2[1]} sets the
model of time-dependence:
\cr - \code{pars2[1] == 0} no time dependence
\cr - \code{pars2[1] == 1} speciation and/or extinction rate is exponentially
declining with time
\cr - \code{pars2[1] == 2} stepwise decline in
speciation rate as in diversity-dependence without extinction
\cr - \code{pars2[1] == 3} decline in speciation rate following deterministic
logistic equation for ddmodel = 1
\cr - \code{pars2[1] == 4} decline in
speciation rate such that the expected number of species matches with that
of ddmodel = 1 with the same mu
\cr \cr \code{pars2[2]} sets the
conditioning:
\cr - \code{pars[2] == 0} conditioning on stem or crown age
\cr - \code{pars[2] == 1} conditioning on stem or crown age and
non-extinction of the phylogeny
\cr - \code{pars[2] == 2} conditioning on
stem or crown age and on the total number of extant taxa (including missing
species)
\cr - \code{pars[2] == 3} conditioning on the total number of
extant taxa (including missing species)
\cr \cr \code{pars2[3]} sets whether
the likelihood is for the branching times (0) or the phylogeny (1)
\cr \cr \code{pars2[4]} sets whether the parameters and likelihood should be 
shown
on screen (1) or not (0)
\cr \cr \code{pars2[5]} sets whether the first data
point is stem age (1) or crown age (2)}

\item{brts}{A set of branching times of a phylogeny, all positive}

\item{missnumspec}{The number of species that are in the clade but missing
in the phylogeny}

\item{methode}{The method used to solve the master equation, default is
'odeint::runge_kutta_cash_karp54'.}
}
\value{
The loglikelihood
}
\description{
This function computes loglikelihood of a diversity-independent
diversification model for a given set of branching times and parameter
values.
}
\examples{
bd_loglik(pars1 = c(0.5,0.1), pars2 = c(0,1,1,0,2), brts = 1:10, 
missnumspec = 0)
}
\references{
- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309,
doi: 10.1098/rspb.2011.1439 \cr - Etienne, R.S. & B. Haegeman 2012. Am. Nat.
180: E75-E89, doi: 10.1086/667574
}
\seealso{
\code{\link{bd_ML}}
}
\author{
Rampal S. Etienne, Bart Haegeman & Cesar Martinez
}
\keyword{models}
