Integration with Diversity.jl

EcoSISTEM is integrated with the Diversity package, so diversity measures can be calculated directly on an ecosystem - an Ecosystem is a Diversity metacommunity, with one subcommunity per grid cell.

See The basics of EcoSISTEM.jl for how to set one up; the example below builds a small one to measure.

Every grid cell is a subcommunity, including inactive ones - sea off a coastline, or a cell a Deactivate intervention has destroyed. That costs nothing for the metacommunity measures, which weight each subcommunity by its share of the total abundance and so give an empty cell zero weight; the partitioned results are identical whether or not the empty cells are there. But a subcommunity measure returns one row per cell, so on a small island in a large grid most of those rows describe empty sea, and an index of an empty community is not defined. Select the occupied cells before asking a per-cell question.

using Diversity

first(norm_sub_alpha(eco, 1.0), 5)   # subcommunity measures - one row per grid cell, 25 here

norm_meta_alpha(eco, 1.0)     # or metacommunity measures - one row for the landscape

Any measure takes several values of the viewpoint parameter q at once - 0 counts rare and common species alike, and larger values weight towards the commonest:

beta = norm_sub_beta(eco, 0.0:3.0)   # one row per cell per q - 100 of them here
beta[beta.partition_name .== first(beta.partition_name), :]   # one cell, all four q