examples/overlap.plot.R

In mlysy/nicheROVER: Niche Region and Niche Overlap Metrics for Multidimensional Ecological Niches

# fish data
data(fish)

# parameter draws from the "default" posteriors of each fish
nsamples <- 500
system.time({
  fish.par <- tapply(1:nrow(fish), fish$species,
                     function(ii) niw.post(nsamples = nsamples,
                                           X = fish[ii,2:4]))
})

# overlap calculation
system.time({
  over <- overlap(fish.par, nreps = nsamples, nprob = nsamples,
                  alpha = c(.95, .99))
})

# overlap plot
clrs <- c("black", "red", "blue", "orange") # color for each species
ii <- 1 # which niche region alpha level to use
overlap.plot(over[,,,ii], col = clrs, mean.cred.col = "turquoise",
             xlab = paste0("Overlap Probability (%) -- Niche Region Size: ",
                           dimnames(over)[[4]][ii]))