R/ecospace.R

In pnovack-gottshall/ecospace: Simulating Community Assembly and Ecological Diversification Using Ecospace Frameworks

#' ecospace: Simulating Community Assembly and Ecological Diversification Using
#' Ecospace Frameworks
#'
#' ecospace is an R package that implements stochastic simulations of community
#' assembly (ecological diversification) using customizable ecospace frameworks
#' (functional trait spaces). Simulations model the 'neutral', 'redundancy',
#' 'partitioning', and 'expansion' models of Bush and Novack-Gottshall (2012)
#' and Novack-Gottshall (2016a,b). It provides a wrapper to calculate common
#' ecological disparity and functional ecology statistical dynamics as a
#' function of species richness. Functions are written so they will work in a
#' parallel-computing environment.
#'
#' The package also contains a sample data set, functional traits for Late
#' Ordovician (Type Cincinnatian) fossil species from the Kope and Waynesville
#' formations, from Novack-Gottshall (2016b).
#'
#' @author Phil Novack-Gottshall \email{pnovack-gottshall@@ben.edu}
#' @name ecospace-package
#' @aliases ecospace-package ecospace
#' @docType package

#' @references Bush, A. and P.M. Novack-Gottshall. 2012. Modelling the
#'   ecological-functional diversification of marine Metazoa on geological time
#'   scales. \emph{Biology Letters} 8: 151-155.
#' @references Novack-Gottshall, P.M. 2016a. General models of ecological
#'   diversification. I. Conceptual synthesis. \emph{Paleobiology} 42: 185-208.
#' @references Novack-Gottshall, P.M. 2016b. General models of ecological
#'   diversification. II. Simulations and empirical applications.
#'   \emph{Paleobiology} 42: 209-239.

#' @seealso The 'calc_metrics' function relies extensively on the functional
#'   diversity package \code{\link[FD]{FD-package}}, and hence lists this package as a
#'   depends, so it is loaded simultaneously.
#'
#' @examples
#' # Get package version, citation, updates, and vignette
#' packageVersion("ecospace")
#' citation("ecospace")
#' news(package = "ecospace")
#' vignette("ecospace")
#'
#' # Create an ecospace framework (functional-trait space) with 15 characters
#' #    (functional traits) of mixed types
#' nchar <- 15
#' ecospace <- create_ecospace(nchar = nchar, char.state = rep(3, nchar),
#'   char.type = rep(c("factor", "ord.fac", "ord.num"), nchar / 3))
#'
#' # Use to assemble a stochastic "neutral" sample of 20 species (from
#' #    initial seeding by 5 species)
#' x <- neutral(Sseed = 5, Smax = 20, ecospace = ecospace)
#' head(x, 10)
#'
#' # Calculate ecological disparity (functional diversity) dynamics as a
#' #    function of species richness
#' # Statistic 'V' [total variance] not calculated because there are factors
#' #    in the sample
#' metrics <- calc_metrics(samples = x, Smax = 20, Model = "Neutral", Param = "NA")
#' metrics
#'
#' # Plot statistical dynamics as function of species richness
#' op <- par()
#' par(mfrow = c(2,4), mar = c(4, 4, 1, .3))
#' attach(metrics)
#' plot(S, H, type = "l", cex = .5)
#' plot(S, D, type = "l", cex = .5)
#' plot(S, M, type = "l", cex = .5)
#' plot(S, V, type = "l", cex = .5)
#' plot(S, FRic, type = "l", cex = .5)
#' plot(S, FEve, type = "l", cex = .5)
#' plot(S, FDiv, type = "l", cex = .5)
#' plot(S, FDis, type = "l", cex = .5)
#'
#' par(op)
#'
# NAMESPACE IMPORTING
#' @import FD
#' @importFrom stats var rmultinom runif
NULL