
Hi,

Newbie question about the pls package.

Setup:
Mac OS 10.3.9
R: Aqua GUI 1.01, v 2.0.1

I want to get R^2 and Q^2 (LOO and Leave-10-Out) values for each 
component for my model.
I was running into a few problems so I played with the example a little 
and the results do not match up with the comments
in the help pages.

$ library(pls)
$ data(NIR)

$ testing.plsNOCV <- plsr(y ~ X, 6, data = NIR, method="kernelpls", 
validation="none")
$ NIR.plsCV <- plsr(y ~ X, 6, data = NIR, CV=TRUE, method="kernelpls")
$ testing.plsCV <- crossval(testing.plsNOCV)
$ R2(NIR.plsCV)
(Intercept)      1 comps      2 comps      3 comps      4 comps      5 
comps
      0.0000       0.9812       0.9825       0.9964       0.9997       
0.9999
     6 comps
      0.9999
$ R2(testing.plsCV)
(Intercept)      1 comps      2 comps      3 comps      4 comps      5 
comps
      0.0000       0.9678       0.9782       0.9941       0.9991       
0.9996
     6 comps
      0.9997

$ ?crossval

"This function performs cross-validation on a model fit by mvr. It can 
handle models such as plsr(y ~ msc(X), ...) or other models where the 
predictor variables need to be recalculated for each segment. When 
recalculation is not needed, the result of crossval(mvr(...)) is 
identical to mvr(..., CV = TRUE), but slower."

If the above result is correct can someone explain the difference to me.

Using the above scheme gives different results for my model (dim(X) ~ 
88 x 1500), of around ~ 0.2 (7th Comp) in R2, and so the question is 
which one should I use?

Your help will be greatly appreciated,

Cheers,

Martin.




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