evaluators {asbio} | R Documentation |
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).
McR.eval(cat, dist) Cindex.eval(cat, Y, index = "steinhaus") morisita.eval(cat, Y) biserial.eval(cat, dist)
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. |
More to come. Note that the function McR.eval
is essentially the partana
function from library labdsv
with only a few minor adjustments.
Returns an evaluator score for a classification solution.
The Morisita evaluator has been tested on a few datasets and appears to respond in a strongly linear fashion to the number of clusters.
David Roberts and Ken Aho
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.