DAISIE_ML3: Computes MLE for single type species under a clade specific...

Description Usage Arguments Value

View source: R/DAISIE_ML3.R

Description

Computes MLE for single type species under a clade specific scenario with ontogeny

Usage

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DAISIE_ML3(
  datalist,
  initparsopt,
  idparsopt,
  parsfix,
  idparsfix,
  res = 100,
  ddmodel = 0,
  cond = 0,
  island_ontogeny,
  tol = c(1e-04, 1e-05, 1e-07),
  maxiter = 1000 * round((1.25)^length(idparsopt)),
  methode = "lsodes",
  optimmethod = "subplex",
  CS_version = 1,
  verbose = 0,
  tolint = c(1e-16, 1e-10),
  jitter = 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.

res

Sets the maximum number of species for which a probability must be computed, must be larger than the size of the largest clade.

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

cond

cond = 0 : conditioning on island age
cond = 1 : conditioning on island age and non-extinction of the island biota
.

island_ontogeny

In DAISIE_sim_time_dependent(), DAISIE_ML_CS and plotting a string describing the type of island ontogeny. Can be "const", "beta" for a beta function describing area through time. String checked by is_island_ontogeny_input().
In all other functions a numeric describing the type of island ontogeny. Can be 0 for constant, 1 for a beta function describing area through time. In ML functions island_ontogeny = NA assumes constant ontogeny.

tol

Sets the tolerances in the optimization. Consists of:
reltolx = relative tolerance of parameter values in optimization
reltolf = relative tolerance of function value in optimization
abstolx = absolute tolerance of parameter values in optimization.

maxiter

Sets the maximum number of iterations in the optimization.

methode

Method of the ODE-solver. See package deSolve for details. Default is "lsodes".

optimmethod

Method used in likelihood optimization. Default is "subplex" (see subplex package). Alternative is 'simplex' which was the method in previous versions.

CS_version

a numeric or list. Default is 1 for the standard DAISIE model, for a relaxed-rate model a list with the following elements:

  • model: the CS model to run, options are 1 for single rate DAISIE model, 2 for multi-rate DAISIE, or 0 for IW test model

  • relaxed_par: the parameter to relax (integrate over). Options are "cladogenesis", "extinction", "carrying_capacity", "immigration", or "anagenesis"

verbose

In simulation and dataprep functions a logical, Default = TRUE gives intermediate output should be printed. For ML functions a numeric determining if intermediate output should be printed, Default = 0 does not print, verbose = 1 prints intermediate output of the parameters and loglikelihood, verbose = 2 means also intermediate progress during loglikelihood computation is shown.

tolint

Vector of two elements containing the absolute and relative tolerance of the integration.

jitter

Numeric for optimizer(). Jitters the parameters being optimized by the specified amount which should be very small, e.g. 1e-5. Jitter when link[subplex]{subplex}() produces incorrect output due to parameter transformation.

Value

The output is a dataframe containing estimated parameters and maximum loglikelihood.

lambda_c

gives the maximum likelihood estimate of lambda^c, the rate of cladogenesis

mu

gives the maximum likelihood estimate of mu, the extinction rate

K

gives the maximum likelihood estimate of K, the carrying-capacity

gamma

gives the maximum likelihood estimate of gamma, the immigration rate

lambda_a

gives the maximum likelihood estimate of lambda^a, the rate of anagenesis

loglik

gives the maximum loglikelihood

df

gives the number of estimated parameters, i.e. degrees of feedom

conv

gives a message on convergence of optimization; conv = 0 means convergence


DAISIE documentation built on Aug. 26, 2020, 5:12 p.m.