micom.algorithms

Implements additional analysis algorithms for communities.

Module Contents

Functions

jaccard(inclusion)

Calculate jaccard distances for a community.

euclidean(inclusion)

Calculate euclidean distances for a community.

reaction_matrix(files)

Create a matrix of reactions x models.

metabolic_dist(reactions, metric=jaccard)

Calculate the metabolic distances between all members.

micom.algorithms.jaccard(inclusion)[source]

Calculate jaccard distances for a community.

micom.algorithms.euclidean(inclusion)[source]

Calculate euclidean distances for a community.

micom.algorithms.reaction_matrix(files)[source]

Create a matrix of reactions x models.

micom.algorithms.metabolic_dist(reactions, metric=jaccard)[source]

Calculate the metabolic distances between all members.