data(rockArt)
rockart.dist <- dist(x = as.matrix(rockArt[, 28:641]), method = "binary")
sum(rockart.dist==1)/length(rockart.dist)
plot(density(rockart.dist, to = 1))
rockart.cmd <- cmdscale(rockart.dist)
tab <- table(rockArt$District)
district <- as.character(rockArt$District)
district[!(rockArt$District %in% names(tab)[tab>5])] <- "other"
library(lattice)
xyplot(rockart.cmd[,2] ~ rockart.cmd[,1], groups=district,
auto.key=list(columns=5),
par.settings=list(superpose.symbol=list(pch=16)))
library(MASS)
## For sammon, need to avoid zero distances
omit <- c(47, 54, 60, 63, 92)
rockart.dist <- dist(x = as.matrix(rockArt[-omit, 28:641]), method = "binary")
rockart.cmd <- cmdscale(rockart.dist)
rockart.sam <- sammon(rockart.dist, rockart.cmd)
xyplot(rockart.sam$points[,2] ~ rockart.sam$points[,1],
groups=district[-omit], auto.key=list(columns=5),
par.settings=list(superpose.symbol=list(pch=16)))
## Notice the very different appearance of the Sammon plot
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