Calculates information criterion from DAISIE ML estimates?
DAISIE_IC(
datalist,
initparsopt,
idparsopt,
parsfix,
idparsfix,
endmc = 1000,
res = 100,
cond = 0,
ddmodel = 0
)List of two numerics with WIC and AICb
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
The initial values of the parameters that must be optimized, they are all positive.
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.
The values of the parameters that should not be optimized.
The ids of the parameters that should not be optimized, e.g. c(1,3) if lambda^c and K should not be optimized.
Numeric for how many simulations should run.
Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade.
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
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