R/DAISIEmainland.R

In joshwlambert/DAISIEmainland: Simulates Data for Phylogenetic Data on Islands for DAISIE with the Addition of Mainland Dynamics

#' `DAISIEmainland`: A package to simulate phylogenetic data on an island
#' with the presence of mainland speciation and extinction to test the
#' `DAISIE` model of island biogeography.
#'
#' `DAISIEmainland` simulates a two data sets for every island: 1) the
#' ideal data set has the full information, 2) the empirical data set has
#' the data as would be seen by the empirical collecting phylogenetic data
#' in the presence of mainland dynamics.
#'
#' @examples
#' # simulate data for 1 island (replicate) with mainland extinction
#' island <- sim_island_with_mainland(
#'   total_time = 1,
#'   m = 100,
#'   island_pars = c(1, 1, 10, 0.1, 1),
#'   mainland_ex = 0.1,
#'   mainland_sample_prob = 1,
#'   mainland_sample_type = "complete",
#'   replicates = 1,
#'   verbose = FALSE
#' )
#' # simulate data for 1 island (replicate) with incomplete sampling of known
#' # mainland species
#' island <- sim_island_with_mainland(
#'   total_time = 1,
#'   m = 100,
#'   island_pars = c(1, 1, 10, 0.1, 1),
#'   mainland_ex = 0,
#'   mainland_sample_prob = 0.8,
#'   mainland_sample_type = "unsampled",
#'   replicates = 1,
#'   verbose = FALSE
#' )
#' @seealso
#' `DAISIEmainland` works in association with the
#' package `DAISIE`(github.com/rsetienne/DAISIE)
#' @author Joshua W. Lambert
#' @name DAISIEmainland
#' @keywords internal
"_PACKAGE"
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