asbio (version 0.2-1)

evaluators: 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, method = "McR")

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, i.e. an object of class="dist".

method

The method used in McR.eval. Options are method="partana" and method="McR".

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

Value

• Returns an list of class="eval". Printed will be the evaluator score for a classification solution; invisible objects will vary with method.

Details

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

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

Examples

library(vegan)
data(dune)
data(dune.env)

McR.eval(dune.env[,3],get.dist(dune,"steinhaus"))
Cindex.eval(dune.env[,3],dune)
biserial.eval(dune.env[,3],get.dist(dune,"steinhaus"))