DAISIE_IC: Calculates information criterion from DAISIE ML estimates?

View source: R/DAISIE_IC.R

DAISIE_ICR 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

Value

List of two numerics with WIC and AICb


DAISIE documentation built on June 2, 2022, 5:07 p.m.