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.