Thaler, Thorn, LAUSANNE, Applied Mathematics
2011-May-11 07:11 UTC
[Rd] stats:::biplot.prcomp: Scaling, typo in the help file?
Dear all,>From the documentation of biplot.prcomp:scale: The variables are scaled by 'lambda ^ scale' and the observations are scaled by 'lambda ^ (1-scale)' where 'lambda' are the singular values as computed by 'princomp'.>From the source code of prcomp:lam <- x$sdev[choices] n <- NROW(scores) lam <- lam * sqrt(n) if (scale < 0 || scale > 1) warning("'scale' is outside [0, 1]") if (scale != 0) lam <- lam^scale else lam <- 1 if (pc.biplot) lam <- lam/sqrt(n) biplot.default(t(t(scores[, choices])/lam), t(t(x$rotation[, choices]) * lam), ...) Thus, the observations are divided by the scale factor, i.e. they are scaled by lambda^(-scale) and not by lambda^(1-scale). Am I missing something? Kind Regards, Thorn Thaler Mathematician Applied Mathematics Group Nestl? Research Center PO Box 44 CH-1000 Lausanne 26, Switzerland Phone: +41 21 785 8220 Fax: +41 21 785 8556