gx.rotate: Function to Perform a Kaiser Varimax Rotaion

In rgr: Applied Geochemistry EDA

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, orgx.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.

See Also

gx.mva, gx.mva.closed, gx.robmva, gx.robmva.closed, varimax, gx.rqpca.loadplot,
gx.rqpca.plot

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 documentation built on May 2, 2019, 6:09 a.m.