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