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Note that this notebook was automatically generated from an RDocumentation page. It depends on the package and the example code whether this code will run without errors. You may need to edit the code to make things work.
if(!require('cluster')) {
install.packages('cluster')
library('cluster')
}
data(ruspini)
pr4 <- pam(ruspini, 4)
str(si <- silhouette(pr4))
(ssi <- summary(si))
plot(si) # silhouette plot
plot(si, col = c("red", "green", "blue", "purple"))# with cluster-wise coloring
si2 <- silhouette(pr4$clustering, dist(ruspini, "canberra"))
summary(si2) # has small values: "canberra"'s fault
plot(si2, nmax= 80, cex.names=0.6)
op <- par(mfrow= c(3,2), oma= c(0,0, 3, 0),
mgp= c(1.6,.8,0), mar= .1+c(4,2,2,2))
for(k in 2:6)
plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE)
mtext("PAM(Ruspini) as in Kaufman & Rousseeuw, p.101",
outer = TRUE, font = par("font.main"), cex = par("cex.main")); frame()
## the same with cluster-wise colours:
c6 <- c("tomato", "forest green", "dark blue", "purple2", "goldenrod4", "gray20")
for(k in 2:6)
plot(silhouette(pam(ruspini, k=k)), main = paste("k = ",k), do.n.k=FALSE,
col = c6[1:k])
par(op)
## clara(): standard silhouette is just for the best random subset
data(xclara)
set.seed(7)
str(xc1k <- xclara[ sample(nrow(xclara), size = 1000) ,]) # rownames == indices
cl3 <- clara(xc1k, 3)
plot(silhouette(cl3))# only of the "best" subset of 46
## The full silhouette: internally needs large (36 MB) dist object:
sf <- silhouette(cl3, full = TRUE) ## this is the same as
s.full <- silhouette(cl3$clustering, daisy(xc1k))
stopifnot(all.equal(sf, s.full, check.attributes = FALSE, tolerance = 0))
## color dependent on original "3 groups of each 1000": % __FIXME ??__
plot(sf, col = 2+ as.integer(names(cl3$clustering) ) %/% 1000,
main ="plot(silhouette(clara(.), full = TRUE))")
## Silhouette for a hierarchical clustering:
ar <- agnes(ruspini)
si3 <- silhouette(cutree(ar, k = 5), # k = 4 gave the same as pam() above
daisy(ruspini))
stopifnot(is.data.frame(di3 <- as.data.frame(si3)))
plot(si3, nmax = 80, cex.names = 0.5)
## 2 groups: Agnes() wasn't too good:
si4 <- silhouette(cutree(ar, k = 2), daisy(ruspini))
plot(si4, nmax = 80, cex.names = 0.5)