#' Calculates the maximum rates for a Gillespie simulation
#' @description Internal function that updates the all the max rates at time t.
#' @family rate calculations
#'
#' @inheritParams default_params_doc
#'
#' @seealso \code{\link{update_rates}}
#'
#' @return a named list with the updated effective rates.
#' @export
update_max_rates <- function(timeval,
totaltime,
gam,
laa,
lac,
mu,
hyper_pars = NULL,
area_pars,
dist_pars = NULL,
ext_pars = NULL,
island_ontogeny = NULL,
sea_level = NULL,
extcutoff,
K,
num_spec,
num_immigrants,
mainland_n,
global_min_area_time,
global_max_area_time) {
immig_max_rate <- get_immig_rate(
timeval = global_max_area_time,
totaltime = totaltime,
gam = gam,
mainland_n = mainland_n,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
num_spec = num_spec,
K = K
)
testit::assert(is.numeric(immig_max_rate))
clado_max_rate <- get_clado_rate(
timeval = global_max_area_time,
lac = lac,
hyper_pars = hyper_pars,
area_pars = area_pars,
dist_pars = dist_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
num_spec = num_spec,
K = K
)
testit::assert(is.numeric(clado_max_rate))
ext_max_rate <- get_ext_rate(
timeval = global_min_area_time,
mu = mu,
hyper_pars = hyper_pars,
area_pars = area_pars,
ext_pars = ext_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
extcutoff = extcutoff,
num_spec = num_spec,
K = K
)
testit::assert(is.numeric(ext_max_rate) && ext_max_rate >= 0.0)
ana_max_rate <- get_ana_rate(
laa = laa,
hyper_pars = hyper_pars,
dist_pars = dist_pars,
num_immigrants = num_immigrants
)
testit::assert(is.numeric(ana_max_rate) && ana_max_rate >= 0.0)
max_rates <- list(
ext_max_rate = ext_max_rate,
immig_max_rate = immig_max_rate,
ana_max_rate = ana_max_rate,
clado_max_rate = clado_max_rate
)
return(max_rates)
}
#' Get the time of maximum area
#'
#' @inheritParams default_params_doc
#'
#' @return Numeric with time at which area is maximum during the simulation.
#'
#' @examples
#' timeval <- 1
#' totaltime <- 10
#' area_pars <- DAISIE::create_area_pars(
#' max_area = 5000,
#' proportional_peak_t = 0.5,
#' peak_sharpness = 1,
#' total_island_age = 15,
#' sea_level_amplitude = 0,
#' sea_level_frequency = 0,
#' island_gradient_angle = 0
#' )
#' island_ontogeny <- 1
#' sea_level <- 0
#'
#' testthat::expect_silent(
#' global_max_area_time <- DAISIE:::get_global_max_area_time(
#' totaltime = totaltime,
#' area_pars = area_pars,
#' island_ontogeny = island_ontogeny,
#' sea_level = sea_level
#' )
#' )
#'
#' @author Pedro Neves, Joshua Lambert, Shu Xie
get_global_max_area_time <- function(totaltime,
area_pars,
island_ontogeny,
sea_level) {
# Intervals are temporarily set so the function computes only the global
# maximum
interval_min <- 0
interval_max <- totaltime
max <- stats::optimize(
f = DAISIE::island_area,
interval = c(interval_min, interval_max),
area_pars = area_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level, # Fixed at no sea_level for the moment
maximum = TRUE,
tol = .Machine$double.eps
)
global_max_area_time <- max$maximum
testit::assert(is.numeric((global_max_area_time)))
global_max_area_time <- DDD::roundn(global_max_area_time, 14)
return(global_max_area_time)
}
#' Get the time when area is minimum
#'
#' @inheritParams default_params_doc
#'
#' @return Numeric with time at which area is minimum during the simulation
#'
#' @examples
#' timeval <- 1
#' totaltime <- 10
#' area_pars <- DAISIE::create_area_pars(
#' max_area = 5000,
#' proportional_peak_t = 0.5,
#' peak_sharpness = 1,
#' total_island_age = 15,
#' sea_level_amplitude = 0,
#' sea_level_frequency = 0,
#' island_gradient_angle = 0
#' )
#' island_ontogeny <- 1
#' sea_level <- 0
#'
#' testthat::expect_silent(
#' DAISIE:::get_global_min_area_time(
#' totaltime = totaltime,
#' area_pars = area_pars,
#' island_ontogeny = island_ontogeny,
#' sea_level = sea_level
#' )
#' )
#'
#' @author Pedro Neves, Joshua Lambert, Shu Xie
get_global_min_area_time <- function(totaltime,
area_pars,
island_ontogeny,
sea_level) {
fx <- function(timeval) {
y <- island_area(
timeval,
area_pars = area_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level
)
if (is.nan(y)) {
return(Inf)
} else {
return(y)
}
}
global_min_area_time <- subplex::subplex(par = 0, fn = fx)$par
testit::assert(is.numeric((global_min_area_time)))
global_min_area_time <- DDD::roundn(global_min_area_time, 14)
return(global_min_area_time)
}
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