R/functClust-package.R

In functClust: Functional Clustering of Redundant Components of a System

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#'
#' @name functClust-package
#'
#' @docType package
#'
#' @title Functional Clustering
#' of Redundant Components of a System
#'
#' @description Cluster together the components
#' that make up an interactive system
#' on the basis of their functional redundancy
#' on one or more collective, systemic performances.
#' Plot the hierarchical tree of component clusters,
#' the modelled and predicted performances of component assemblages,
#' and other results associated with a functional clustering.
#' Test and prioritize the significance of the different components
#' that make up the interactive system,
#' of the different assemblages of components that make up the dataset,
#' and of the different performances observed on the component assemblages.
#' The package contains three groups of functions: \cr
#'
#' \code{\link{fclust}}, \code{\link{fclust_plot}},
#' \code{\link{fclust_write}} and \code{\link{fclust_read}},
#' fits a clustering tree of functional components
#' to observed assemblage performances,
#' plots, saves and loads the results obtained
#' using the function \code{fclust}, respectively; \cr
#'
#' \code{\link{ftest}}, \code{\link{ftest_plot}},
#' \code{\link{ftest_write}} and \code{\link{ftest_read}},
#' tests the significance of the different components,
#' assemblages and performances depending on the option choisen,
#' plots, saves and loads the results obtained
#' using the function \code{ftest}, respectively; \cr
#'
#' \code{\link{fboot}}, \code{\link{fboot_plot}},
#' \code{\link{fboot_write}} and \code{\link{fboot_read}},
#' evaluates the robustness of a functional clustering
#' by bootstrapping from 1 to (all-1) observations
#' of assemblages or performances depending on the option choisen,
#' plots, saves and loads the results obtained
#' using the function \code{fboot}, respectively; \cr
#'
#' The function \code{\link{fclust}} needs to be run first.
#' The functions \code{\link{ftest}} and \code{\link{fboot}}
#' use the result of the function \code{\link{fclust}}.
#' Both the last ones are time-consumming.
#'
#' @details
#'   None.
#'
#' @author Benoît Jaillard (maintainer)
#'
#' @references{
#'
#'   Jaillard B., Richon C., Deleporte P., Loreau M. and Violle C. (2018)
#'   \emph{An a posteriori species clustering
#'   for quantifying the effects of species
#'   interactions on ecosystem functioning}.
#'   Methods in Ecology and Evolution, 9:704-715.
#'   \url{https://doi.org/10.1111/2041-210X.12920}. \cr
#'
#'   Jaillard B., Deleporte P., Loreau M. and Violle C. (2018)
#'   \emph{A combinatorial analysis using observational data
#'   identifies species that govern ecosystem functioning}.
#'   PLoS ONE 13(8): e0201135.
#'   \url{https://doi.org/10.1371/journal.pone.0201135}. \cr
#'}
#'
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