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#' @title Simulate islands with given trait-dependent parameters.
#' @description This function simulates islands with given cladogenesis,
#' extinction, K, immigration and anagenesis parameters for binary states.
#'
#' Returns R list object that contains the simulated islands
#'
#' @inheritParams default_params_doc
#'
#' @return
#' A list. The highest level of the least corresponds to each individual
#' replciate. The first element of each replicate is composed of island
#' information containing:
#' \itemize{
#' \item{\code{$island_age}: A numeric with the island age.}
#' \item{\code{$not_present}: A numeric with the number of mainland lineages
#' that are not present on the island.}
#' \item{\code{$stt_all}: STT table for all species on the island
#' (nI - number of non-endemic species; nA - number of anagenetic species,
#' nC - number of cladogenetic species, present - number of independent
#' colonisations present)}
#' \item{\code{$brts_table}: Only for simulations under \code{"IW"}. Table
#' containing information on order of events in the data, for use in maximum
#' likelihood optimization.).}
#' }
#' The subsequent elements of the list pertaining to each replcate contain
#' information on a single colonist lineage on the island and have 4 components:
#' \itemize{
#' \item{\code{$branching_times}: island age and stem age of the
#' population/species in the case of Non-endemic, Non-endemic_MaxAge and
#' Endemic anagenetic species. For cladogenetic species these should
#' be island age and branching times of the radiation including the
#' stem age of the radiation.}
#' \item{\code{$stac}: An integer ranging from 1 to 4
#' indicating the status of the colonist:}
#' \item{\code{$missing_species}: number of island species that were
#' not sampled for particular clade (only applicable for endemic clades)}
#' \item{\code{$type_1or2}: whether the colonist belongs to type 1 or type 2}
#' }
#' @author Luis Valente and Albert Phillimore
#' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
#' Lake expansion increases equilibrium diversity via the target effect of
#' island biogeography.
#' @keywords models
#' @export
DAISIE_sim_trait_dep <- function(
time,
M,
pars,
replicates,
divdepmodel = "CS",
sample_freq = 25,
plot_sims = TRUE,
island_ontogeny = "const",
sea_level = "const",
hyper_pars = create_hyper_pars(d = 0, x = 0),
area_pars = DAISIE::create_area_pars(
max_area = 1,
current_area = 1,
proportional_peak_t = 0,
total_island_age = 0,
sea_level_amplitude = 0,
sea_level_frequency = 0,
island_gradient_angle = 0),
extcutoff = 1000,
cond = 0,
verbose = TRUE,
trait_pars = NULL,
...
) {
total_time <- time
island_replicates <- list()
island_ontogeny <- translate_island_ontogeny(island_ontogeny)
sea_level <- translate_sea_level(sea_level)
#### IW ####
if (divdepmodel == "IW") {
for (rep in 1:replicates) {
island_replicates[[rep]] <- DAISIE_sim_core_trait_dep(
time = total_time,
mainland_n = M,
pars = pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
extcutoff = extcutoff,
trait_pars = trait_pars
)
if (verbose == TRUE) {
message("Island replicate ", rep)
}
}
island_replicates <- DAISIE_format_IW(
island_replicates = island_replicates,
time = total_time,
M = M,
sample_freq = sample_freq,
verbose = verbose,
trait_pars = trait_pars)
}
#### CS ####
if (divdepmodel == "CS") {
for (rep in 1:replicates) {
island_replicates[[rep]] <- list()
full_list <- list()
if (cond == 0) {
number_present <- -1
} else {
number_present <- 0
}
while (number_present < cond) {
if(M == 0 || is.null(trait_pars)){
stop("One state exist on mainland, should use constant rate DAISIE.")
}else{
for (m_spec in 1:M) {
### M1 = 1, M2 = 0
trait_pars_onecolonize <- create_trait_pars(
trans_rate = trait_pars$trans_rate,
immig_rate2 = trait_pars$immig_rate2,
ext_rate2 = trait_pars$ext_rate2,
ana_rate2 = trait_pars$ana_rate2,
clado_rate2 = trait_pars$clado_rate2,
trans_rate2 = trait_pars$trans_rate2,
M2 = 0)
full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
time = total_time,
mainland_n = 1,
pars = pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
extcutoff = extcutoff,
trait_pars = trait_pars_onecolonize
)
}
for(m_spec in (M + 1):(M + trait_pars$M2)) {
### M1 = 0, M2 = 1
trait_pars_onecolonize <- create_trait_pars(
trans_rate = trait_pars$trans_rate,
immig_rate2 = trait_pars$immig_rate2,
ext_rate2 = trait_pars$ext_rate2,
ana_rate2 = trait_pars$ana_rate2,
clado_rate2 = trait_pars$clado_rate2,
trans_rate2 = trait_pars$trans_rate2,
M2 = 1)
full_list[[m_spec]] <- DAISIE_sim_core_trait_dep(
time = total_time,
mainland_n = 0,
pars = pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
extcutoff = extcutoff,
trait_pars = trait_pars_onecolonize
)
}
}
stac_vec <- unlist(full_list)[which(names(unlist(full_list)) == "stac")]
present <- which(stac_vec != 0)
number_present <- length(present)
}
island_replicates[[rep]] <- full_list
if (verbose == TRUE) {
message("Island replicate ", rep)
}
}
island_replicates <- DAISIE_format_CS(
island_replicates = island_replicates,
time = total_time,
M = M,
sample_freq = sample_freq,
verbose = verbose,
trait_pars = trait_pars
)
}
if (plot_sims == TRUE) {
DAISIE_plot_sims(
island_replicates = island_replicates,
sample_freq = sample_freq,
trait_pars = trait_pars
)
}
return(island_replicates)
}
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