default_params_doc: Defailt parameter documentation

In xieshu95/Trait_dependent_TraiSIE: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

Description

Defailt parameter documentation

Usage

default_params_doc(datalist, datatype, initparsopt, idparsopt, parsfix,
  idparsfix, idparsnoshift, idparsmat, res, ddmodel, cond, island_ontogeny,
  eqmodel, x_E, x_I, tol, maxiter, methode, optimmethod, CS_version,
  verbose, tolint, time, M, pars, replicates, mainland_params, divdepmodel,
  prop_type2_pool, replicates_apply_type2, sample_freq, ddmodel_sim,
  island_type, nonoceanic, plot_sims, Apars, Epars, Tpars,
  keep_final_state, stored_data, island_replicates)

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 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 and stem age of the population/species in the case of Non-endemic, Non-endemic_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_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
datatype	Sets the type of data: 'single' for a single island or archipelago treated as one, and 'multiple' for multiple archipelagoes potentially sharing the same parameters
initparsopt	The initial values of the parameters that must be optimized
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.
idparsnoshift	For datatype = 'single' only: The ids of the parameters that should not be different between two groups of species; This can only apply to ids 6:10, e.g. idparsnoshift = c(6,7) means that lambda^c and mu have the same values for both groups
idparsmat	For datatype = 'multiple' only: Matrix containing the ids of the parameters, linking them to initparsopt and parsfix. Per island system we use the following order: * lac = (initial) cladogenesis rate * mu = extinction rate * K = maximum number of species possible in the clade * gam = (initial) immigration rate * laa = (initial) anagenesis rate Example: idparsmat = rbind(c(1,2,3,4,5),c(1,2,3,6,7)) has different rates of immigration and anagenesis for the two islands.
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	type of island ontonogeny. A string describing the type of island ontogeny. If NA, then constant ontogeny is assumed.Can be "const", "beta".
eqmodel	Sets the equilibrium constraint that can be used during the likelihood optimization. Only available for datatype = 'single'. eqmodel = 0 : no equilibrium is assumed eqmodel = 13 : near-equilibrium is assumed on endemics using deterministic equation for endemics and immigrants. Endemics must be within x_E of the equilibrium value eqmodel = 15 : near-equilibrium is assumed on endemics and immigrants using deterministic equation for endemics and immigrants. Endemics must be within x_E of the equilibrium value, while non-endemics must be within x_I of the equilibrium value
x_E	Sets the fraction of the equlibrium endemic diversity above which the endemics are assumed to be in equilibrium; only active for eqmodel = 13 or 15
x_I	Sets the fraction of the equlibrium non-endemic diversity above which the system is assumed to be in equilibrium; only active for eqmodel = 15
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	For internal testing purposes only. Default is 1, the original DAISIE code.
verbose	sets whether parameters and likelihood should be printed (1) or not (0)
tolint	Vector of two elements containing the absolute and relative tolerance of the integration
time	Length of the simulation in time units. For examples, if an island is known to be 4 million years old, setting time = 4 will simulate the entire life span of the island; setting time = 2 will stop the simulation at the mid-life of the island.
M	The size of mainland pool, i.e. the number of species that can potentially colonize the island.
pars	Contains the model parameters: pars[1] corresponds to lambda^c (cladogenesis rate) pars[2] corresponds to mu (extinction rate) pars[3] corresponds to K (clade-level carrying capacity). Set K=Inf for non-diversity dependence. pars[4] corresponds to gamma (immigration rate) pars[5] corresponds to lambda^a (anagenesis rate) pars[6] corresponds to lambda^c (cladogenesis rate) for type 2 species pars[7] corresponds to mu (extinction rate) for type 2 species pars[8] corresponds to K (clade-level carrying capacity) for type 2 species. Set K=Inf for non-diversity dependence. pars[9] corresponds to gamma (immigration rate) for type 2 species pars[10] corresponds to lambda^a (anagenesis rate) for type 2 species The elements 6:10 are optional and are required only when type 2 species are included.
replicates	Number of island replicates to be simulated.
mainland_params	mainland_params parameters for simulation mainland processes. If NULL, the mainland is assumed to be static, following the assumptions of Valente et al., 2015.
divdepmodel	Option divdepmodel = 'CS' runs a model with clade-specific carrying capacity, where diversity-dependence operates only within single clades, i.e. only among species originating from the same mainland colonist. Option divdepmodel = 'IW' runs a model with island-wide carrying capacity, where diversity-dependence operates within and among clades.
prop_type2_pool	Fraction of mainland species that belongs to the second subset of species (type 2). Applies only when two types of species are simulated (length(pars) = 10).
replicates_apply_type2	Applies only when two types of species are being simulated. Default replicates_apply_type2 = TRUE runs simulations until the number of islands where a type 2 species has colonised is equal to the specified number of replicates. This is recommended if prop_type2_pool is small of if the rate of immigration of type two species (pars[9]) is low, meaning that more replicates are needed to achieved an adequate sample size of islands with type 2 species. Setting replicates_apply_type2 = FALSE simulates islands up to the specified number of replicates regardless of whether type 2 species have colonised or not.
sample_freq	Specifies the number of units times should be divided by for plotting purposes. Larger values will lead to plots with higher resolution, but will also run slower.
ddmodel_sim	A numeric which sets the model of diversity-depedence when running simulations.
island_type	oceanic or non-oceanic island
nonoceanic	parameters for non-oceanic island model
plot_sims	Default = TRUE plots species-through-time (STT) plots.
Apars	A numeric vector: [1]: maximum area [2]: vale from 0 to 1 indicating where in the island's history the peak area is achieved [3]: sharpness of peak [4]: total island age
Epars	A numeric vector: [1]: minimum extinction when area is at peak [2]: extinction rate when current area is 0.10 of maximum area
Tpars	A named list containing diversification rates considering two trait states: [1]:A numeric with the per capita transition rate with state1 [2]:A numeric with the per capita immigration rate with state2 [3]:A numeric with the per capita extinction rate with state2 [4]:A numeric with the per capita anagenesis rate with state2 [5]:A numeric with the per capita cladogenesis rate with state2 [6]:A numeric with the per capita transition rate with state2 [7]:A carrying capacity with trait state 2 on mainland [8]:A numeric with the number of species with trait state 2 on mainland
keep_final_state	logical indicating if final state of simulation should be returned. Default is FALSE.
stored_data	output of DAISIE_sim function when run with keep_final_state. If not NULL.
island_replicates	Island replicates in DAISIE format (produced in DAISIE_sim with format = TRUE option). Minimally, this must be a list, that has as much elements as replicates. Each element must be a list with the elements island_age, not_present and stt_all. stt_all must be a data frame with the column names Time, nI, nA, nC and present.

Value

Nothing

xieshu95/Trait_dependent_TraiSIE documentation built on Nov. 22, 2019, 7:51 a.m.