concordance: Concordance between two classifications

Description

Computes an index to compare two classifications.

Usage

concordance(x, y, method="adjustedRand",...)

Arguments

x,y

Classification vector or membership matrix. Alternatively, objects of type vegclust or vegclass.

method

A string vector to indicate the desired indices (see details).

...

Additional parameters for function defuzzify, which will be called if x or y are of type matrix, vegclust or vegclass.

Value

A numeric vector with the desired index values.

Details

Several indices for comparison of partitions are available:

method="Rand": Rand (1971) index.
method="adjustedRand": Rand index adjusted for random effects (Hubert & Arabie 1985).
method="Wallace": Wallace (1983) index (for asymmetrical comparisons). This index (and its adjusted version) is useful to quantify how much x is nested into y.
method="adjustedWallace": Wallace index adjusted for random effects (Pinto et al. 2008).

References

Hubert, L. & Arabie, P. (1985). Comparing partitions. Journal of Classification, 2, 193<U+2013>218.

Pinto, F.R., Melo-Cristino, J. & Ramirez, M. (2008). A confidence interval for the wallace coefficient of concordance and its application to microbial typing methods. PLoS ONE, 3.

Rand, W.M. (1971). Objective Criteria for the Evaluation of Clustering Methods. Journal of the American Statistical Association, 66, 846<U+2013>850.

Wallace, D.L. (1983). A method for comparing two hierarchical clusterings: Comment. Journal of the American Statistical Association, 78, 569<U+2013>576.