% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/dd_MS_loglik.R
\name{dd_MS_loglik}
\alias{dd_MS_loglik}
\title{Loglikelihood for macro-evolutionary succession under diversity-dependent
diversification with the key innovation at time t = t_d}
\usage{
dd_MS_loglik(
  pars1,
  pars2,
  brtsM,
  brtsS,
  missnumspec,
  methode = "odeint::runge_kutta_cash_karp54"
)
}
\arguments{
\item{pars1}{Vector of parameters: \cr \cr
\code{pars1[1]} corresponds to lambda_M (speciation rate) of the main clade \cr
\code{pars1[2]} corresponds to mu_M (extinction rate) of the main clade \cr
\code{pars1[3]} corresponds to K_M (clade-level carrying capacity) of
the main clade \cr
\code{pars1[4]} corresponds to lambda_M (speciation rate) of the subclade \cr
\code{pars1[5]} corresponds to mu_S (extinction rate) of the subclade \cr
\code{pars1[6]} corresponds to t_d (the time of the key innovation)}

\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 \cr
\code{pars2[4]} sets the time of splitting of the branch that will undergo
the key innovation leading to different parameters \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)
\code{pars2[7]} sets whether the old (incorrect) likelihood should be used (0)
or whether new corrected version should be used (1)}

\item{brtsM}{A set of branching times of the main clade in the phylogeny,
all positive}

\item{brtsS}{A set of branching times of the subclade in the phylogeny, all
positive}

\item{missnumspec}{The number of species that are in the clade but missing
in the phylogeny. One can specify the sum of the missing species in main
clade and subclade or a vector c(missnumspec_M,missnumspec_S) with missing
species in main clade and subclade respectively.}

\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 the loglikelihood of a diversity-dependent
diversification model for a given set of branching times and parameter
values where the diversity-dependent dynamics of an innovative subclade have
different parameters from the dynamics of the main clade from time t_d, but
both are governed by the same carrying capacity and experience each other's
diversity.
}
\examples{

pars1 = c(0.2,0.1,40,1.0,0.1,9.8)
pars2 = c(200,1,0,18.8,1,2)
missnumspec = 0
brtsM = c(25.2,24.6,24.0,22.5,21.7,20.4,19.9,19.7,18.8,17.1,15.8,11.8,9.7,8.9,5.7,5.2)
brtsS = c(9.6,8.6,7.4,4.9,2.5)
dd_MS_loglik(pars1,pars2,brtsM,brtsS,missnumspec)

}
\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_MS_ML}}, \code{\link{dd_loglik}},
\code{\link{dd_KI_loglik}}, \code{\link{dd_SR_loglik}}
}
\author{
Rampal S. Etienne & Bart Haegeman
}
\keyword{models}
