pbd_ML function

Maximization of loglikelihood under protracted birth-death model of diversification

Likelihood maximization for protracted birth-death model of diversification

pbd_ML(
   brts,
   initparsopt = c(0.2,0.1,1),
   idparsopt = 1:length(initparsopt),
   idparsfix = NULL,
   parsfix = NULL,
   exteq = 1,
   parsfunc = c(function(t,pars) {pars[1]},function(t,pars) {pars[2]},
function(t,pars) {pars[3]}, function(t,pars) {pars[4]}),
   missnumspec = 0,
   cond = 1,
   btorph = 1,
   soc = 2,
   methode = "lsoda",
   n_low = 0,
   n_up = 0,
   tol = c(1E-6, 1E-6, 1E-6),
   maxiter = 1000 * round((1.25)^length(idparsopt)),
   optimmethod = 'subplex',
   verbose = TRUE
)

Arguments

• brts: A set of branching times of a phylogeny, all positive

• initparsopt: The initial values of the parameters that must be optimized

• idparsopt: The ids of the parameters that must be optimized, e.g. 1:4 for all parameters. The ids are defined as follows:

  id == 1 corresponds to b (speciation-initiation rate)

  id == 2 corresponds to mu_1 (extinction rate of good species)

  id == 3 corresponds to la_1 (speciation-completion rate)

  id == 4 corresponds to mu_2 (extinction rate of incipient species)

• idparsfix: The ids of the parameters that should not be optimized, e.g. c(2,4) if mu_1 and mu_2 should not be optimized, but only b and la_1. In that case idparsopt must be c(1,3).

• parsfix: The values of the parameters that should not be optimized

• exteq: Sets whether incipient species have the same (1) or different (0) extinction rate as good species. If exteq = 0, then idparsfix and idparsopt should together have all parameters 1:4

• parsfunc: Specifies functions how the rates depend on time, default functions are constant functions

• missnumspec: The number of species that are in the clade but missing in the phylogeny

• cond: Conditioning:

  cond == 0 : conditioning on stem or crown age

  cond == 1 : conditioning on stem or crown age and non-extinction of the phylogeny

  cond == 2 : conditioning on stem or crown age and number of extant taxa

• btorph: Sets whether the likelihood is for the branching times (0) or the phylogeny (1)

• soc: Sets whether the first element of the branching times is the stem (1) or the crown (2) age

• methode: Sets which method should be used in the ode-solver. Default is 'lsoda'. See package deSolve for details.

• n_low: Sets the lower bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)

• n_up: Sets the upper bound of the number of species on which conditioning should be done when cond = 2. Set this to 0 when conditioning should be done on precisely the number of species (default)

• tol: Sets the tolerances in the optimization. Consists of:

  reltolx = relative tolerance of parameter values in optimization

  reltolf = relative tolerance of function value in optimization

  abstolx = absolute tolerance of parameter values in optimization

• maxiter: Sets the maximum number of iterations in the optimization

• optimmethod: Method used in optimization of the likelihood. Current default is 'subplex'. Alternative is 'simplex' (default of previous versions)

• verbose: if TRUE, explanatory text will be shown

Returns

A data frame with the following components:

• b: gives the maximum likelihood estimate of b

• mu_1: gives the maximum likelihood estimate of mu_1

• la_1: gives the maximum likelihood estimate of la_1

• mu_2: gives the maximum likelihood estimate of mu_2

• loglik: gives the maximum loglikelihood

• df: gives the number of estimated parameters, i.e. degrees of feedom

• conv: gives a message on convergence of optimization; conv = 0 means convergence

Author(s)

Rampal S. Etienne

See Also

pbd_loglik

Examples

pbd_ML(1:10,initparsopt = c(4.640321,4.366528,0.030521), exteq = 1)