#' @title Simulate islands with given parameters.
#' @description This function simulates islands with given cladogenesis,
#' extinction, Kprime, immigration and anagenesis parameters. If a single
#' parameter set is provided (5 parameters) it simulates islands where all
#' species have the same macro-evolutionary process. If two paramater sets
#' (10 parameters) are provided, it simulates islands where two different
#' macro-evolutionary processes operate, one applying to type 1 species and
#' other to type 2 species. If two parameter sets and a time shift (11
#' parameters) are provided, it simulates islands where at the given time
#' a shift between the parameter sets will occur.
#'
#' Returns R list object that contains the simulated islands
#'
#' @inheritParams default_params_doc
#'
#' @return Each simulated dataset is an element of the list, which can be
#' called using [[x]]. For example if the object is called island_replicates,
#' the last replicates is a list in itself. The first (e.g.
#' \code{island_replicates[[x]][[1]]}) element of that list has the following
#' components: \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
#' \code{$stt_all} - STT table for all species on the island (nI - number of
#' non-endemic species; nA - number of anagenetic species, nC - number of
#' cladogenetic species, present - number of independent colonisations present
#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
#' only if 2 types of species were simulated (nI - number of non-endemic
#' species; nA - number of anagenetic species, nC - number of cladogenetic
#' species, present - number of independent colonisations present )\cr
#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
#' 2 types of species were simulated (nI - number of non-endemic species; nA -
#' number of anagenetic species, nC - number of cladogenetic species, present -
#' number of independent colonisations present )\cr \code{$brts_table} - Only
#' for simulations under 'IW'. Table containing information on order of events
#' in the data, for use in maximum likelihood optimization.)\cr
#'
#' The subsequent elements of the list each contain information on a single
#' colonist lineage on the island and has 4 components:\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 * Non_endemic_MaxAge: 1 \cr *
#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
#' \code{$missing_species} - number of island species that were not sampled for
#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
#' - whether the colonist belongs to type 1 or type 2 \cr
#' @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
#' @examples
#' \donttest{
#' ##### Ontogeny simulation with 5 replicates ######
#' n_mainland_species <- 1000
#' island_age <- 0.4
#' clado_rate <- 0.0001 # cladogenesis rate
#' ext_rate <- 2.683454548 # extinction rate (not used)
#' clade_carr_cap <- 0.05 # clade-level carrying capacity
#' imm_rate <- 0.001 # immigration rate
#' ana_rate <- 0.1 # anagenesis rate
#' max_area <- 1000
#' peak_time <- 0.1
#' sharpness <- 1
#' total_island_age <- 10
#' sea_level_amplitude <- 0
#' sea_level_frequency <- 0
#' island_gradient_angle <- 0
#' mu_min <- 0.5
#' mu_max <- 100
#' island_ontogeny <- "beta"
#' sea_level <- "const"
#' extcutoff <- 1000
#' out <- DAISIE_sim_time_dependent(
#' time = island_age,
#' M = n_mainland_species,
#' pars = c(clado_rate, ext_rate, clade_carr_cap, imm_rate, ana_rate),
#' replicates = 5,
#' island_ontogeny = island_ontogeny,
#' sea_level = sea_level,
#' area_pars = create_area_pars(max_area,
#' peak_time,
#' sharpness,
#' total_island_age,
#' sea_level_amplitude,
#' sea_level_frequency,
#' island_gradient_angle),
#' ext_pars = c(mu_min, mu_max),
#' extcutoff = extcutoff,
#' plot_sims = TRUE,
#' verbose = TRUE
#' )
#' }
#' @export
DAISIE_sim_trait_dependent <- function(
time,
M,
pars,
replicates,
divdepmodel = "CS",
nonoceanic_pars = c(0, 0),
num_guilds = NULL,
sample_freq = 25,
plot_sims = TRUE,
island_ontogeny = "const",
sea_level = "const",
hyper_pars = NULL,
area_pars = NULL,
dist_pars = NULL,
ext_pars = NULL,
extcutoff = 1000,
verbose = TRUE,
trait_pars = NULL,
...
) {
testit::assert(
"island_ontogeny is not valid input. Specify 'const',\n
or 'beta'", is_island_ontogeny_input(island_ontogeny)
)
testit::assert(
"sea_level is not valid input. Specify 'const, \n or 'sine'",
is_sea_level_input(sea_level)
)
testit::assert(
"length(pars) is not five",
length(pars) == 5
)
totaltime <- 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_dependent(
time = totaltime,
mainland_n = M,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
ext_pars = ext_pars,
extcutoff = extcutoff,
trait_pars = trait_pars
)
if (verbose == TRUE) {
print(paste("Island replicate ", rep, sep = ""))
}
}
island_replicates <- DAISIE_format_IW(island_replicates = island_replicates,
time = totaltime,
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(M == 0){
if(is.null(trait_pars)){
stop("There is no species on mainland.")
}else{ ## only have state2 species on mainland
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)
for (m_spec in 1:trait_pars$M2) {
full_list[[m_spec]] <- DAISIE_sim_core_trait_dependent(
time = totaltime,
mainland_n = 0,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
ext_pars = ext_pars,
extcutoff = extcutoff,
trait_pars = trait_pars_onecolonize
)
}
}
}else{
trait_pars_addcol <- create_trait_pars(trans_rate = 0,
immig_rate2 = 0,
ext_rate2 = 0,
ana_rate2 = 0,
clado_rate2 = 0,
trans_rate2 = 0,
M2 = 0)
for (m_spec in 1:M) {
full_list[[m_spec]] <- DAISIE_sim_core_trait_dependent(
time = totaltime,
mainland_n = 1,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
ext_pars = ext_pars,
extcutoff = extcutoff,
trait_pars = trait_pars_addcol
)
}
for(m_spec in (M + 1):(M + trait_pars$M2))
{
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_dependent(
time = totaltime,
mainland_n = 0,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
ext_pars = ext_pars,
extcutoff = extcutoff,
trait_pars = trait_pars_onecolonize
)
}
}
island_replicates[[rep]] <- full_list
if (verbose == TRUE) {
print(paste("Island replicate ", rep, sep = ""))
}
}
island_replicates <- DAISIE_format_CS(
island_replicates = island_replicates,
time = totaltime,
M = M,
sample_freq = sample_freq,
verbose = verbose,
trait_pars = trait_pars
)
}
#### GW ####
if (divdepmodel == "GW") {
if (!is.numeric(num_guilds)) {
stop("num_guilds must be numeric")
}
guild_size <- M / num_guilds
testit::assert(num_guilds < M)
testit::assert(M %% num_guilds == 0)
for (rep in 1:replicates) {
island_replicates[[rep]] <- list()
full_list <- list()
for (m_spec in 1:num_guilds) {
full_list[[m_spec]] <- DAISIE_sim_core_trait_dependent(
time = totaltime,
mainland_n = guild_size,
pars = pars,
nonoceanic_pars = nonoceanic_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
ext_pars = ext_pars,
extcutoff = extcutoff
)
}
island_replicates[[rep]] <- full_list
if (verbose == TRUE) {
print(paste("Island replicate ", rep, sep = ""))
}
}
island_replicates <- DAISIE_format_GW(island_replicates = island_replicates,
time = totaltime,
M = M,
sample_freq = sample_freq,
num_guilds = num_guilds,
verbose = verbose)
}
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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