DAMOCLES_loglik: Likelihood for DAMOCLES model

In rsetienne/DAMOCLES: Dynamic Assembly Model of Colonization, Local Extinction and Speciation

Description

Computes likelihood for the presence-absence data of species in a local community for a given phylogeny of species in the region.

Usage

DAMOCLES_loglik(
  phy,
  pa,
  pars,
  pchoice = 0,
  edgeTList = NULL,
  methode = "analytical",
  model = 0,
  Mlist = NULL,
  verbose = FALSE
)

Arguments

phy	phylogeny in phylo format
pa	presence-absence table with the first column the species labels and the second column the presence (1) or absence (0) of the species
pars	Vector of model parameters: pars[1] corresponds to mu (extinction rate in local community) pars[2] corresponds to gamma_0 in formula gamma(t) = gamma_0/(1 + gamma_1 * t) where gamma(t) is immigration rate into local community) pars[3] corresponds to gamma_1 in formula gamma(t) = gamma_0/(1 + gamma_1 * t) where gamma(t) is immigration rate into local community)
pchoice	sets the p-value to optimize: pchoice == 0 corresponds to the sum of p_0f + p_1f pchoice == 1 corresponds to p_0f pchoice == 2 corresponds to p_1f
edgeTList	list of edge lengths that need to be succesively pruned; if not specified, it will computed using compute_edgeTList
methode	method used to solve the ODE. Either 'analytical' for the analytical solution, 'Matrix' for matrix exponentiation using package Matrix or 'expm' using package 'expm' or any of the numerical solvers, used in deSolve.
model	model used. Default is 0 (standard null model). Other options are 1 (binary traits) 2 (trinary environmental trait) or 3 (diversity-dependent colonization - beta version)
Mlist	list of M matrices that can be specified when methode = 'analytical'. If set at NULL (default) and methode = 'analytical', Mlist will be computed.
verbose	Whether intermediate output should be printed. Default is FALSE.

Value

The loglikelihood

Author(s)

Rampal S. Etienne

References

Pigot, A.L. & R.S. Etienne (2015). A new dynamic null model for phylogenetic community structure. Ecology Letters 18: 153-163.

See Also

DAMOCLES_ML DAMOCLES_sim

Examples

  #TEST IT WORKS
  library(ape)
  phy = ape::rcoal(100)
  pars = c(0.5,0.1,0.1)
  pa = rbinom(100,c(0,1),0.5)
  pa = matrix(c(phy$tip.label,pa),nrow = length(phy$tip.label),ncol = 2)

  # - without a root edge
  loglik = DAMOCLES_loglik(phy,pa,pars)
  loglik

  # - with a root edge
  phy$root.edge = 2
  loglik = DAMOCLES_loglik(phy,pa,pars)
  loglik

rsetienne/DAMOCLES documentation built on Feb. 8, 2021, 1:35 p.m.