Z : ndarray
The hierarchical clustering encoded with the matrix returned
by the linkage function.
t : float
The threshold to apply when forming flat clusters.
criterion : str, optional
The criterion to use in forming flat clusters. This can
be any of the following values:
- inconsistent : If a cluster node and all its
descendants have an inconsistent value less than or equal
to t then all its leaf descendants belong to the
same flat cluster. When no non-singleton cluster meets
this criterion, every node is assigned to its own
- distance : Forms flat clusters so that the original
observations in each flat cluster have no greater a
cophenetic distance than t.
- maxclust : Finds a minimum threshold r so that
the cophenetic distance between any two original
observations in the same flat cluster is no more than
r and no more than t flat clusters are formed.
- monocrit : Forms a flat cluster from a cluster node c
with index i when monocrit[j] <= t.
For example, to threshold on the maximum mean distance
as computed in the inconsistency matrix R with a
threshold of 0.8 do:
MR = maxRstat(Z, R, 3)
cluster(Z, t=0.8, criterion=’monocrit’, monocrit=MR)
- maxclust_monocrit : Forms a flat cluster from a
non-singleton cluster node c when monocrit[i] <=
r for all cluster indices i below and including
c. r is minimized such that no more than t
flat clusters are formed. monocrit must be
monotonic. For example, to minimize the threshold t on
maximum inconsistency values so that no more than 3 flat
clusters are formed, do:
MI = maxinconsts(Z, R)
cluster(Z, t=3, criterion=’maxclust_monocrit’, monocrit=MI)
depth : int, optional
The maximum depth to perform the inconsistency calculation.
It has no meaning for the other criteria. Default is 2.
R : ndarray, optional
The inconsistency matrix to use for the ‘inconsistent’
criterion. This matrix is computed if not provided.
monocrit : ndarray, optional
An array of length n-1. monocrit[i] is the
statistics upon which non-singleton i is thresholded. The
monocrit vector must be monotonic, i.e. given a node c with
index i, for all node indices j corresponding to nodes
below c, monocrit[i] >= monocrit[j].