evaluators {asbio}R Documentation

Cluster analysis evaluators.

Description

A collection of classification evaluators are included here; McR.eval provides both the McClain & Rao evaluator (W/B) (McClain and Rao 1975) and the PARTANA ratio (Roberts 2005); Cindex.eval = The C-index (Hubert and Levin 1976); morisita.eval = the Morisita index (adapted from Horn 1966); biserial.eval = point biserial correlation evaluator (Brogden 1949).

Usage


McR.eval(cat, dist)

Cindex.eval(cat, Y, index = "steinhaus")

morisita.eval(cat, Y)

biserial.eval(cat, dist)

Arguments

cat Classification solution, a categorical vector.
dist A dissimilarity or distance matrix.
Y A matrix of raw data, e.g. a community matrix.
index Type of dissimilarity or distance metric to use. Any measure from get.dist is allowed.

Details

More to come. Note that the function McR.eval is essentially the partana function from library labdsv with only a few minor adjustments.

Value

Returns an evaluator score for a classification solution.

Note

The Morisita evaluator has been tested on a few datasets and appears to respond in a strongly linear fashion to the number of clusters.

Author(s)

David Roberts and Ken Aho

References

Brogden, H. E.(1949) A new coefficient: application to biserial correlation and to estimation of selective efficiency. Psychometrika. 14: 169-182.

Horn, H. S. (1966) Measurement of "overlap" in comparative ecological studies. Am. Naturalist. 100: 419-424.

Hubert, L. J. & Levin, J. R. (1976) A general framework for assessing categorical clustering in free recall. Psychol. Bull. 83: 1072-1080.

McClain, J. O. & Rao, V. R. (1975) CLUSTISZ: A program to test for the quality of clustering of a set of objects. J. Marketing Res. 12: 456-460.

Milligan, G. W. (1981) A Monte Carlo study of thirty internal criterion measures for cluster analysis. Psychometrika. 46(2): 187-199.

Milligan, G. W. & Cooper, M. C. (1985) An examination of procedures for determining the number of clusters in a dataset. Psychometrika. 50 (2): 159-179.

Milligan, G. W. & Isaac, P. D. (1980) The validation of four ultrametric clustering algorithms. Pattern Recogn. 12: 41-50.

Roberts, D. (2005) Vegetation classification in R, for labdsv ver. 1.1-1, vegetation ecology package. www.cran.r-project.org. unpubl.

See Also

get.dist


[Package asbio version 0.1 Index]