R/overallNiche.R

In Irstea/chocR: Exploring the temporal CHange of OCcurence of events in multivariate time series

#' overallNiche
#' computes the average niche over the whole study period
#'
#' @param mychoc a chocR object of realised niche \link{choc}
#' with chocRealised
#'
#' @return a data.frame with the grid and and the corresponding density
#'
#' @importFrom ks kde
#' @export
overallNiche <- function(mychoc) {
  if (class(mychoc) != "chocR")
    stop("chocRealised should be a chocR object")
  grid <- mychoc$grid[, -ncol(mychoc$grid)]

  overallData <- do.call(rbind.data.frame, mychoc$list_data)
  overallWeights <- do.call(c, mychoc$list_weights)
  niche <- kde(eval.points = as.matrix(grid),
               x = as.matrix(overallData),
               w = overallWeights / sum(overallWeights),
               H = mychoc$H,
               binned = TRUE)$estimate
  res <- cbind.data.frame(grid,
                          data.frame(dens = niche))
  return(res)
}