gputools (version 0.1-1)

gpuHclust: Perform Hierarchical Clustering for Vectors with a GPU

Description

This function performs clustering on a set of points. The distance between each pair of points should be calculated first using a function like 'gpuDist' or 'dist'.

Usage

gpuHclust(distances, method = "single")

Arguments

distances

a matrix of floating point numbers whose i, j entry represents the distance between point i and point j. To use this with the dist function, be sure to generate the whole matrix of distances, and wrap the output with 'as.matrix'.

method

a string representing the name of the clustering method to be applied to distances. Currently supported method names include "average", "centroid", "complete", "flexible", "flexible group", "mcquitty", "median", "single", "ward", and "wpgma".

Value

• Copied from the native R function 'hclust' documentation. A list with the following components.
• merge
  an n-1 by 2 matrix. Row i of 'merge' describes the merging of clusters at step i of the clustering. If an element j in the row is negative, then observation -j was merged at this stage. If j is positive then the merge was with the cluster formed at the (earlier) stage j of the algorithm. Thus negative entries in 'merge' indicate agglomerations of singletons, and positive entries indicate agglomerations of non-singletons. Copied from the native R function 'hclust' documentation.
• order
  a vector giving the permutation of the original observations suitable for plotting, in the sense that a cluster plot using this ordering and matrix 'merge' will not have crossings of the branches.
• height
  a set of n-1 non-decreasing real values. The clustering height: that is, the value of the criterion associated with the clustering 'method' for the particular agglomeration.

See Also

hclust, gpuDistClust

Examples

numVectors <- 5
dimension <- 10
Vectors <- matrix(runif(numVectors*dimension), numVectors, dimension)
distMat <- gpuDist(Vectors, "euclidean")
gpuHclust(distMat, "single")
gpuHclust(as.matrix(dist(Vectors)), "single")