plot3darcs: Modes of variation plots for PCA and PNSS

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plot3darcsR Documentation

Modes of variation plots for PCA and PNSS

Description

Modes of variation plots for PCA and PNSS based on 3D views and arcs along a mode. c * sd : the extent along lower and upper principal arcs.

The lower principal arc -> 0 -> upper principal arc has a total of 2*nn+1 configurations with: nn configurations along the negative principal arc to 0; one configuration at the PNS mean; nn configurations along the positive principal arc.

Usage

plot3darcs(x,pcno=1,c=1,nn=100,boundary.data=TRUE,view.theta=0,view.phi=0,type="pnss")

Arguments

x

Output from pnss3d

pcno

The number of the PC/PNSS component. The default is 1, the first PC/PNSS

c

Number of standard deviations along each arc

nn

In total 2 * nn + 1 configurations: n configurations on arc from negative to 0; 1 configuration at 0; nn configurations from 0 to positive

boundary.data

Logical for whether to use boundary data or not.

view.theta

Viewing angle theta

view.phi

Viewing angle phi

type

"pnss" principal nested sphere mean and arc, or "pca" Procrustes mean and linear PC.

Value

A list with components

PNSmean

the PNSS mean

lu.arc

the configurations along the arc

Author(s)

Kwang-Rae Kim, Ian Dryden

References

Dryden, I.L., Kim, K., Laughton, C.A. and Le, H. (2019). Principal nested shape space analysis of molecular dynamics data. Annals of Applied Statistics, 13, 2213-2234.

Jung, S., Dryden, I.L. and Marron, J.S. (2012). Analysis of principal nested spheres. Biometrika, 99, 551-568.

See Also

pns, pns4pc, pnss3d

Examples

ans <- pnss3d(digit3.dat, sphere.type="BIC", n.pc=5)
#aa <- plot3darcs(ans,c=2,pcno=1)
#bb <- plot3darcs(ans,c=2,pcno=1,type="pca")

shapes documentation built on Feb. 16, 2023, 8:16 p.m.