R/default_params_doc.R

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

#' Defailt parameter documentation
#'
#' @param time Numeric defining the 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.
#' @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{pars[1]: lambda^c (cladogenesis rate)}
#'   \item{pars[2]: mu (extinction rate)}
#'   \item{pars[3]: K (carrying capacity), set K=Inf for diversity
#'   independence.}
#'   \item{pars[4]: gamma (immigration rate)}
#'   \item{pars[5]: lambda^a (anagenesis rate)}
#'   \item{pars[6]: lambda^c (cladogenesis rate) for either type 2 species
#'   or rate set 2 in rate shift model}
#'   \item{pars[7]: mu (extinction rate) for either type 2 species or rate
#'   set 2 in rate shift model}
#'   \item{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{pars[9]: gamma (immigration rate) for either type 2 species or
#'   rate set 2 in rate shift model}
#'   \item{pars[10]: lambda^a (anagenesis rate) for either type 2 species
#'   or rate set 2 in rate shift model}
#' }
#' The elements 6:10 are required only when type 2 species are included
#' or in the rate shift model.
#' @param replicates 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 "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 prop_type2_pool
#' is small or 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.
#' @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 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 In simulation and dataprep functions a logical,
#' \code{Default = TRUE} gives intermediate output should be printed.
#' For ML functions a numeric determining if intermediate output should be
#' printed, \code{Default = 0} does not print, \code{verbose = 1} prints
#' intermediate output of the parameters and loglikelihood, \code{verbose = 2}
#' means also intermediate progress during loglikelihood computation is shown.
#' @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]: value from 0 to 1 indicating where in the island's history the
#'   peak area is achieved}
#'   \item{[3]: sharpness of peak}
#'   \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_0 the scaling parameter for exponent for calculating
#' cladogenesis rate}
#' \item{[2]: is x the exponent for calculating extinction rate}
#' \item{[3]: is alpha, the exponent for calculating the immigration rate}
#' \item{[4]: is beta the exponent for calculating the anagenesis rate.}
#' }
#' @param dist_pars A named list of a numeric distance from the mainland as
#' created by \code{\link{create_dist_pars}}:
#' \itemize{
#' \item{[1]: is D distance from the mainland}
#' }
#' @param ext_pars A numeric vector:
#' \itemize{
#'   \item{[1]: minimum extinction when area is at peak}
#'   \item{[2]: extinction rate when current area is 0.10 of maximum area}
#' }
#' @param island_ontogeny In \code{\link{DAISIE_sim_time_dependent}},
#' \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. String checked by
#' \code{\link{is_island_ontogeny_input}}. \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.
#' @param sea_level In \code{\link{DAISIE_sim_time_dependent}} 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. String
#' checked by \code{\link{is_sea_level_input}}.
#' \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_constant_rate}},
#' \code{\link{DAISIE_sim_core_time_dependent}},
#' \code{\link{DAISIE_sim_core_constant_rate_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_rates}}.
#' @param timeval Numeric defining current time of simulation.
#' @param totaltime 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 peak_sharpness Numeric defining sharpness of peak.
#' @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_0 Numeric defining the scaling parameter for exponent for
#' calculating cladogenesis rate.
#' @param x Numeric defining the exponent for calculating extinction rate.
#' @param alpha Numeric defining the exponent for calculating the immigration
#' rate.
#' @param beta Numeric defining the exponent for calculating the anagenesis
#' rate.
#' @param D A numeric defining the distance parameters for the rate
#' calculations.
#' @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 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.\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: 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.
#' @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. See package deSolve for details.
#' Default is "lsodes".
#' @param optimmethod Method used in likelihood optimization. Default is
#' "subplex" (see subplex package). Alternative is 'simplex' which was the
#' method in previous versions.
#' @param CS_version For internal testing purposes only. Default is 1, the
#' original DAISIE code.
#' @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
#' Galapagos_datatable.Rdata 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.\cr
#' @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 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. list_type2_clades = "Finches").  If 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 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} 
#' }
#' @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,
  dist_pars,
  ext_pars,
  island_ontogeny,
  sea_level,
  extcutoff,
  shift_times,
  mainland_n,
  island_replicates,
  island_spec,
  stt_table,
  rates,
  max_rates,
  timeval,
  totaltime,
  possible_event,
  maxspecID,
  mainland_spec,
  max_area,
  proportional_peak_t,
  peak_sharpness,
  total_island_age,
  sea_level_amplitude,
  sea_level_frequency,
  island_gradient_angle,
  d_0,
  x,
  alpha,
  beta,
  D,
  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,
  trait_pars
) {
  # Nothing
}