The recommended measure of nestedness (working both for deterministic and probabilistic networks) is η:
EcologicalNetwork.η — Function.
Nestedness η of a matrix
This returns the nestedness of the entire matrix, of the columns, and of the rows.
We also implement NODF, for deterministic networks, and its quantitative variant WNODF:
EcologicalNetwork.nodf — Function.
Nestedness based on Overlap and Decreasing Fill
If the network is quantitative, then WNODF is measured instead of NODF. Note that in all situations, the value goes between 0 (not nested) to 1 (perfectly nested). This is a change with regard to the original papers, in which the maximal value is 100. The values returned are the nestedness of the network, of the columns, and of the rows.