Hi Liviu,
However, I'm still confused on how to compute the scores when rotations (such as 'varimax' or other methods in GPArotation) are applied.
PCA does an orthogonal rotation of the coordinate system (axes) and further rotation is not usually done (in contrast to factor analysis). Neither prcomp nor princomp do any further rotation and any rotate= argument in the call is simply being passed through. You can get what you want from by feeding the scores from prcomp/princomp (or something else) to GPArotation. This returns rotated scores and the rotating matrix. ## library(GPArotation) .PC <- princomp(~am+carb+cyl+disp+drat+gear+hp+mpg, cor=TRUE, data=mtcars) .PCs <- .PC$scores .PCrs <- entropy(.PCs) .PCs .PCrs Regards, Mark.
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