Description
Usage
Arguments
Details
Value
Author(s)
References
See Also
View source: R/DAISIE_loglik_IW.R
Computes the loglikelihood of the DAISIE model given colonization and
branching times for lineages on an island, and a set of model parameters for
the DAISIE model with islandwide diversitydependence
 (
pars1,
pars2,
datalist,
methode = "ode45",
abstolint = 1e16,
reltolint = 1e14,
verbose =
)

pars1 
Contains the model parameters:
pars1[1] corresponds to lambda^c (cladogenesis rate)
pars1[2] corresponds to mu (extinction rate)
pars1[3] corresponds to K (cladelevel carrying capacity)
pars1[4] corresponds to gamma (immigration rate)
pars1[5] corresponds to lambda^a (anagenesis rate)
pars1[6] is optional; it may contain M, the total number of species
on the mainland

pars2 
Contains the model settings
pars2[1] corresponds to lx = length of ODE variable x
pars2[2] corresponds to ddmodel = diversitydependent model, model of diversitydependence, which can be one
of
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
Only ddmodel = 11 is currently implemented
pars2[3] corresponds to cond = setting of conditioning
cond = 0 : conditioning on island age
cond = 1 : conditioning on island age and nonextinction of the island biota
pars2[4] Specifies whether intermediate output should be provided,
because computation may take long. Default is 0, no output. A value of 1
means the parameters and loglikelihood are printed. A value of 2 means also
intermediate progress during loglikelihood computation is shown.

datalist 
Data object containing information on colonisation and
branching times. This object can be generated using the DAISIE_dataprep
function, which converts a userspecified 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 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 and stem
age of the population/species in the case of Nonendemic, Nonendemic_MaxAge
and Endemic anagenetic species. For cladogenetic species these should be
island age and branching times of the radiation including the stem age of
the radiation.
$stac  the status of the colonist
* Non_endemic_MaxAge: 1
* Endemic: 2
* Endemic&Non_Endemic: 3
* Non_endemic: 4
* Endemic_MaxAge: 5
$missing_species 
number of island species that were not sampled for particular clade (only
applicable for endemic clades)

methode 
Method of the ODEsolver. See package deSolve for details.
Default is "ode45"

abstolint 
Absolute tolerance of the integration

reltolint 
Relative tolerance of the integration

verbose 
Logical controling if progress is printed to console.

The output is a loglikelihood value
The loglikelihood
Rampal S. Etienne & Bart Haegeman
Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
Equilibrium and nonequilibrium dynamics simultaneously operate in the
Galapagos islands. Ecology Letters 18: 844852.
DAISIE_ML_IW
, DAISIE_loglik_CS
,
DAISIE_sim_constant_rate
DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.