DAISIE_SR_loglik_CS: Computes the loglikelihood of the DAISIE model with...
In xieshu95/Test-Trasie: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

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

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 that may shift at some time

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

`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) after the shift `pars1[7]` corresponds to mu (extinction rate) after the shift `pars1[8]` corresponds to K (clade-level carrying capacity) after the shift `pars1[9]` corresponds to gamma (immigration rate) after the shift `pars1[10]` corresponds to lambda^a (anagenesis rate) after the shift `pars1[11]` corresponds to the time of shift
`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 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 "lsodes"
`CS_version`	For internal testing purposes only. Default is 1, the original DAISIE code.
`abstolint`	Absolute tolerance of the integration
`reltolint`	Relative tolerance of the integration
`verbose`	Logical controling if progress is printed to console.

The output is a loglikelihood value

The loglikelihood

Rampal S. Etienne & Bart Haegeman

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.

DAISIE_ML, DAISIE_sim

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)