Re: [R] Can't reproduce clusplot princomp results.
Thomas M. Parris writes: clusplot reports that the first two principal components explain 99.7% of the variability. [...] loadings(pca) [...] 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 This has nothing to do with how much of the variability of the original data that is captured by each component; it merely measures the variability in the coefficients of the loading vectors (and they are standardised to length one in princomp) What you want to look at is pca$sdev, for instance something like totvar - sum(pca$sdev^2) rbind(explained var = pca$sdev^2, prop. expl. var = pca$sdev^2/totvar, cum.prop.expl.var = cumsum(pca$sdev^2)/totvar) Comp.1Comp.2 Comp.3 Comp.4 explained var 3.4093746 0.5785399 0.011560142 0.0005252824 prop. expl. var 0.8523437 0.1446350 0.002890036 0.0001313206 cum.prop.expl.var 0.8523437 0.9969786 0.999868679 1.00 And as you can see, two comps explain 99.7%. :-) -- Bjørn-Helge Mevik __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
[R] 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 major2 minor0.1 year 2004 month11 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 -0.5400.837 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 __ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html
