Can't reproduce clusplot princomp results.
Dear R folk: Perhaps I'm just dense today, but I am having trouble reproducing the principal components plotted and summarized by clusplot. Here is a brief example using the pluton dataset. clusplot reports that the first two principal components explain 99.7% of the variability. But this is not what princomp is reporting. I would greatly appreciate any advice. With best regards, -- Tom
R.version
_ platform i386-pc-mingw32 arch i386 os mingw32 system i386, mingw32 status major 2 minor 0.1 year 2004 month 11 day 15 language R
require("cluster")
[1] TRUE
pluton.agnes <- agnes(pluton) clusters <- cutree(as.hclust(pluton.agnes), h=4.00) clusplot(pluton, clusters, lines=0) pca <- princomp(pluton, cor=TRUE) loadings(pca)
Loadings:
Comp.1 Comp.2 Comp.3 Comp.4
Pu238 0.521 0.348 0.714 0.313
Pu239 -0.540 0.837
Pu240 0.418 -0.835 0.353
Pu241 0.512 0.418 -0.698 0.277
Comp.1 Comp.2 Comp.3 Comp.4
SS loadings 1.00 1.00 1.00 1.00
Proportion Var 0.25 0.25 0.25 0.25
Cumulative Var 0.25 0.50 0.75 1.00