DAISIE (version 1.4)

DAISIE_loglik_all: Computes the loglikelihood of the DAISIE model 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

Usage

DAISIE_loglik_all(
   pars1,
   pars2,
   datalist,
   methode = "lsodes"
   )

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 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_MaxAge: 5 $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"

Value

The loglikelihood

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.

See Also

DAISIE_ML, DAISIE_sim

Examples

# NOT RUN {
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)
# }