These functions cut hierarchical clusterings into flat clusterings
or find the roots of the forest formed by a cut by providing the flat
cluster ids of each observation.
|fcluster(Z, t[, criterion, depth, R, monocrit])
||Forms flat clusters from the hierarchical clustering defined by the given linkage matrix.
|fclusterdata(X, t[, criterion, metric, ...])
||Cluster observation data using a given metric.
||Returns the root nodes in a hierarchical clustering.
These are routines for agglomerative clustering.
|linkage(y[, method, metric])
||Performs hierarchical/agglomerative clustering.
||Performs single/min/nearest linkage on the condensed distance matrix y
||Performs complete/max/farthest point linkage on a condensed distance matrix
||Performs average/UPGMA linkage on a condensed distance matrix
||Performs weighted/WPGMA linkage on the condensed distance matrix.
||Performs centroid/UPGMC linkage.
||Performs median/WPGMC linkage.
||Performs Ward’s linkage on a condensed distance matrix.
These routines compute statistics on hierarchies.
||Calculates the cophenetic distances between each observation in the hierarchical clustering defined by the linkage Z.
||Converts a linkage matrix generated by MATLAB(TM) to a new linkage matrix compatible with this module.
||Calculates inconsistency statistics on a linkage matrix.
||Returns the maximum inconsistency coefficient for each non-singleton cluster and its descendents.
||Returns the maximum distance between any non-singleton cluster.
|maxRstat(Z, R, i)
||Returns the maximum statistic for each non-singleton cluster and its descendents.
||Converts a linkage matrix to a MATLAB(TM) compatible one.
Routines for visualizing flat clusters.
|dendrogram(Z[, p, truncate_mode, ...])
||Plots the hierarchical clustering as a dendrogram.
These are data structures and routines for representing hierarchies as
|ClusterNode(id[, left, right, dist, count])
||A tree node class for representing a cluster.
||Returns a list of leaf node ids
||Converts a linkage matrix into an easy-to-use tree object.
|cut_tree(Z[, n_clusters, height])
||Given a linkage matrix Z, return the cut tree.
These are predicates for checking the validity of linkage and
inconsistency matrices as well as for checking isomorphism of two
flat cluster assignments.
|is_valid_im(R[, warning, throw, name])
||Returns True if the inconsistency matrix passed is valid.
|is_valid_linkage(Z[, warning, throw, name])
||Checks the validity of a linkage matrix.
||Determines if two different cluster assignments are equivalent.
||Returns True if the linkage passed is monotonic.
||Checks for correspondence between linkage and condensed distance matrices
||Returns the number of original observations of the linkage matrix passed.
Utility routines for plotting:
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|[R4]||Ward Jr, JH. “Hierarchical grouping to optimize an objective
function.” Journal of the American Statistical Association. 58(301):
pp. 236–44. 1963.|
|[R5]||Johnson, SC. “Hierarchical clustering schemes.” Psychometrika.
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|[R6]||Sneath, PH and Sokal, RR. “Numerical taxonomy.” Nature. 193: pp.
|[R7]||Batagelj, V. “Comparing resemblance measures.” Journal of
Classification. 12: pp. 73–90. 1995.|
|[R8]||Sokal, RR and Michener, CD. “A statistical method for evaluating
systematic relationships.” Scientific Bulletins. 38(22):
pp. 1409–38. 1958.|
|[R9]||Edelbrock, C. “Mixture model tests of hierarchical clustering
algorithms: the problem of classifying everybody.” Multivariate
Behavioral Research. 14: pp. 367–84. 1979.|
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