DAMOCLES (version 1.1)

DAMOCLES_loglik: Likelihood for DAMOCLES model

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 = compute_edgeTList(phy)
   )

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

Value

The loglikelihood

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

# NOT RUN {
  #TEST IT WORKS
  phy = 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
# }