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#' Default parameter documentation
#'
#' @param time Numeric defining the length of the simulation in time units.
#' For example, 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.
#' @param M Numeric defining the size of mainland pool, i.e. the number of
#' species that can potentially colonize the island.
#' @param pars A numeric vector containing the model parameters:
#' \itemize{
#' \item{\code{pars[1]}: lambda^c (cladogenesis rate)}
#' \item{\code{pars[2]}: mu (extinction rate)}
#' \item{\code{pars[3]}: K (carrying capacity), set K=Inf for diversity
#' independence.}
#' \item{\code{pars[4]}: gamma (immigration rate)}
#' \item{\code{pars[5]}: lambda^a (anagenesis rate)}
#' \item{\code{pars[6]}: lambda^c (cladogenesis rate) for either type 2 species
#' or rate set 2 in rate shift model}
#' \item{\code{pars[7]}: mu (extinction rate) for either type 2 species or rate
#' set 2 in rate shift model}
#' \item{\code{pars[8]}: K (carrying capacity) for either type 2 species or rate
#' set 2 in rate shift model, set K=Inf for diversity independence.}
#' \item{\code{pars[9]}: gamma (immigration rate) for either type 2 species
#' or rate set 2 in rate shift model}
#' \item{\code{pars[10]}: lambda^a (anagenesis rate) for either type 2
#' species or rate set 2 in rate shift model}
#' }
#' Elements 6:10 are required only when type 2 species are included
#' or in the rate shift model. For \code{\link{DAISIE_sim_relaxed_rate}()}
#' \code{pars[6]} is the standard deviation of the gamma distribution for the
#' relaxed parameter and the parameter chosen by the \code{relaxed_par}
#' argument is the mean of the gamma distribution for the relaxed parameter.
#' @param replicates Integer specifying number of island replicates to be
#' simulated.
#' @param 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. Option divdepmodel = 'GW' runs a model with diversity-dependence
#' operates within a guild.
#' @param nonoceanic_pars A vector of length two with:
#' \itemize{
#' \item{[1]: the probability of sampling a species from the mainland}
#' \item{[2]: the probability of the species sampled from the mainland
#' being nonendemic}
#' }
#' @param num_guilds The number of guilds on the mainland. The number of
#' mainland species is divided by the number of guilds when
#' \code{divdepmodel = "GW"}
#' @param 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). For \code{\link{DAISIE_dataprep}()}
#' applies only if number_clade_types = 2. In \code{\link{DAISIE_dataprep}()}
#' the default \code{"proportional"} sets the fraction to be proportional to
#' the number of clades of distinct macroevolutionary process that have
#' colonised the island.
#' @param 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
#' \code{prop_type2_pool} is small or if the rate of immigration of type two
#' species (\code{pars[9]}) is low, meaning that more replicates are needed to
#' achieved an adequate sample size of islands with type 2 species. Setting
#' \code{replicates_apply_type2 = FALSE} simulates islands up to the
#' specified number of replicates regardless of whether type 2 species have
#' colonised or not.
#' @param sample_freq Numeric specifing 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.
#' @param plot_sims \code{Default = TRUE} plots species-through-time (STT)
#' plots. It detects how many types of species are present. If only one type
#' of species is present, STT is plotted for all species. If two types are
#' present, three plots are produced: STT for all, STT for type 1 and STT for
#' type 2.
#' @param verbose A numeric vector of length 1, which in simulations and
#' `DAISIEdataprep()` can be `1` or `0`, where `1` gives intermediate output
#' should be printed.
#' For ML functions a numeric determining if intermediate output should be
#' printed. The default: `0` does not print, `1` prints the initial
#' likelihood and the settings that were selected (which parameters are
#' to be optimised, fixed or shifted), `2` prints the same as `1 and also the
#' intermediate output of the parameters and loglikelihood, while `3` the
#' same as `2` and prints intermediate progress during likelihood computation.
#' @param area_pars A named list containing area and sea level parameters as
#' created by \code{\link{create_area_pars}()}:
#' \itemize{
#' \item{[1]: maximum area}
#' \item{[2]: current area}
#' \item{[3]: value from 0 to 1 indicating where in the island's history the
#' peak area is achieved}
#' \item{[4]: total island age}
#' \item{[5]: amplitude of area fluctuation from sea level}
#' \item{[6]: frequency of sine wave of area change from sea level}
#' \item{[7]: angle of the slope of the island}
#' }
#' @param hyper_pars A named list of numeric hyperparameters for the rate
#' calculations as returned by \code{\link{create_hyper_pars}()}:
#' \itemize{
#' \item{[1]: is d the scaling parameter for exponent for calculating
#' cladogenesis rate}
#' \item{[2]: is x the exponent for calculating extinction rate}
#' }
#' @param island_ontogeny In \code{\link{DAISIE_sim_time_dep}()},
#' \code{\link{DAISIE_ML_CS}} and plotting a string describing the type of
#' island ontogeny. Can be \code{"const"}, \code{"beta"} for a beta function
#' describing area through time. \cr In all other functions a
#' numeric describing the type of island ontogeny. Can be \code{0} for
#' constant, \code{1} for a beta function describing area through time. In ML
#' functions \code{island_ontogeny = NA} assumes constant ontogeny. Time
#' dependent estimation is not yet available as development is still ongoing.
#' Will return an error if called in that case.
#' @param sea_level In \code{\link{DAISIE_sim_time_dep}()} and plotting a
#' string describing the type of sea level. Can be \code{"const"} or
#' \code{"sine"} for a sine function describing area through time.
#' \cr In all other functions a numeric describing the type of sea level. Can
#' be \code{0} for constant, \code{1} for a sine function describing area
#' through time.
#' @param extcutoff A numeric with the cutoff for the the maximum extinction
#' rate preventing it from being too large and slowing down simulation.
#' @param shift_times a numeric vector specifying when the rate shifts occur
#' before the present.
#' @param mainland_n A numeric stating the number of mainland species, that
#' is the number of species that can potentially colonize the island.
#' If using a clade-specific diversity dependence, this value is set to 1.
#' If using an island-wide diversity dependence, this value is set to the
#' number of mainland species.
#' @param island_replicates List output from
#' \code{\link{DAISIE_sim_core_cr}()},
#' \code{\link{DAISIE_sim_core_time_dep}()},
#' \code{\link{DAISIE_sim_core_cr_shift}()} or
#' \code{\link{DAISIE_sim_min_type2}()} functions. Minimally, this must be a
#' list that has as many elements as replicates. Each element must be a list
#' with the elements \code{island_age}, \code{not_present} and \code{stt_all}.
#' \code{stt_all} must be a data frame with the column names \code{Time},
#' \code{nI}, \code{nA}, \code{nC} and \code{present}.
#' @param island_spec Matrix with current state of simulation containing number
#' of species.
#' @param stt_table Matrix with number of species at each time step.
#' @param rates named list of numeric rates as returned by
#' \code{\link{update_rates}()}.
#' @param max_rates named list of numeric max rates as returned by
#' \code{\link{update_max_rates}()}.
#' @param timeval Numeric defining current time of simulation.
#' @param total_time Numeric defining the length of the simulation in time
#' units.
#' @param possible_event Numeric defining what event will happen.
#' @param maxspecID Current species IDs.
#' @param mainland_spec Number of mainland species.
#' @param max_area Numeric defining maximum area.
#' @param proportional_peak_t Numeric value from 0 to 1 indicating
#' where in the island's history the peak area is achieved.
#' @param total_island_age Numeric defining total island age.
#' @param sea_level_amplitude Numeric defining amplitude of area fluctuation
#' from sea level.
#' @param sea_level_frequency Numeric defining frequency of sine wave of
#' area change from sea level.
#' @param island_gradient_angle Numeric defining the angle in degrees
#' specifying the slope of the island.
#' @param d Numeric defining the scaling parameter for exponent for
#' calculating cladogenesis rate.
#' @param x Numeric defining the exponent for calculating extinction rate.
#' @param simulation_outputs A list with matrices and vectors of simulation
#' produced by DAISIE_sim functions.
#' @param plot_plus_one Boolean to indicate to plot all values plus one.
#' Set to \code{TRUE} for default behavior. Set to \code{FALSE} to plot all
#' values without adding one. Only works when there is one type of species.
#' @param type String to indicate if stt of all species or all possible stt
#' should be plotted. Default is \code{"all_species"}, \code{"type1_species"}
#' or \code{"type2_species"} should be plotted.
#' @param plot_lists List of lists containing average and quantile species
#' through time.
#' @param ... Any arguments to pass on to plotting functions.
#' @param 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.\cr The first element
#' of the list has two or three components: \cr \cr \code{$island_age} - the
#' island age \cr Then, depending on whether a distinction between types is
#' made, we have:\cr \code{$not_present} - the number of mainland lineages
#' that are not present on the island \cr or:\cr \code{$not_present_type1} -
#' the number of mainland lineages of type 1 that are not present on the
#' island \cr \code{$not_present_type2} - the number of mainland lineages of
#' type 2 that are not present on the island \cr \cr The remaining elements of
#' the list each contains information on a single colonist lineage on the
#' island and has 5 components:\cr \cr \code{$colonist_name} - the name of the
#' species or clade that colonized the island \cr \code{$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\cr \code{$stac} - the
#' status of the colonist \cr \cr * Non_endemic_MaxAge: 1 \cr * Endemic: 2
#' \cr * Endemic&Non_Endemic: 3 \cr * Non_Endemic: 4 \cr
#' * Endemic_Singleton_MaxAge: 5 \cr * Endemic_Clade_MaxAge: 6
#' \cr * Endemic&Non_Endemic_Clade_MaxAge: 7 \cr
#' \cr \code{$missing_species} - number of island species that were not
#' sampled for particular clade (only applicable for endemic clades) \cr
#' \code{$type1or2} - whether the colonist belongs to type 1 or type 2 \cr
#' @param 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.
#' @param initparsopt The initial values of the parameters that must be
#' optimized, they are all positive.
#' @param idparsopt The ids of the parameters that must be optimized. The ids
#' are defined as follows: \cr \cr id = 1 corresponds to lambda^c
#' (cladogenesis rate) \cr id = 2 corresponds to mu (extinction rate) \cr
#' id = 3 corresponds to K (clade-level carrying capacity) \cr id = 4
#' corresponds to gamma (immigration rate) \cr id = 5 corresponds to lambda^a
#' (anagenesis rate) \cr id = 6 corresponds to lambda^c (cladogenesis rate)
#' for an optional subset of the species \cr id = 7 corresponds to mu
#' (extinction rate) for an optional subset of the species\cr id = 8
#' corresponds to K (clade-level carrying capacity) for an optional subset of
#' the species\cr id = 9 corresponds to gamma (immigration rate) for an
#' optional subset of the species\cr id = 10 corresponds to lambda^a
#' (anagenesis rate) for an optional subset of the species\cr id = 11
#' corresponds to p_f (fraction of mainland species that belongs to the second
#' subset of species.
#' @param 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.
#' @param parsfix The values of the parameters that should not be optimized.
#' @param 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.
#' @param 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: \cr \cr * lac = (initial) cladogenesis
#' rate \cr * mu = extinction rate \cr * K = maximum number of species possible
#' in the clade \cr * gam = (initial) immigration rate \cr * laa = (initial)
#' anagenesis rate \cr Example:
#' \code{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.
#' @param res Sets the maximum number of species for which a probability must
#' be computed, must be larger than the size of the largest clade.
#' @param ddmodel Sets the model of diversity-dependence: \cr \cr ddmodel = 0 :
#' no diversity dependence \cr ddmodel = 1 : linear dependence in speciation
#' rate \cr ddmodel = 11: linear dependence in speciation rate and in
#' immigration rate \cr ddmodel = 2 : exponential dependence in speciation
#' rate\cr ddmodel = 21: exponential dependence in speciation rate and in
#' immigration rate\cr
#' @param cond cond = 0 : conditioning on island age \cr cond = 1 :
#' conditioning on island age and non-extinction of the island biota \cr.
#' 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 \cr
#' @param eqmodel Sets the equilibrium constraint that can be used during the
#' likelihood optimization. Only available for datatype = 'single'.\cr\cr
#' eqmodel = 0 : no equilibrium is assumed \cr 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\cr 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.
#' @param 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.
#' @param 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.
#' @param tol Sets the tolerances in the optimization. Consists of: \cr reltolx
#' = relative tolerance of parameter values in optimization \cr reltolf =
#' relative tolerance of function value in optimization \cr abstolx = absolute
#' tolerance of parameter values in optimization.
#' @param maxiter Sets the maximum number of iterations in the optimization.
#' @param methode Method of the ODE-solver. Supported Boost \code{ODEINT}
#' solvers (steppers) are:
#' \code{"odeint::runge_kutta_cash_karp54"}
#' \code{"odeint::runge_kutta_fehlberg78"}
#' \code{"odeint::runge_kutta_dopri5"}
#' \code{"odeint::bulirsch_stoer"}
#' without \code{odeint::}-prefix, \code{\link{deSolve}{ode}} method is
#' assumed. The default method overall is
#' \code{"lsodes"} for \code{\link{DAISIE_ML_CS}()}
#' and \code{"ode45"} from \code{\link[deSolve]{ode}()} for
#' \code{\link{DAISIE_ML_IW}()}.
#' @param optimmethod Method used in likelihood optimization. Default is
#' `subplex` (see `\link[subplex]{subplex}()` for full details).
#' Alternative is \code{"simplex"} which was the method in previous versions.
#' @param tolint Vector of two elements containing the absolute and relative
#' tolerance of the integration.
#' @param datatable Data frame (table) with user-specified data. See file
#' \code{Galapagos_datatable} for a template of an input table. Each row on the
#' table represents and independent colonisation event. Table has the
#' following four columns. \cr \cr \code{$Clade_name} - name of independent
#' colonization event \cr \code{$Status} - One of the following categories:
#' \cr * "Non_endemic": applies to non-endemic species for cases where both
#' island and non-island populations of the species have been sampled) \cr *
#' "Non_endemic_MaxAge": applies to non-endemic species for cases where island
#' individuals of the species have not been sampled and only the age of the
#' species is available) \cr * "Endemic": applies to endemic species and is
#' applicable for both cladogenetic and anagenetic species \cr *
#' "Endemic_MaxAge": applies to endemic species for cases where island
#' individuals of the species have not been sampled and only the age of the
#' species is available. This could apply to endemic species that have
#' recently gone extinct because of antropogenic causes that are (evidently)
#' not modelled, and for which no DNA data is available.\cr *
#' "Endemic&Non_Endemic": when endemic clade is present and its mainland
#' ancestor has re-colonized \cr \code{$Missing_species} - Number of island
#' species that were not sampled for particular clade (only applicable for
#' "Endemic" clades) \cr \code{$Branching_times} - Stem age of the
#' population/species in the case of "Non-endemic", "Non-endemic_MaxAge" and
#' "Endemic" anagenetic species. For "Endemic" cladogenetic species these
#' should be branching times of the radiation including the stem age of the
#' radiation.
#' @param island_age Age of island in appropriate units. In
#' \code{\link{DAISIE_plot_age_diversity}()} and
#' \code{\link{DAISIE_plot_island}()} if island input is in table format,
#' the age of the island must be specified. If island input is in DAISIE list
#' format, this option will override the island age specified in the island
#' list.
#' @param number_clade_types Number of clade types. Default: number_clade_types
#' = 1 all species are considered to belong to same macroevolutionary process.
#' If number_clade_types = 2, there are two types of clades with distinct
#' macroevolutionary processes.
#' @param list_type2_clades If \code{number_clade_types = 2}, list_type2_clades
#' specifies the names of the clades that have a distinct macroevolutionary
#' process. The names must match those in the $Clade_name column of the source
#' data table (e.g. \code{list_type2_clades = "Finches"}). If
#' \code{number_clade_types = 1}, then list_type2_clades = NA should be
#' specified (default).
#' @param epss Default= 1E-5 should be appropriate in most cases. This value
#' is used to set the maximum age of colonisation of "Non_endemic_MaxAge" and
#' "Endemic_MaxAge" species to an age that is slightly younger than the island
#' for cases when the age provided for that species is older than the island.
#' The new maximum age is then used as an upper bound to integrate over all.
#' @param t The time at which the expectations need to be computed.
#' @param initEI The initial values for the number of endemics and
#' non-endemics. In \code{\link{DAISIE_probdist}()} or
#' \code{\link{DAISIE_margprobdist}()} either this or initprobs must be NULL. In
#' \code{\link{DAISIE_numcol}()} when it is NULL, it is assumed that the island
#' is empty.
#' @param data_table data table
#' @param endmc Numeric for how many simulations should run.
#' @param archipelago something
#' @param phylo_data something
#' @param archipelago_data something
#' @param gam A numeric with the per capita immigration rate.
#' @param laa A numeric with the per capita anagenesis rate.
#' @param lac A numeric with the per capita cladogenesis rate.
#' @param mu A numeric with the per capita extinction rate.
#' @param K A numeric with carrying capacity.
#' @param num_spec A numeric with the current number of species.
#' @param num_immigrants A numeric with the current number of non-endemic
#' species (a.k.a non-endemic species).
#' @param global_min_area_time stub
#' @param global_max_area_time stub
#' @param distance_type Use 'continent' if the distance to the continent should
#' be used, use 'nearest_big' if the distance to the nearest big landmass
#' should be used, and use 'biologically_realistic' if the distance should
#' take into account some biologically realism, e.g. an average of the
#' previous two if both are thought to contribute.
#' @param distance_dep Sets what type of distance dependence should be used.
#' Default is a power law, denoted as 'power'. Alternatives are an exponantial
#' relationship denoted by 'exp' or sigmoids, either 'sigmoidal_col' for a
#' sigmoid in the colonization, 'sigmoidal_ana' for sigmoidal anagenesis,
#' 'sigmoidal_clado' for sigmoidal cladogenesis, and 'sigmoidal_col_ana' for
#' signoids in both colonization and anagenesis.
#' @param parallel Sets whether parallel computation should be used. Use 'no'
#' if no parallel computing should be used, 'cluster' for parallel computing
#' on a unix/linux cluster, and 'local' for parallel computation on a local
#' machine.
#' @param cpus Number of cpus used in parallel computing. Default is 3. Will
#' not have an effect if parallel = 'no'.
#' @param pars1 Vector of model parameters: \cr \cr \code{pars1[1]} corresponds
#' to lambda^c (cladogenesis rate) \cr \code{pars1[2]} corresponds to mu
#' (extinction rate) \cr \code{pars1[3]} corresponds to K (clade-level
#' carrying capacity) \cr \code{pars1[4]} corresponds to gamma
#' (immigration rate) \cr \code{pars1[5]} corresponds to lambda^a
#' (anagenesis rate).
#' @param pars2 Vector of settings: \cr \cr \code{pars2[1]} corresponds to res,
#' the maximum number of endemics or non-endemics for which the ODE system is
#' solved; this must be much larger than the actual number for which the
#' probability needs to be calculated.) \cr \code{pars2[2]} corresponds to M,
#' size of the mainland pool, i.e the number of species that can potentially
#' colonize the island.
#' @param tvec The times at which the probabilities need to be computed.
#' @param initprobs The initial probability distribution for the number of
#' endemics and non-endemics; either this or initEI must be NULL.
#' @param pb Probability distribution in matrix format as output by
#' \code{\link{DAISIE_probdist}()}.
#' @param island Island data object. Can be in DAISIE list format (see
#' Galapagos_datalist and DAISIE_data_prep for examples) or in table format
#' (see Galapagos_datatable for an example).
#' @param title Title of the plot
#' @param plot_lists_simulations List with simulation output after parsing by
#' \code{DAISIE_prepare_data_plotting}.
#' @param plot_lists_simulations_MLE List with simulation output after parsing
#' by \code{DAISIE_prepare_data_plotting}, but obtained by simulating MLE
#' output.
#' @param kind_of_plot Character vector stating how STT plot resulting from MLE
#' based simulations should be plotted. Default is \code{"line"} for multiple
#' individual lines. Can also be \code{"shade"} for the 5\% quantile.
#' @param resolution numeric indicating resolution of plot. Should be < 0.
#' @param resol numeric for resolution of summary stats calculation. Should be
#' > 1.
#' @param removed_timepoints Positive integer with number of first datapoints
#' to be removed from rate plots (to prevent Inf)
#' @param A A numeric value for island area at a given point in time.
#' @param Amin A numeric value for minimum island area during the simulation.
#' @param Amax A numeric value for maximum island area during the simulation.
#' @param peak A numeric value specifying the peakiness (or shaprness) of the
#' ontogeny curve. Higher values imply peakier ontogeny. This value is
#' internally calculated by \code{\link{calc_peak}()} given the area at the
#' present and the \code{area_pars}.
#' @param proptime A numeric from 0 to 1. The proportion of time that has
#' elapsed in the simulation, in relation to the total island age (NB: not
#' the simulation time, but island age).
#' @param proptime_max A numeric from 0 to 1. The same as
#' \code{proportional_peak_t}. Indicates, in proportion to the total island
#' age when the ontogeny peak should occur (i.e. 0.5 means a peak halfway in
#' time).
#' @param current_area A numeric with the current island area at present (i.e.,
#' at the end of the simulation).
#' @param jitter Numeric for \code{\link[DDD]{optimizer}()}. Jitters the
#' parameters being optimized by the specified amount which should be very
#' small, e.g. 1e-5. Jitter when \code{link{subplex}{subplex}()} produces
#' incorrect output due to parameter transformation.
#' @param num_cycles The number of cycles the optimizer will go through.
#' Default is 1.
#' @param trait_pars A named list containing diversification rates considering
#' two trait states created by \code{\link{create_trait_pars}}:
#' \itemize{
#' \item{[1]:A numeric with the per capita transition rate with state1}
#' \item{[2]:A numeric with the per capita immigration rate with state2}
#' \item{[3]:A numeric with the per capita extinction rate with state2}
#' \item{[4]:A numeric with the per capita anagenesis rate with state2}
#' \item{[5]:A numeric with the per capita cladogenesis rate with state2}
#' \item{[6]:A numeric with the per capita transition rate with state2}
#' \item{[7]:A numeric with the number of species with trait state 2 on
#' mainland}
#' }
#' @param relaxed_par A string determining which parameter is relaxed in a
#' relaxed rate model.
#' @param relaxed_rate_pars A list of two numbers, element one is the
#' distribution mean, element two is the distribution standard deviation (sd).
#' Currently the distribution is the gamma distribution. The list can be created
#' with \code{create_relaxed_rate_pars()}.
#' @param brts Numeric vector of branching times
#' @param stac Numeric of Endemicity status
#' @param missnumspec Numeric of missing species
#' @param 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:
#' \itemize{
#' \item{model: the CS model to run, options are \code{1} for single rate
#' DAISIE model, \code{2} for multi-rate DAISIE, or \code{0} for IW test
#' model.}
#' \item{relaxed_par: the parameter to relax (integrate over). Options are
#' \code{"cladogenesis"}, \code{"extinction"}, \code{"carrying_capacity"},
#' \code{"immigration"}, or \code{"anagenesis"}.}
#' }
#' @param DAISIE_par A numeric parameter to evaluate the integral of the
#' function.
#' @param DAISIE_dist_pars A numeric vector of two elements, first is the mean
#' and second the standard deviation of the distribution.
#' @param abstolint Numeric absolute tolerance of the integration
#' @param reltolint Numeric relative tolerance of the integration
#' @param pick Numeric determining which parameter is selected for the
#' relaxed-rate model
#' @param mean Numeric mean of the distribution
#' @param sd Numeric standard deviation of the distribution
#' @keywords internal
#' @note This is an internal function, so it should be marked with
#' \code{@noRd}. This is not done, as this will disallow all
#' functions to find the documentation parameters
#' @param clado_rate Numeric rate of cladogenesis
#' @param ext_rate Numeric rate of extinction
#' @param carr_cap Numeric carrying capacity
#' @param immig_rate Numeric rate of immigration
#' @param ana_rate Numeric rate of anagenesis
#' @param islands Island datalist or simulated data in DAISIE datalist format.
#' Can be a single island (empirical data) generated with DAISIE_dataprep or
#' DAISIEprep. Can also be simulated data generated with DAISIE_sim function.
#' @param sort_clade_sizes Default sort_clade_sizes = T outputs clade sizes
#' sorted in ascending order of number of species. sort_clade_sizes=F outputs
#' clade sizes in the same order as they appear in the input datalist.
#'
#'
#' @return Nothing
default_params_doc <- function(
time,
M,
pars,
replicates,
divdepmodel,
nonoceanic_pars,
num_guilds,
prop_type2_pool,
replicates_apply_type2,
sample_freq,
plot_sims,
verbose,
area_pars,
hyper_pars,
island_ontogeny,
sea_level,
extcutoff,
shift_times,
mainland_n,
island_replicates,
island_spec,
stt_table,
rates,
max_rates,
timeval,
total_time,
possible_event,
maxspecID,
mainland_spec,
max_area,
proportional_peak_t,
total_island_age,
sea_level_amplitude,
sea_level_frequency,
island_gradient_angle,
d,
x,
simulation_outputs,
plot_plus_one,
type,
plot_lists,
...,
datalist,
datatype,
initparsopt,
idparsopt,
idparsfix,
parsfix,
idparsnoshift,
idparsmat,
res,
ddmodel,
cond,
eqmodel,
x_E,
x_I,
tol,
maxiter,
methode,
optimmethod,
CS_version,
tolint,
datatable,
island_age,
number_clade_types,
list_type2_clades,
epss,
t,
initEI,
data_table,
endmc,
archipelago,
phylo_data,
archipelago_data,
gam,
laa,
lac,
mu,
K,
num_spec,
num_immigrants,
global_min_area_time,
global_max_area_time,
distance_type,
distance_dep,
parallel,
cpus,
pars1,
pars2,
tvec,
initprobs,
pb,
island,
title,
plot_lists_simulations,
plot_lists_simulations_MLE,
kind_of_plot,
resolution,
resol,
removed_timepoints,
A,
Amin,
Amax,
peak,
proptime,
proptime_max,
current_area,
jitter,
num_cycles,
trait_pars,
relaxed_par,
relaxed_rate_pars,
brts,
stac,
missnumspec,
DAISIE_par,
DAISIE_dist_pars,
abstolint,
reltolint,
pick,
mean,
sd,
clado_rate,
ext_rate,
carr_cap,
immig_rate,
ana_rate,
islands,
sort_clade_sizes
) {
# Nothing
}
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