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Composition Statistics

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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.

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