Python module for compositional data analysis. Install with pip:
pip install composition_stats
The following functions are provided:
closure |
Performs closure to ensure that all elements add up to 1. |
multiplicative_replacement |
Replace all zeros with small non-zero alues |
perturb |
Performs the perturbation operation. |
perturb_inv |
Performs the inverse perturbation operation. |
power |
Performs the power operation. |
inner |
Calculates the Aitchson inner product. |
clr |
Performs centre log ratio transformation. |
clr_inv |
Performs inverse centre log ratio transformation. |
ilr |
Performs isometric log ratio transformation. |
ilr_inv |
Performs inverse isometric log ratio transform. |
alr |
Performs additive log ratio transformation. |
alr_inv |
Performs inverse additive log ratio transform. |
center |
Computes the geometric average of data. |
centralize |
Center data around its geometric average. |
sbp_basis |
Builds an orthogonal basis from a sequential binary partition (SBP). |
Please see the documentation for details and a complete function reference.
This is a fork of the essential compositional data functions of the
skbio.stats.composition module from scikit-bio. However, for reasons of
performance, the functions in this module expect inputs where compositions
already sum to unity, and do not call closure() on inputs internally.