pcm: Compute Pairwise Co-occurrence Matrix
In T4cluster: Tools for Cluster Analysis

Description Usage Arguments Value See Also Examples

Let clustering be a label from data of N observations and suppose we are given M such labels. Co-occurrent matrix counts the number of events where two observations X_i and X_j belong to the same category/class. PCM serves as a measure of uncertainty embedded in any algorithms with non-deterministic components.

1	pcm(partitions)

partitions

partitions can be provided in either (1) an (M\times N) matrix where each row is a clustering for N objects, or (2) a length-M list of length-N clustering labels.

an (N\times N) matrix, whose elements (i,j) are counts for how many times observations i and j belong to the same cluster, ranging from 0 to M.

psm

# -------------------------------------------------------------
#               PSM with 'iris' dataset + k-means++
# -------------------------------------------------------------
## PREPARE WITH SUBSET OF DATA
data(iris)
X     = as.matrix(iris[,1:4])
lab   = as.integer(as.factor(iris[,5]))

## EMBEDDING WITH PCA
X2d = Rdimtools::do.pca(X, ndim=2)$Y

## RUN K-MEANS++ 100 TIMES
partitions = list()
for (i in 1:100){
  partitions[[i]] = kmeanspp(X)$cluster
}

## COMPUTE PCM
iris.pcm = pcm(partitions)

## VISUALIZATION
opar <- par(no.readonly=TRUE)
par(mfrow=c(1,2), pty="s")
plot(X2d, col=lab, pch=19, main="true label")
image(iris.pcm[,150:1], axes=FALSE, main="PCM")
par(opar)