% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/dd_SR_loglik.R
\name{dd_SR_loglik}
\alias{dd_SR_loglik}
\title{Loglikelihood for diversity-dependent diversification models with a shift in
the parameters at time t = tshift}
\usage{
dd_SR_loglik(pars1, pars2, brts, missnumspec, methode = "analytical")
}
\arguments{
\item{pars1}{Vector of parameters: \cr \cr \code{pars1[1]} corresponds to
lambda (speciation rate) before the shift \cr \code{pars1[2]} corresponds to
mu (extinction rate) before the shift \cr \code{pars1[3]} corresponds to K
(clade-level carrying capacity) before the shift \cr \code{pars1[4]}
corresponds to lambda (speciation rate) after the shift \cr \code{pars1[5]}
corresponds to mu (extinction rate) after the shift \cr \code{pars1[6]}
corresponds to K (clade-level carrying capacity) after the shift \cr
\code{pars1[7]} corresponds to tshift (the time of shift)}

\item{pars2}{Vector of model settings: \cr \cr \code{pars2[1]} sets the
maximum number of species for which a probability must be computed.  This
must be larger than 1 + missnumspec + length(brts). \cr \cr \code{pars2[2]}
sets the model of diversity-dependence: \cr - \code{pars2[2] == 1} linear
dependence in speciation rate with parameter K (= diversity where speciation
= extinction)\cr - \code{pars2[2] == 1.3} linear dependence in speciation
rate with parameter K' (= diversity where speciation = 0)\cr -
\code{pars2[2] == 2} exponential dependence in speciation rate with
parameter K (= diversity where speciation = extinction)\cr - \code{pars2[2]
== 2.1} variant of exponential dependence in speciation rate with offset at
infinity\cr - \code{pars2[2] == 2.2} 1/n dependence in speciation rate\cr -
\code{pars2[2] == 2.3} exponential dependence in speciation rate with
parameter x (= exponent)\cr - \code{pars2[2] == 3} linear dependence in
extinction rate \cr - \code{pars2[2] == 4} exponential dependence in
extinction rate \cr - \code{pars2[2] == 4.1} variant of exponential
dependence in extinction rate with offset at infinity\cr - \code{pars2[2] ==
4.2} 1/n dependence in extinction rate\cr\cr \code{pars2[3]} sets the
conditioning: \cr - \code{pars2[3] == 0} no conditioning \cr -
\code{pars2[3] == 1} conditioning on non-extinction of the phylogeny \cr -
\code{pars2[3] == 2} conditioning on non-extinction of the phylogeny and on
the total number of extant taxa (including missing species) \cr \cr
\code{pars2[4]} sets whether the likelihood is for the branching times (0)
or the phylogeny (1) \cr \cr \code{pars2[5]} sets whether the parameters and
likelihood should be shown on screen (1) or not (0) \cr \cr \code{pars2[6]}
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
'analytical' which uses matrix exponentiation; alternatively numerical ODE
solvers can be used, such as 'odeint::runge_kutta_cash_karp54'. These were used in the
package before version 3.1.}
}
\value{
The loglikelihood
}
\description{
This function computes loglikelihood of a diversity-dependent
diversification model for a given set of branching times and parameter
values where the parameters are allowed to shift at time t = tshift
}
\examples{
dd_SR_loglik(pars1 = c(0.2,0.1,50,0.2,0.1,70,5), pars2 = c(100,1,1,1,0,2),
   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{dd_SR_ML}}, \code{\link{dd_loglik}},
\code{\link{dd_KI_loglik}}
}
\author{
Rampal S. Etienne & Bart Haegeman
}
\keyword{models}
