\HeaderA{hdist-class}{Class "hdist" - S4 class to hold distance matrices.}{hdist.Rdash.class}
\aliasA{as.hdist}{hdist-class}{as.hdist}
\aliasA{as.hdist,matrix-method}{hdist-class}{as.hdist,matrix.Rdash.method}
\aliasA{as.matrix,hdist-method}{hdist-class}{as.matrix,hdist.Rdash.method}
\aliasA{as.vector,hdist,missing-method}{hdist-class}{as.vector,hdist,missing.Rdash.method}
\aliasA{coerce,hdist,matrix-method}{hdist-class}{coerce,hdist,matrix.Rdash.method}
\aliasA{coerce,matrix,hdist-method}{hdist-class}{coerce,matrix,hdist.Rdash.method}
\aliasA{dim,hdist-method}{hdist-class}{dim,hdist.Rdash.method}
\aliasA{hdist}{hdist-class}{hdist}
\aliasA{is.hdist}{hdist-class}{is.hdist}
\aliasA{labels,hdist-method}{hdist-class}{labels,hdist.Rdash.method}
\aliasA{length,hdist-method}{hdist-class}{length,hdist.Rdash.method}
\aliasA{show,hdist-method}{hdist-class}{show,hdist.Rdash.method}
\aliasA{[,hdist-method}{hdist-class}{[,hdist.Rdash.method}
\keyword{classes}{hdist-class}
\begin{Description}\relax
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)
\end{Description}
\begin{Section}{Slots}
\describe{
\item[\code{Data}:] Object of class \code{"numeric"} a vector containing the stacked columns of
the lower triangle of a symmetric matrix -- often the symmetric matrix is a
distance matrix.
\item[\code{Size}:] Object of class \code{"numeric"} the dimension of the 
symmetric matrix, from which \code{Data} was constructed.
\item[\code{Labels}:] Object of class \code{"numeric"} a list of values of 
length \code{Size} to allow for pretty printing.
\item[\code{Call}:] Object of class \code{"character"} a character string 
specifying the method used to create the distance matrix
from which \code{Data} was constructed.
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[hdist] \code{signature\{Data = "numeric", Size = "numeric", Labels = "numeric", Call = "character"\}}: Create a new hdist object. 
\item[as.hdist] \code{signature\{from = "matrix"\}}: Converts a matrix to a hdist object. 
\item[as.matrix] \code{signature(x = "hdist")}: Converts a hdist object to a matrix. 
\item[as.vector] \code{signature(x = "hdist", mode = "missing")}: Returns the hdist object as a vector. 
\item[[] \code{signature(x = "hdist")}: Subsetting function for hdist objects. See examples and warning. 
\item[coerce] \code{signature(from = "matrix", to = "hdist")}: Converts a matrix to a hdist object. 
\item[coerce] \code{signature(from = "hdist", to = "matrix")}: Converts a hdist object to a matrix. 
\item[dim] \code{signature(x = "hdist")}: Returns the dimension of the hdist object if expanded to a square matrix.
\item[labels] \code{signature(object = "hdist")}: Returns the labels used for printing. 
\item[length] \code{signature(x = "hdist")}: Returns the number of rows in hdist object. 
\item[show] \code{signature(object = "hdist")}: Prints the hdist object. 
}
\end{Section}
\begin{Section}{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)
\end{Section}
\begin{Note}\relax
Thank you to Larry Tai for his assistance creating run-time comparisons.
\end{Note}
\begin{Author}\relax
Katherine S. Pollard \textless{}kpollard@gladstone.ucsf.edu\textgreater{} and Gregory D. Wall \textless{}gwall@wald.ucdavis.edu\textgreater{}
\end{Author}
\begin{References}\relax
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.

\url{http://www.stat.berkeley.edu/~laan/Research/Research_subpages/Papers/hopach.pdf}

\url{http://www.bepress.com/ucbbiostat/paper107/}

\url{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.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{hopach}{hopach}}
\end{SeeAlso}
\begin{Examples}
\begin{ExampleCode}
        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)

\end{ExampleCode}
\end{Examples}

