prototype code

data-raw/temp/niche_overlap.R

@@ -0,0 +1,22 @@
+
+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)}