riem.kmeans {Riemann} | R Documentation |
K-Means Clustering
Description
Given N
observations X_1, X_2, \ldots, X_N \in \mathcal{M}
,
perform k-means clustering by minimizing within-cluster sum of squares (WCSS).
Since the problem is NP-hard and sensitive to the initialization, we provide an
option with multiple starts and return the best result with respect to WCSS.
Usage
riem.kmeans(riemobj, k = 2, geometry = c("intrinsic", "extrinsic"), ...)
Arguments
riemobj |
a S3 |
k |
the number of clusters. |
geometry |
(case-insensitive) name of geometry; either geodesic ( |
... |
extra parameters including
|
Value
a named list containing
- cluster
a length-
N
vector of class labels (from1:k
).- means
a 3d array where each slice along 3rd dimension is a matrix representation of class mean.
- score
within-cluster sum of squares (WCSS).
References
Lloyd S (1982). “Least squares quantization in PCM.” IEEE Transactions on Information Theory, 28(2), 129–137. ISSN 0018-9448.
MacQueen J (1967). “Some methods for classification and analysis of multivariate observations.” In Proceedings of the fifth berkeley symposium on mathematical statistics and probability, volume 1: Statistics, 281–297.
See Also
Examples
#-------------------------------------------------------------------
# Example on Sphere : a dataset with three types
#
# class 1 : 10 perturbed data points near (1,0,0) on S^2 in R^3
# class 2 : 10 perturbed data points near (0,1,0) on S^2 in R^3
# class 3 : 10 perturbed data points near (0,0,1) on S^2 in R^3
#-------------------------------------------------------------------
## GENERATE DATA
mydata = list()
for (i in 1:10){
tgt = c(1, stats::rnorm(2, sd=0.1))
mydata[[i]] = tgt/sqrt(sum(tgt^2))
}
for (i in 11:20){
tgt = c(rnorm(1,sd=0.1),1,rnorm(1,sd=0.1))
mydata[[i]] = tgt/sqrt(sum(tgt^2))
}
for (i in 21:30){
tgt = c(stats::rnorm(2, sd=0.1), 1)
mydata[[i]] = tgt/sqrt(sum(tgt^2))
}
myriem = wrap.sphere(mydata)
mylabs = rep(c(1,2,3), each=10)
## K-MEANS WITH K=2,3,4
clust2 = riem.kmeans(myriem, k=2)
clust3 = riem.kmeans(myriem, k=3)
clust4 = riem.kmeans(myriem, k=4)
## MDS FOR VISUALIZATION
mds2d = riem.mds(myriem, ndim=2)$embed
## VISUALIZE
opar <- par(no.readonly=TRUE)
par(mfrow=c(2,2), pty="s")
plot(mds2d, pch=19, main="true label", col=mylabs)
plot(mds2d, pch=19, main="K=2", col=clust2$cluster)
plot(mds2d, pch=19, main="K=3", col=clust3$cluster)
plot(mds2d, pch=19, main="K=4", col=clust4$cluster)
par(opar)