DAISIE_IC: Calculates information criterion from DAISIE ML estimates?
In DAISIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

DAISIE_IC

R Documentation

Calculates information criterion from DAISIE ML estimates?

Description

Calculates information criterion from DAISIE ML estimates?

Usage

DAISIE_IC(
  datalist,
  initparsopt,
  idparsopt,
  parsfix,
  idparsfix,
  endmc = 1000,
  res = 100,
  cond = 0,
  ddmodel = 0
)

Arguments

`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 followed by stem age of the population/species in the case of Non-endemic, Non-endemic_MaxAge species and Endemic species with no close relatives on the island. For endemic clades with more than one species on the island (cladogenetic clades/ radiations) these should be island age followed by the branching times of the island clade including the stem age of the clade `$stac` - the status of the colonist * Non_endemic_MaxAge: 1 * Endemic: 2 * Endemic&Non_Endemic: 3 * Non_Endemic: 4 * Endemic_Singleton_MaxAge: 5 * Endemic_Clade_MaxAge: 6 * Endemic&Non_Endemic_Clade_MaxAge: 7 `$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
`initparsopt`	The initial values of the parameters that must be optimized, they are all positive.
`idparsopt`	The ids of the parameters that must be optimized. The ids are defined as follows: id = 1 corresponds to lambda^c (cladogenesis rate) id = 2 corresponds to mu (extinction rate) id = 3 corresponds to K (clade-level carrying capacity) id = 4 corresponds to gamma (immigration rate) id = 5 corresponds to lambda^a (anagenesis rate) id = 6 corresponds to lambda^c (cladogenesis rate) for an optional subset of the species id = 7 corresponds to mu (extinction rate) for an optional subset of the species id = 8 corresponds to K (clade-level carrying capacity) for an optional subset of the species id = 9 corresponds to gamma (immigration rate) for an optional subset of the species id = 10 corresponds to lambda^a (anagenesis rate) for an optional subset of the species id = 11 corresponds to p_f (fraction of mainland species that belongs to the second subset of species.
`parsfix`	The values of the parameters that should not be optimized.
`idparsfix`	The ids of the parameters that should not be optimized, e.g. c(1,3) if lambda^c and K should not be optimized.
`endmc`	Numeric for how many simulations should run.
`res`	Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade.
`cond`	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. This last option is not yet available for the IW model
`ddmodel`	Sets the model of diversity-dependence: 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