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

Description Usage Arguments Details Value Author(s) References See Also

View source: R/DAISIE_loglik_IW.R

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

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DAISIE_loglik_IW(
  pars1,
  pars2,
  datalist,
  methode = "ode45",
  abstolint = 1e-16,
  reltolint = 1e-14,
  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. See package deSolve for details. Default is "ode45"

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.

See Also

DAISIE_ML_IW, DAISIE_loglik_CS, DAISIE_sim_constant_rate


DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.