R: Validity Measures for Partitions and Hierarchies

cl_validity {clue} | R Documentation

## Validity Measures for Partitions and Hierarchies

### Description

Compute validity measures for partitions and hierarchies, attempting to measure how well these clusterings capture the underlying structure in the data they were obtained from.

### Usage

    cl_validity(x, ...)
    ## Default S3 method:
    cl_validity(x, d, ...)

### Arguments

`x` | an object representing a partition or hierarchy.
`d` | a dissimilarity object from which `x` was obtained.
`...` | arguments to be passed to or from methods.

### Details

`cl_validity` is a generic function.

For partitions, its default method gives the “dissimilarity accounted for”, defined as 1 - a_w / a_t, where a_t is the average total dissimilarity, and the “average within dissimilarity” a_w is given by

∑_{i,j} ∑_k m_{ik}m_{jk} d_{ij} / ∑_{i,j} ∑_k m_{ik}m_{jk}

where d and m are the dissimilarities and memberships, respectively, and the sums are over all pairs of objects and all classes.

For hierarchies, the validity measures computed by default are “variance accounted for” (VAF, e.g., Hubert, Arabie & Meulman, 2006) and “deviance accounted for” (DEV, e.g., Smith, 2001). If `u` is the ultrametric corresponding to the hierarchy `x` and `d` the dissimilarity `x` was obtained from, these validity measures are given by

max(0, 1 - sum_{i,j} (d_{ij} - u_{ij})^2 / sum_{i,j} (d_{ij} - mean(d))^2)

and

max(0, 1 - sum_{i,j} |d_{ij} - u_{ij}| / sum_{i,j} |d_{ij} - median(d)|)

respectively. Note that VAF and DEV are not invariant under rescaling `u`, and may be “arbitrarily small” (i.e., 0 using the above definitions) even though `u` and `d` are “structurally close” in some sense.

For the results of using `agnes` and `diana`, the agglomerative and divisive coefficients are provided in addition to the default ones.

### Value

A list of class `"cl_validity"` with the computed validity measures.

### References

L. Hubert, P. Arabie and J. Meulman (2006). The structural representation of proximity matrices with MATLAB. Philadelphia, PA: SIAM.

T. J. Smith (2001). Constructing ultrametric and additive trees based on the L_1 norm. Journal of Classification, 18/2, 185–207. https://link.springer.com/article/10.1007/s00357-001-0015-0.

### See Also

`cluster.stats` in package fpc for a variety of cluster validation statistics; `fclustIndex` in package e1071 for several fuzzy cluster indexes; `clustIndex` in package cclust; `silhouette` in package cluster.

[Package clue version 0.3-54 Index]