DAISIE_loglik_IW  R Documentation 
Computes the loglikelihood of the DAISIE model with islandwide
diversitydependence given data and a set of model parameters
Description
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
Usage
DAISIE_loglik_IW(
pars1,
pars2,
datalist,
methode = "lsodes",
abstolint = 1e12,
reltolint = 1e10,
verbose = FALSE
)
Arguments
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. Supported Boost ODEINT
solvers (steppers) are:
'odeint::runge_kutta_cash_karp54'
'odeint::runge_kutta_fehlberg78' [default]
'odeint::runge_kutta_dopri5'
'odeint::bulirsch_stoer'
'odeint::adams_bashforth_[12345678]}
\code{'odeint::adams_bashforth_moulton_[12345678]
without odeint:: prefix, ode method is
assumed.

abstolint 
Absolute tolerance of the integration

reltolint 
Relative tolerance of the integration

verbose 
Logical controling if progress is printed to console.

Details
The output is a loglikelihood value
Value
The loglikelihood
Author(s)
Rampal S. Etienne & Bart Haegeman
References
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.
See Also
DAISIE_ML_IW
, DAISIE_loglik_CS
,
DAISIE_sim_cr