dd_MS_loglik: Loglikelihood for macro-evolutionary succession under...
In DDD: Diversity-Dependent Diversification

dd_MS_loglik

R Documentation

Loglikelihood for macro-evolutionary succession under diversity-dependent diversification with the key innovation at time t = t_d

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.

Usage

dd_MS_loglik(
  pars1,
  pars2,
  brtsM,
  brtsS,
  missnumspec,
  methode = "odeint::runge_kutta_cash_karp54"
)

Arguments

`pars1`	Vector of parameters: `pars1[1]` corresponds to lambda_M (speciation rate) of the main clade `pars1[2]` corresponds to mu_M (extinction rate) of the main clade `pars1[3]` corresponds to K_M (clade-level carrying capacity) of the main clade `pars1[4]` corresponds to lambda_M (speciation rate) of the subclade `pars1[5]` corresponds to mu_S (extinction rate) of the subclade `pars1[6]` corresponds to t_d (the time of the key innovation)
`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 - `pars2[3] == 1` conditioning on non-extinction of the phylogeny `pars2[4]` sets the time of splitting of the branch that will undergo the key innovation leading to different parameters `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 new corrected version should be used (1)
`brtsM`	A set of branching times of the main clade in the phylogeny, all positive
`brtsS`	A set of branching times of the subclade in the phylogeny, all positive
`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.
`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

Author(s)

Rampal S. Etienne & Bart Haegeman

References

- Etienne, R.S. et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi: 10.1098/rspb.2011.1439
- Etienne, R.S. & B. Haegeman 2012. Am. Nat. 180: E75-E89, doi: 10.1086/667574

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)

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