I'm looking for someone to explain the difference between these
procedures. The function prcomp() does principal components anaylsis,
and the function cmdscale() does classical multi-dimensional scaling
(also called principal coordinates analysis).
My confusion stems from the fact that they give very similar results:
my.d <- matrix(rnorm(50), ncol=5)
rownames(my.d) <- paste("c", 1:10, sep="")
# prcomp
prc <- prcomp(my.d)
# cmdscale
mds <- cmdscale(dist(my.d))
cor(prc$x[,1], mds[,1]) # produces 1 or -1
cor(prc$x[,2], mds[,2]) # produces 1 or -1
Presumably, under the defaults for these commands in R, they carry out
the same (or very similar) procedures?
Thanks
Mick
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