Cluster Algorithms (clustering and extra)


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.