PyDiver is a lightweight software package for calculating Simpson diversity with error bars.
It provides a reference implementation of the unbiased variance estimates proposed in Tiffeau-Mayer 2024.
The quickest way to install Pyrepseq is via pip:
pip install python-diver
Note that this package is called python-diver on PyPI.
You can find API documentation on readthedocs. You can also create a local copy of the API documentation by running:
make htmlin the docs folder.
You can find usage examples by looking at the code in the pub_simpsonvar directory.
If this software is useful to you please cite the following article, which derives and benchmarks the unbiased variance estimator:
Tiffeau-Mayer, A., 2024. Unbiased estimation of sampling variance for Simpson's diversity index. Physical Review E, 109(6), p.064411, doi:PhysRevE.109.064411