Hi all,
I think I may be confused by different people/programs using the word
rotation differently.

Does prcomp not perform rotations by default?
If I understand it correctly retx=TRUE returns ordinated data, that I can
plot for individual samples (prcomp()$x: which is the scaled and centered
(rotated?) data multiplied by loadings).

What does it mean that the data is rotated from the "?prcomp" description?
Is this referring to the data matrix orientation (i.e. looking at
differences among samples (columns) based on variables (rows) vs.
differences among variables (columns) based on samples(rows))?

Thank you,
Colin Wahl
Graduate student,
Western Washington University


code & background:
I am looking at the ordination of abiotic stream variables between different
sampling locations.

   abiot.pca=prcomp(all24[, c(10, 13:18)], retx=TRUE, center=TRUE, scale=
TRUE)


   summary(abiot.pca)

Importance of components:

                          PC1    PC2    PC3    PC4     PC5     PC6     PC7

Standard deviation     1.5925 1.0814 1.0697 0.9536 0.76624 0.68444 0.43037

Proportion of Variance 0.3623 0.1671 0.1635 0.1299 0.08387 0.06692 0.02646

Cumulative Proportion  0.3623 0.5294 0.6928 0.8227 0.90662 0.97354 1.00000


loadings[,1:3]

                 PC1         PC2         PC3

avg.dmax  -0.1879223  0.55792480 -0.04962935

scond.med -0.4327223  0.04779998 -0.43369560

docon.med  0.1976094 -0.30384127  0.67222550

cb.per     0.4134302 -0.17550281 -0.40171318

gc.per     0.4136933 -0.26997129 -0.39960398

gf.per     0.3419349  0.63917223  0.16174661

fine.per  -0.5285840 -0.28616200  0.10168155

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