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
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initparsopt |
The initial values of the parameters that must be
optimized, they are all positive.
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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.
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parsfix |
The values of the parameters that should not be optimized.
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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
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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
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