rgr: gx.rotate – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

gx.rotate

Function to Perform a Kaiser Varimax Rotaion

Description

Function to perform a Kaiser Varimax rotation on Principal Component (PCA) loadings and scores in an object saved from gx.mva, gx.mva.closed, gx.robmva or gx.robmva.closed.

Usage

gx.rotate(save, nrot = 2)

Arguments

`save`	a saved object from the execution of function `gx.mva`, `gx.mva.closed`, `gx.robmva`, or`gx.robmva.closed`.
`nrot`	the number of component loadings to be rotated, by default the first two components are rotated, `nrot = 2`.

Value

The value of nr is modified in, and the following are appended to, the object that was saved from gx.mva, gx.mva.closed, gx.robmva, or gx.robmva.closed:

`nr`	modified to equal the number of components rotated.
`vload`	the new loadings after Varimax rotation.
`vscore`	the new scores after Varimax rotation.
`vvcontrib`	the contribution of the rotated Varimax component to the total data variability.
`pvvcontrib`	the contribution of the rotated Varimax component to the total data variability as a percentage.
`cpvvcontrib`	the cumulative contribution of the rotated Varimax component to the total data variability as a percentage.

Author(s)

Robert G. Garrett

References

Reimann, C., Filzmoser, P., Garrett, R. and Dutter, R., 2008. Statistical Data Analysis Explained: Applied Environmental Statistics with R. John Wiley & Sons, Ltd., 362 p.

Venables, W.N. and Ripley, B.D., 2001. Modern Applied Statistics with S-Plus, 3rd Edition, Springer, 501 p.

Examples

## Make test data available
data(sind.mat2open)

## Save PCA results and display biplots before and after Varimax rotation
sind.save <- gx.mva(clr(sind.mat2open))
gx.rqpca.plot(sind.save)
gx.rqpca.plot(sind.save,
main = "Howarth & Sinding Larsen Stream Sediments\nclr transform",
pch = 4, cex.main = 0.9)
sind.save.rot2 <- gx.rotate(sind.save)
gx.rqpca.plot(sind.save.rot2,
main = "Howarth & Sinding Larsen Stream Sediments\nclr transform",
pch = 4, cex.main = 0.9)

## Clean-up
rm(sind.save)
rm(sind.save.rot2)

rgr

Applied Geochemistry EDA

v1.1.15

GPL-2

Authors

Robert G. Garrett

Initial release

2018-03-05