scipy.cluster.hierarchy.fclusterdata

scipy.cluster.hierarchy.fclusterdata(X, t, criterion='inconsistent', metric='euclidean', depth=2, method='single', R=None)

Cluster observation data using a given metric.

Clusters the original observations in the n-by-m data matrix X (n observations in m dimensions), using the euclidean distance metric to calculate distances between original observations, performs hierarchical clustering using the single linkage algorithm, and forms flat clusters using the inconsistency method with t as the cut-off threshold.

A one-dimensional array T of length n is returned. T[i] is the index of the flat cluster to which the original observation i belongs.

Parameters:

X : (N, M) ndarray

N by M data matrix with N observations in M dimensions.

t : float

The threshold to apply when forming flat clusters.

criterion : str, optional

Specifies the criterion for forming flat clusters. Valid values are ‘inconsistent’ (default), ‘distance’, or ‘maxclust’ cluster formation algorithms. See fcluster for descriptions.

metric : str, optional

The distance metric for calculating pairwise distances. See distance.pdist for descriptions and linkage to verify compatibility with the linkage method.

depth : int, optional

The maximum depth for the inconsistency calculation. See inconsistent for more information.

method : str, optional

The linkage method to use (single, complete, average, weighted, median centroid, ward). See linkage for more information. Default is “single”.

R : ndarray, optional

The inconsistency matrix. It will be computed if necessary if it is not passed.

Returns:

fclusterdata : ndarray

A vector of length n. T[i] is the flat cluster number to which original observation i belongs.

See also

scipy.spatial.distance.pdist

pairwise distance metrics

Notes

This function is similar to the MATLAB function clusterdata.