R/data_doc.R

In Neves-P/utilSIE: Utility Functions for DAISIE

#' @title Matrix with island ontogeny simulation parameters
#'
#' @description An example dataset useful for DAISIE pilot studies assuming
#' island ontogeny.
#' Area parameters are inspired in Hawaii. Extinction parameters are purposefuly
#' high, to ensure ontogeny effects are noticeable. Format is generated by
#' \code{\link{experiment_setup}} and ready to be passed to
#' \code{\link{execute_next_setup}}.
#'
#' @format A data frame with 3 rows, each corresponding to a
#' scenario, made up of 14 variables (in each column):
#' \describe{
#'   \item{time}{Numeric double containing length of the simulation in time
#'   units. For example, if an island is know to be 4 million years old,
#'  setting time = 4 will simulate entire life span of the island;
#'  setting time = 2 will stop the simulation at the mid-life of the island.}
#'   \item{M}{Numeric integer containing the size of the mainland pool, i.e
#'  the number of species that can potentially colonize the island.}
#'   \item{lac}{Numeric double containing the cladogenesis rate (lambda^c).}
#'   \item{mu}{Numeric double containing the extinction rate. Used only on
#' non ontogeny scenarios.}
#'   \item{K}{Numeric double containing the carrying capacity (clade level).
#' Set \code{K = Inf} for no diversity dependence.}
#'   \item{gam}{Numeric double containing the immigration rate (gamma).}
#'   \item{laa}{Numeric double containing the anagenesis rate (lambda^a).}
#'   \item{replicates}{Numeric integer stating how many replicates should be
#'   run per scenario.}
#'   \item{mu_min}{Numeric double containing the minimum extinction when area is
#'  at peak, used only on ontogeny scenarios.}
#'   \item{mu_max}{Numeric double containing the extinction rate when current
#' area is 0.10 of maximum area, used only on ontogeny scenarios.}
#'   \item{Amax}{Numeric double containing the maximum area,
#'   used only on ontogeny scenarios.}
#'   \item{Apeak}{Numeric double containing the value from 0 to 1
#'   indicating where in the island's history the peak area is achieved,
#'  used only on ontogeny scenarios.}
#'   \item{Asharpness}{Numeric double containing the sharpness of peak,
#'  used only on ontogeny scenarios.}
#'   \item{Atotalage}{Numeric double containing the total island age, used
#'  only on ontogeny scenarios.}
#' }
#' @source Generated in-house by Pedro Neves.
"pilot_study_parameters"