hdist-class: Class "hdist" - S4 class to hold distance matrices.
In hopach: Hierarchical Ordered Partitioning and Collapsing Hybrid (HOPACH)

Description Slots Methods Warning Note Author(s) References See Also Examples

Class hdist was created to take advantage of the structure innate to symmetric matrices. It stores only the lower triangle of the matrix, thus reducing the size (and memory usage) from n x n to [n x (n - 1)] / 2.

Like a matrix, a hdist object is subsettable; thus, hdist[i,j] will return the value at row 'i' column 'j'. Most valid indices for a matrix are also valid for a hdist object. (See examples below)

Data:: Object of class "numeric" a vector containing the stacked columns of the lower triangle of a symmetric matrix – often the symmetric matrix is a distance matrix.
Size:: Object of class "numeric" the dimension of the symmetric matrix, from which Data was constructed.
Labels:: Object of class "numeric" a list of values of length Size to allow for pretty printing.
Call:: Object of class "character" a character string specifying the method used to create the distance matrix from which Data was constructed.

hdist: signature{Data = "numeric", Size = "numeric", Labels = "numeric", Call = "character"}: Create a new hdist object.
as.hdist: signature{from = "matrix"}: Converts a matrix to a hdist object.
as.matrix: signature(x = "hdist"): Converts a hdist object to a matrix.
as.vector: signature(x = "hdist"): Returns the hdist object as a vector.
[: signature(x = "hdist"): Subsetting function for hdist objects. See examples and warning.
coerce: signature(from = "matrix", to = "hdist"): Converts a matrix to a hdist object.
coerce: signature(from = "hdist", to = "matrix"): Converts a hdist object to a matrix.
dim: signature(x = "hdist"): Returns the dimension of the hdist object if expanded to a square matrix.
labels: signature(object = "hdist"): Returns the labels used for printing.
length: signature(x = "hdist"): Returns the number of rows in hdist object.
show: signature(object = "hdist"): Prints the hdist object.

A hdist object is NOT closed under the subsetting operation. For instance, if a 100 x 100 symmetric matrix is stored as an hdist object, hdist[c(3,4,5),c(7,8,9)] will return a 3 x 3 matrix, since the subsetting will not result in a symmetric matrix. However, if index i = j, then subsetting a hdist object will result in a symmetric matrix, and thus a hdist object will be returned. (See examples below)

Thank you to Larry Tai for his assistance creating run-time comparisons.

Katherine S. Pollard <kpollard@gladstone.ucsf.edu> and Gregory D. Wall <gwall@wald.ucdavis.edu>

van der Laan, M.J. and Pollard, K.S. A new algorithm for hybrid hierarchical clustering with visualization and the bootstrap. Journal of Statistical Planning and Inference, 2003, 117, pp. 275-303.

http://www.stat.berkeley.edu/~laan/Research/Research_subpages/Papers/hopach.pdf

http://www.bepress.com/ucbbiostat/paper107/

http://www.stat.berkeley.edu/~laan/Research/Research_subpages/Papers/jsmpaper.pdf

Kaufman, L. and Rousseeuw, P.J. (1990). Finding Groups in Data: An Introduction to Cluster Analysis. Wiley, New York.

hopach

	showClass("hdist")

	library(hopach) 
	X <- matrix(rnorm(60,mean=10,sd=2),nrow=10,ncol=6,byrow=TRUE)
	dmat <- disscosangle(X) 
	dmat
	str(dmat) 
	
	# Examples where subsetting a hdist object returns a matrix...	
	dmat[c(3,4,5),c(5,6,7,8)]
	dmat[c(TRUE,FALSE),c(FALSE,TRUE)]
	dmat[c(4,5,6), ] 

	# Examples where subsetting a hdist object returns a hdist object...
	dmat[c(3,4,5,6,7),c(3,4,5,6,7)]
	dmat[c(TRUE,FALSE),c(TRUE,FALSE)]
	
	# Expand hdist object to a symmetric matrix...
	as.matrix(dmat)