cba (version 0.2-5)

seriation: Seriation heuristics for symmetric matrices

Description

Seriation heuristics for symmetric matrices used for cluproxplot. Seriation tries to move large values towards the main diagonal by reordering columns and rows at the same time.

Usage

seriation(x, method = NULL, args = NULL)

Arguments

x

a symmetric matrix to be seriated.

method

a character string with the name of the seriation method.

args

"list"; contains arguments for the seriation heuristic.

Value

• The order as a vector of integer. The attribute "method" contains the method as a character string.

Details

Currently the following methods are implemented: [object Object],[object Object],[object Object],[object Object]

References

F. Murtagh (1985). Multidimensional Cluster Algorithms. Lectures in Computational Statistics, Physica Verlag, pp. 15.

Gruvaeus, G. and Wainer, H. (1972), "Two Additions to Hierarchical Cluster Analysis", British Journal of Mathematical and Statistical Psychology, 25, 200-206.

Hurley, Catherine B. Clustering Visualizations of Multidimensional Data. Journal of Computational and Graphical Statistics, 13(4), pages 788-806, 2004.

Z. Bar-Joseph, E. D. Demaine, D. K. Gifford, and T. Jaakkola. (2001). Fast Optimal Leaf Ordering for Hierarchical Clustering. Bioinformatics, Vol. 17 Suppl. 1, pp. 22-29.

Examples

data("Votes")

### create dummy coding (with removed party affiliation)
x <- as.dummy(Votes[-17])

### calculate distance matrix
d <- dists(x, method = "binary")


### use standard method
order <- seriation(d)
order

### use hclust w/complete linkage + optimal leaf ordering
order2 <- seriation(d, method = "Optimal")
order2


### use hclust w/single linkage + optimal leaf ordering
order3 <- seriation(d, method = "Optimal", args = list(method = "single"))
order3