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Likelihood for DAMOCLES model

DAMOCLES_loglik.Rd

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,
  cond = 0
)

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, or any of the solvers used in odeint (preceded by 'odeint'), e.g. 'odeint::runge_kutta_cash_karp54', 'odeint::runge_kutta_fehlberg78', 'odeint::runge_kutta_dopri5', 'odeint::runge_kutta_bulirsch_stoer'

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.

cond

Whether likelihood should be conditioned on non-empty community. Default is no conditioning.

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

Author

Rampal S. Etienne

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
#> [1] -171.0041

  # - with a root edge
  phy$root.edge = 2
  loglik = DAMOCLES_loglik(phy,pa,pars)
  loglik
#> [1] -171.3912