Cluster Algorithms (clustering and extra)

Functions

flat_cluster(method, threshold, matrix[, …])

Carry out a flat cluster analysis based on linkage algorithms.

flat_upgma(threshold, matrix[, taxa, revert])

Carry out a flat cluster analysis based on the UPGMA algorithm (Sokal1958).

fuzzy(threshold, matrix, taxa[, method, revert])

Create fuzzy cluster of a given distance matrix.

link_clustering(threshold, matrix, taxa[, …])

Carry out a link clustering analysis using the method by Ahn2010.

mcl(threshold, matrix, taxa[, max_steps, …])

Carry out a clustering using the MCL algorithm (Dongen2000).

neighbor(matrix, taxa[, distances])

Function clusters data according to the Neighbor-Joining algorithm (Saitou1987).

upgma(matrix, taxa[, distances])

Carry out a cluster analysis based on the UPGMA algorithm (Sokal1958).

infomap_clustering(threshold, matrix[, …])

Compute the Infomap clustering analysis of the data.

affinity_propagation(threshold, matrix, taxa)

Compute affinity propagation from the matrix.

valid_cluster(sequence)

Only allow to have sequences which have consecutive ordering of elements.

generate_all_clusters(numbers)

Generate all possible clusters for a number of elements.

generate_random_cluster(numbers[, bias])

Generate a random cluster for a number of elements.

order_cluster(clr)

Order a cluster into the form of a valid cluster.

mutate_cluster(clr[, chance])

Mutate a cluster.