DAISIE_loglik_CS: Computes the loglikelihood of the DAISIE model with...
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAISIE_loglik_CS

R Documentation

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

Description

Computes the loglikelihood of the DAISIE model with clade-specific diversity-dependence given colonization and branching times for lineages on an island, and a set of model parameters. The output is a loglikelihood value

Usage

DAISIE_loglik_CS(
  pars1,
  pars2,
  datalist,
  methode = "lsodes",
  CS_version = 1,
  abstolint = 1e-16,
  reltolint = 1e-10
)

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]` corresponds to lambda^c (cladogenesis rate) for an optional subset of the species `pars1[7]` corresponds to mu (extinction rate) for an optional subset of the species `pars1[8]` corresponds to K (clade-level carrying capacity) for an optional subset of the species `pars1[9]` corresponds to gamma (immigration rate) for an optional subset of the species `pars1[10]` corresponds to lambda^a (anagenesis rate) for an optional subset of the species `pars1[11]` corresponds to p_f (fraction of mainland species that belongs to the second subset of species The elements 6:10 and 11 are optional, that is, pars1 should either contain 5, 10 or 11 elements. If 10, then the fraction of potential colonists of type 2 is computed from the data. If 11, then pars1[11] is used, overruling any information in the data.
`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 `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 whether parameters and likelihood should be printed (1) or not (0)
`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
`methode`	Method of the ODE-solver. See package deSolve for details. Default is "lsodes"
`CS_version`	a numeric or list. Default is 1 for the standard DAISIE model, for a relaxed-rate model a list with the following elements: model: the CS model to run, options are `1` for single rate DAISIE model, `2` for multi-rate DAISIE, or `0` for IW test model. relaxed_par: the parameter to relax (integrate over). Options are `"cladogenesis"`, `"extinction"`, `"carrying_capacity"`, `"immigration"`, or `"anagenesis"`.
`abstolint`	Absolute tolerance of the integration
`reltolint`	Relative tolerance of the integration

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.

Examples


utils::data(Galapagos_datalist_2types)
pars1 = c(0.195442017,0.087959583,Inf,0.002247364,0.873605049,
          3755.202241,8.909285094,14.99999923,0.002247364,0.873605049,0.163)
pars2 = c(100,11,0,1)
DAISIE_loglik_all(pars1,pars2,Galapagos_datalist_2types)

DAISIE documentation built on Oct. 22, 2023, 1:06 a.m.