dd_multiple_KI_loglik: Loglikelihood for diversity-dependent diversification models...

In DDD: Diversity-Dependent Diversification

Loglikelihood for diversity-dependent diversification models with multiple decoupling (rate shift) events

Description

This function computes loglikelihood of a diversity-dependent diversification model for a given set of branching times and parameter values where the diversity-dependent dynamics of subclades decouple from the dynamics of main clades, potentially accompanied by a shift in parameters.

Usage

dd_multiple_KI_loglik(
  pars1_list,
  pars2,
  brts_k_list,
  missnumspec_list,
  reltol = 1e-14,
  abstol = 1e-16,
  methode = "odeint::runge_kutta_cash_karp54"
)

Arguments

pars1_list	list of paramater sets one for each rate regime (subclade). The parameters are: lambda (speciation rate), mu (extinction rate), and K (clade-level carrying capacity).
pars2	Vector of model settings: pars2[1] sets the maximum number of species for which a probability must be computed. This must be larger than 1 + missnumspec + length(brts). pars2[2] sets the model of diversity-dependence: - pars2[2] == 1 linear dependence in speciation rate with parameter K (= diversity where speciation = extinction) - pars2[2] == 1.3 linear dependence in speciation rate with parameter K' (= diversity where speciation = 0) - pars2[2] == 2 exponential dependence in speciation rate with parameter K (= diversity where speciation = extinction) - pars2[2] == 2.1 variant of exponential dependence in speciation rate with offset at infinity - pars2[2] == 2.2 1/n dependence in speciation rate - pars2[2] == 2.3 exponential dependence in speciation rate with parameter x (= exponent) - pars2[2] == 3 linear dependence in extinction rate - pars2[2] == 4 exponential dependence in extinction rate - pars2[2] == 4.1 variant of exponential dependence in extinction rate with offset at infinity - pars2[2] == 4.2 1/n dependence in extinction rate pars2[3] sets the conditioning: - pars2[3] == 0 no conditioning (or just crown age) - pars2[3] == 1 conditioning on non-extinction of the phylogeny - pars2[3] == 2 conditioning on number of species and crown age; not yet implemented - pars2[3] == 3 conditioning on number of species only; not yet implemented - pars2[3] == 4 conditioning on survival of the subclade - pars2[3] == 5 conditioning on survival of all subclades and of both crown lineages in the main clade. This assumes that subclades that have already shifted do not undergo another shift, i.e. shifts only occur in the main clade. pars2[4] Obsolete. pars2[5] sets whether the parameters and likelihood should be shown on screen (1) or not (0) pars2[6] sets whether the first data point is stem age (1) or crown age (2) pars2[7] sets whether the old (incorrect) likelihood should be used (0), or whether the new corrected likelihood should be used (1).
brts_k_list	list of matrices, one for each rate regime (subclade). Each matrix has in the first row the branching times including the shift/decoupling time and the present time (0) in negative time (i.e. 10 mya = -10). In the second row it has the number of lineages, i.e. starting at 2 for a phylogeny with a crown and increasing by one at each branching time and decreasing by one at each decoupling/shift time. The last element is the same as the second last.
missnumspec_list	list containing the number of missing species for each clade. If only a single number m of missing species is known for the entire phylogeny, then each element of the list should be 0:m. One can also create this from m using the function create_missnumspec_list
reltol	relative tolerance in integration of the ODE system, default at 1e-14
abstol	tolerance tolerance in integration of the ODE system, default at 1e-16
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.

DDD documentation built on July 26, 2023, 5:25 p.m.