DAISIE_DE_loglik_CS: Computes the loglikelihood of the DAISIE_DE model given data and a set of model parameters

Description

Computes the loglikelihood of the DAISIE_DE model given colonization and branching times for lineages on an island, and a set of model parameters. The output is a loglikelihood value

Usage

DAISIE_DE_loglik_CS(
  pars1,
  pars2,
  datalist,
  methode = "odeint::runge_kutta_cash_karp54",
  abstolint = 1e-15,
  reltolint = 1e-15,
  equal_extinction = TRUE,
  sampling = "n"
)

Value

The loglikelihood

Arguments

pars1: Contains the model parameters:

pars1[1] corresponds to lambda^c (cladogenesis rate)
pars1[2] corresponds to mu (extinction rate of endemic species)
pars1[3] corresponds to mu2 (extinction rate of non-endemic species)
pars1[4] corresponds to gamma (immigration rate)
pars1[5] corresponds to lambda^a (anagenesis rate)
pars2: Contains the model settings

pars2[1] irrelevant for DAISIE_DE
pars2[2] irrelevant for DAISIE_DE
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

cond > 1 : conditioning on island age and having at least cond colonizations on the island

pars2[4] sets the level of verbosity. When equal to 0, no output is generated. At higher values (1 or 2) more output will be generated.
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
or:
$not_present_type1 - the number of mainland lineages of type 1 that are not present on the island
$not_present_type2 - the number of mainland lineages of type 2 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_Singleton_MaxAge: 5
- Endemic_Clade_MaxAge: 6
- Endemic&Non_Endemic_Clade_MaxAge: 7
- Non_endemic_MaxAge_MinAge: 8
- Endemic_Singleton_MaxAge_MinAge: 9
$missing_species - number of island species that were not sampled for particular clade (only applicable for endemic clades)
$type1or2 - whether the colonist belongs to type 1 or type 2. Currently not implemented for DAISIE_DE
methode: Method of the ODE-solver. See package deSolve for details. Default is "odeint::runge_kutta_cask_karp54"
abstolint: Absolute tolerance of the integration
reltolint: Relative tolerance of the integration
equal_extinction: If FALSE the extinction rates of endemic and non-endemic species are different, otherwise they are set equal in optimization
sampling: Determines whether n-sampling or rho-sampling should be used when function_to_optimize = 'DAISIE_DE'.

Author

Rampal S. Etienne & Bart Haegeman

References