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

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"
)

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'.

Value

The loglikelihood

References

O.N. Dehayem et al. 2026. Preprint.

See also

DAISIE_ML

Author

Rampal S. Etienne & Bart Haegeman