R/spatialwarnings.R

In spatialwarnings: Spatial Early Warning Signals of Ecosystem Degradation

# 
# This is the main page for the package documentation. 
# 
#' @rdname spatialwarnings
#' 
#' @title Early Spatial-Warnings of Ecosystem Degradation
#' 
#' @description 
#' 
#' Many dynamical systems such as ecosystems exhibit non-linear responses to 
#' changes in their external drivers, resulting in possible wide state shifts 
#' with strong ecological or economical consequences. This often happens when 
#' a system exhibit a change in its stability properties as a threshold is 
#' crossed, \emph{e.g.} going from multiple stable states to a single stable 
#' state. For a few decades, much research has been dedicated to finding a 
#' way to anticipate these tipping points in ecological systems. This has led 
#' to the development of several indicators, i.e. metrics based on spatial
#' structure, that could reflect the proximity of an ecosystem to a tipping
#' point. 
#' 
#' This package implements the computation of these indicators, or 
#' \emph{early-warning signals} (EWS), on spatial raster data. High-level 
#' functions and methods provide familiar workflows to compute the indicators 
#' and display their variations along environmental gradients or time-series. 
#' Lower-level functions are also available to integrate early-warning signals 
#' into different workflows. 
#' 
#' Main functions provided by this package: 
#' 
#' "Workflow" functions, which may compute several indicators at once:
#' \itemize{ 
#'   \item \code{\link{generic_sews}}: Generic spatial EWS
#'   \item \code{\link{spectral_sews}}: Spectrum-based EWS
#'   \item \code{\link{patchdistr_sews}}: EWS based on patch-size distributions
#'   \item \code{\link{kbdm_sews}}: Kolmogorov complexity
#'   \item \code{\link{flowlength_sews}}: Flow length 
#'   \item \code{\link{variogram_sews}}: Variogram-based indicators
#' }
#' 
#' Individual indicators, which may be used to compute raw indicator values 
#'   on a single matrix: 
#' 
#' \itemize{ 
#'   \item \code{\link{raw_cg_moran}}: lag-1 spatial autocorrelation 
#'   \item \code{\link{raw_cg_variance}}: Spatial variance
#'   \item \code{\link{raw_cg_skewness}}: Spatial skewness
#'   \item \code{\link{raw_sdr}}: Spectral density ratio (SDR)
#'   \item \code{\link{indicator_psdtype}}: Patch-size distribution shape 
#'   \item \code{\link{indicator_plrange}}, 
#'           \code{\link{raw_plrange}} : Power-law range
#'   \item \code{\link{raw_kbdm}}: Kolmogorov complexity
#'   \item \code{\link{raw_flowlength_uniform}}: Flow Length
#'   \item \code{\link{raw_variogram_metrics}}: Variogram-based metrics
#' }
#' 
#' The package homepage is available at 
#' \href{https://github.com/spatial-ews/spatialwarnings}{Github}
#' and a  
#' \href{https://alex.lecairn.org/spatialwarnings-faq.html}{user guide} is 
#' also available. 
#' 
#' @docType package
#' @name spatialwarnings
#' 
#' @aliases spatialwarnings-package
#' 
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