Nestedness Calculator for Python

Ths package provides a nestedness calculator for binary matrices, written in Python.

Currently implemented algorithms are:

NODF (Nestedness based on Overlap and Decreasing Fill) [AlmeidaNeto2008]

Author

Mika J. Straka

This Version

The newest version can be found at https://github.com/tsakim/nestedness

Usage

Be mat a two-dimensional binary NumPy array.

The NODF nestedness can be calculated directly without initializing a class instance::

>>> from nestedness_calculator import NestednessCalculator
>>> nodf_score = NestednessCalculator(mat).nodf(mat)

When calling NestednessCalculator(mat), the algorithm checks that the matrix is binary and raises an error if it is not. Furthermore, if one or more columns or rows consist only of zeros, the program aborts.

Dependencies

The module has been written in Python 2.7 and uses the following packages:

NumPy

References

[AlmeidaNeto2008] M. Almeida-Neto, P. Guimareas, P. R. Guimaraes, R. D Loyala, W. Ulrich, A consistent metric for nestedness analysis in ecological systems: reconciling concept and measurement, Oikos 117: 1227-1239 (2008).