hopach (version 2.32.0)

hdist-class: Class "hdist" - S4 class to hold distance matrices.

Description

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)

Slots

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.

Methods

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.

Warning

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)

References

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.

See Also

hopach

Examples

	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)