# Shepard-like diagrams
par(mfrow = c(2, 2))
plot(
spe.ch,
spe.ch.single.coph,
xlab = "Chord distance",
ylab = "Cophenetic distance",
asp = 1,
xlim = c(0, sqrt(2)),
ylim = c(0, sqrt(2)),
main = c("Single linkage", paste("Cophenetic correlation =",
round(cor(spe.ch, spe.ch.single.coph), 3)))
)
abline(0, 1)
lines(lowess(spe.ch, spe.ch.single.coph), col = "red")
plot(
spe.ch,
spe.ch.comp.coph,
xlab = "Chord distance",
ylab = "Cophenetic distance",
asp = 1,
xlim = c(0, sqrt(2)),
ylim = c(0, sqrt(2)),
main = c("Complete linkage", paste("Cophenetic correlation =",
round(cor(spe.ch, spe.ch.comp.coph), 3)))
)
abline(0, 1)
lines(lowess(spe.ch, spe.ch.comp.coph), col = "red")
plot(
spe.ch,
spe.ch.UPGMA.coph,
xlab = "Chord distance",
ylab = "Cophenetic distance",
asp = 1,
xlim = c(0, sqrt(2)),
ylim = c(0, sqrt(2)),
main = c("UPGMA", paste("Cophenetic correlation =",
round(cor(spe.ch, spe.ch.UPGMA.coph), 3)))
)
abline(0, 1)
lines(lowess(spe.ch, spe.ch.UPGMA.coph), col = "red")
plot(
spe.ch,
spe.ch.ward.coph,
xlab = "Chord distance",
ylab = "Cophenetic distance",
asp = 1,
xlim = c(0, sqrt(2)),
ylim = c(0, max(spe.ch.ward$height)),
main = c("Ward", paste("Cophenetic correlation =",
round(cor(spe.ch, spe.ch.ward.coph), 3)))
)
abline(0, 1)
lines(lowess(spe.ch, spe.ch.ward.coph), col = "red")
4.7 Interpreting and Comparing Hierarchical Clustering Results
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