R: Computes the loglikelihood of the DAISIE model with...

DAISIE_loglik_IW {DAISIE}

R Documentation

Computes the loglikelihood of the DAISIE model with island-wide diversity-dependence given data and a set of model parameters

Description

Computes the loglikelihood of the DAISIE model given colonization and branching times for lineages on an island, and a set of model parameters for the DAISIE model with island-wide diversity-dependence

Usage

DAISIE_loglik_IW(
  pars1,
  pars2,
  datalist,
  methode = "lsodes",
  abstolint = 1e-12,
  reltolint = 1e-10,
  verbose = FALSE
)

Arguments

`pars1`	Contains the 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) `pars1[6]` is optional; it may contain M, the total number of species on the mainland
`pars2`	Contains the model settings `pars2[1]` corresponds to lx = length of ODE variable x `pars2[2]` corresponds to ddmodel = diversity-dependent model, model of diversity-dependence, which can be one of ddmodel = 0 : no diversity dependence ddmodel = 1 : linear dependence in speciation rate ddmodel = 11: linear dependence in speciation rate and in immigration rate ddmodel = 2 : exponential dependence in speciation rate ddmodel = 21: exponential dependence in speciation rate and in immigration rate Only ddmodel = 11 is currently implemented `pars2[3]` corresponds to cond = setting of conditioning cond = 0 : conditioning on island age cond = 1 : conditioning on island age and non-extinction of the island biota `pars2[4]` Specifies whether intermediate output should be provided, because computation may take long. Default is 0, no output. A value of 1 means the parameters and loglikelihood are printed. A value of 2 means also intermediate progress during loglikelihood computation is shown.
`datalist`	Data object containing information on colonisation and branching times. This object can be generated using the DAISIE_dataprep function, which converts a user-specified data table into a data object, but the object can of course also be entered directly. It is an R list object with the following elements. The first element of the list has two or three components: `$island_age` - the island age Then, depending on whether a distinction between types is made, we have: `$not_present` - the number of mainland lineages that are not present on the island The remaining elements of the list each contains information on a single colonist lineage on the island and has 5 components: `$colonist_name` - the name of the species or clade that colonized the island `$branching_times` - island age and stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic species. For cladogenetic species these should be island age and branching times of the radiation including the stem age of the radiation. `$stac` - the status of the colonist * Non_endemic_MaxAge: 1 * Endemic: 2 * Endemic&Non_Endemic: 3 * Non_endemic: 4 * Endemic_MaxAge: 5 `$missing_species` - number of island species that were not sampled for particular clade (only applicable for endemic clades)
`methode`	Method of the ODE-solver. Supported Boost `ODEINT` solvers (steppers) are: `'odeint::runge_kutta_cash_karp54'` `'odeint::runge_kutta_fehlberg78'` [default] `'odeint::runge_kutta_dopri5'` `'odeint::bulirsch_stoer'` `'odeint::adams_bashforth_[1\|2\|3\|4\|5\|6\|7\|8]} \code{'odeint::adams_bashforth_moulton_[1\|2\|3\|4\|5\|6\|7\|8]` without `odeint::`-prefix, `ode` method is assumed.
`abstolint`	Absolute tolerance of the integration
`reltolint`	Relative tolerance of the integration
`verbose`	Logical controling if progress is printed to console.

Details

The output is a loglikelihood value

Value

The loglikelihood

Author(s)

Rampal S. Etienne & Bart Haegeman

References

Valente, L.M., A.B. Phillimore and R.S. Etienne (2015). Equilibrium and non-equilibrium dynamics simultaneously operate in the Galapagos islands. Ecology Letters 18: 844-852.