DAISIE_loglik_integrate: Integrates the loglikelihood of a single clade across a...
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

View source: R/DAISIE_loglik_integrate.R

Integrates the loglikelihood of a single clade across a parameter weighted by a given distribution

DAISIE_loglik_integrate(
  pars1,
  pars2,
  brts,
  stac,
  missnumspec,
  CS_version,
  methode,
  abstolint,
  reltolint,
  verbose
)

`pars1`	Vector of model parameters: `pars1[1]` corresponds to lambda^c (cladogenesis rate) `pars1[2]` corresponds to mu (extinction rate) `pars1[3]` corresponds to K (clade-level carrying capacity) `pars1[4]` corresponds to gamma (immigration rate) `pars1[5]` corresponds to lambda^a (anagenesis rate).
`pars2`	Vector of settings: `pars2[1]` corresponds to res, the maximum number of endemics or non-endemics for which the ODE system is solved; this must be much larger than the actual number for which the probability needs to be calculated.) `pars2[2]` corresponds to M, size of the mainland pool, i.e the number of species that can potentially colonize the island.
`brts`	Numeric vector of branching times
`stac`	Numeric of Endemicity status
`missnumspec`	Numeric of missing species
`CS_version`	a numeric or list. Default is 1 for the standard DAISIE model, for a relaxed-rate model a list with the following elements: model: the CS model to run, options are `1` for single rate DAISIE model, `2` for multi-rate DAISIE, or `0` for IW test model relaxed_par: the parameter to relax (integrate over). Options are `"cladogenesis"`, `"extinction"`, `"carrying_capacity"`, `"immigration"`, or `"anagenesis"`
`methode`	Method of the ODE-solver. See package deSolve for details. Default is "lsodes".
`abstolint`	Numeric absolute tolerance of the integration
`reltolint`	Numeric relative tolerance of the integration
`verbose`	In simulation and dataprep functions a logical, `Default = TRUE` gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, `Default = 0` does not print, `verbose = 1` prints intermediate output of the parameters and loglikelihood, `verbose = 2` means also intermediate progress during loglikelihood computation is shown.