skbio.stats.composition.closure#

skbio.stats.composition.closure(mat)[source]#

Perform closure to ensure that all elements add up to 1.

Parameters:

matarray_like of shape (n_compositions, n_components): A matrix of proportions.

Returns:

ndarray of shape (n_compositions, n_components): The matrix where all of the values are non-zero and each composition (row) adds up to 1.

Raises:

ValueError: If any values are negative.
ValueError: If the matrix has more than two dimensions.
ValueError: If there is a row that has all zeros.

Examples

>>> import numpy as np
>>> from skbio.stats.composition import closure
>>> X = np.array([[2, 2, 6], [4, 4, 2]])
>>> closure(X)
array([[ 0.2,  0.2,  0.6],
       [ 0.4,  0.4,  0.2]])