data-raw/temp/niche_overlap.R

In EvolEcolGroup/pastclim: Manipulate Time Series of Palaeoclimate Reconstructions

niche_overlap <- function (x, y, method=c("Schoener","Hellinger")){
  # standardise the two distributions
  # divide by sum so that integral of pdf is one
  x <- x / sum(x,na.rm = TRUE)
  y <- y / sum(y, na.rm = TRUE)
  
  res_list <- list()
  #Schoeners D
  if ("Schoener" %in% method){
    res_list$D <- 1 - 0.5 * sum(abs(x - y), na.rm = TRUE)
  }
  
  Hellinger's Distance 
if ("Hellinger" %in% method){
H <- sqrt(sum((sqrt(x) - sqrt(y))^2, na.rm = TRUE))
# scaling in https://onlinelibrary.wiley.com/doi/10.1111/j.1558-5646.2008.00482.x
# is incorrect, as it uses 2 rather than sqrt(2) as the max value of H
# scaling to 1 following https://www.sciencedirect.com/science/article/pii/S2287884X18300153
res_list$I <- 1 - H /sqrt(2)
}
return(res_list)}