projShapes: Helper function for plotting the shapes

In Anthropometry: Statistical Methods for Anthropometric Data

Helper function for plotting the shapes

Description

Helper function for plotting the projections of the shapes. It displays the projection on the xy plane of the recorded points and mean shape for a given cluster. To that end, first it is needed to carry out a generalized Procrustes analysis in the cluster to obtain the full Procrustes rotated data.

Usage

projShapes(clust,array3D,asig,prototypes)

Arguments

clust	Cluster for which represent its mean shape together with the recorded points.
array3D	Array with the 3D landmarks of the sample points. Each row corresponds to an observation, and each column corresponds to a dimension (x,y,z).
asig	Clustering optimal results.
prototypes	Vector of optimal prototypes.

Value

Numerical vector with the percentile values of an archetypoid.

Author(s)

Guillermo Vinue

References

Vinue, G., Simo, A., and Alemany, S., (2016). The k-means algorithm for 3D shapes with an application to apparel design, Advances in Data Analysis and Classification 10(1), 103–132.

See Also

LloydShapes, HartiganShapes, trimmedLloydShapes

Examples

landmarksNoNa <- na.exclude(landmarksSampleSpaSurv)
dim(landmarksNoNa) 
#[1] 574 198 
numLandmarks <- (dim(landmarksNoNa)[2]) / 3
#[1] 66
#As a toy example, only the first 15 individuals are used.
landmarksNoNa_First10 <- landmarksNoNa[1:10, ] 
(numIndiv <- dim(landmarksNoNa_First10)[1])
#[1] 10         
    
array3D <- array3Dlandm(numLandmarks, numIndiv, landmarksNoNa_First10)
#shapes::plotshapes(array3D[,,1]) 
#calibrate::textxy(array3D[,1,1], array3D[,2,1], labs = 1:numLandmarks, cex = 0.7) 

numClust <- 2 ; algSteps <- 1 ; niter <- 1 ; stopCr <- 0.0001
resLL <- LloydShapes(array3D, numClust, algSteps, niter, stopCr, FALSE, FALSE)
clust_kmeansProc <- resLL$asig

prototypes <- anthrCases(resLL)

projShapes(1, array3D, clust_kmeansProc, prototypes)
#legend("topleft", c("Registrated data", "Mean shape"), pch = 1, col = 1:2, text.col = 1:2)
#title("Procrustes registrated data for cluster 1 \n with its mean shape superimposed", 
#      sub = "Plane xy")

Anthropometry documentation built on March 7, 2023, 6:58 p.m.