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#' Plot per capita STT and per-capita rate change thourgh simulation
#'
#' @inheritParams default_params_doc
#'
#' @return A composite plot containing the STT plot, and variation in area,
#' extinction rate, cladogenesis rate and immigration rate
#' @keywords internal
#'
#' @author Pedro Neves
DAISIE_plot_pc_rates <- function(total_time,
pars,
island_ontogeny,
sea_level = "const",
area_pars,
peak,
hyper_pars,
mainland_n = 1000,
resolution = 0.001,
simulation_outputs = NULL) {
testit::assert(is_island_ontogeny_input(island_ontogeny))
testit::assert(are_area_pars(area_pars))
testit::assert(resolution < 1 && is.numeric(resolution) && !is.infinite(resolution))
if (!requireNamespace("ggplot2", quietly = TRUE) && !requireNamespace("gridExtra", quietly = TRUE)) {
stop("Packages \"ggplot2\" and \"gridExtra\" needed for this function to work. Please install them.",
call. = FALSE)
}
lac <- pars[1]
mu <- pars[2]
K <- pars[3]
gam <- pars[4]
area_plot <- DAISIE_plot_area(
total_time = total_time,
area_pars = area_pars,
peak = peak,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
resolution = resolution
)
clado_plot <- DAISIE_plot_cladogenesis(
total_time = total_time,
K = K,
area_pars = area_pars,
peak = peak,
hyper_pars = hyper_pars,
lac = lac,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
removed_timepoints = 1,
resolution = resolution
)
ext_plot <- DAISIE_plot_extinction(
total_time = total_time,
area_pars = area_pars,
peak = peak,
mu = mu,
hyper_pars = hyper_pars,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
removed_timepoints = 1,
resolution = resolution)
immig_plot <- DAISIE_plot_immigration(
total_time = total_time,
K = K,
area_pars = area_pars,
peak = peak,
gam = gam,
mainland_n = 1,
island_ontogeny = island_ontogeny,
sea_level = sea_level,
removed_timepoints = 1,
resolution = resolution
)
if (!is.null(simulation_outputs)) {
sims_plot <- DAISIE_plot_sims(simulation_outputs)
}
gridExtra::grid.arrange(area_plot, clado_plot, immig_plot, ext_plot, nrow = 2)
}
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