DAISIE_loglik_IW: 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
)

Value

The loglikelihood

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.

Author

Rampal S. Etienne & Bart Haegeman

Details

The output is a loglikelihood value

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.