rGPA: Generalized Procrustes analysis routine

In jinyung/otolith: Identification of fish otolith using digital images

Description

a wrapper function for routine use to run generalized Procrustes analysis.

Usage

rGPA(A, fix = NULL, plotpca = FALSE, class)

Arguments

A	p x k x n array of raw semilandmarks configurations
fix	a numeric vector giving the semi-landmakrs that not to be slided. Default is all semilandmarks will be slided (See Note for issue).
plotpca	logical. whether to plot PCA for preliminary assessment of the data
class	factor giving the species/grouping, used for plotting purpose and calculation of within class range of Procrustes distance, e.g. using sp value from routine1 or using getclass

Value

tanc	Procrustes aligned configurations projected onto tangent shape space
size	centroid size
expvar	summary of expalined variations by each PC
score	matrix contain the PC scores, to be used for training
rdist	see sprdist
pca	the PCA model, to be used by otopred
meanshape	meanshape of each species/ groups
mshape	meanshape of all species/ groups

Note

There is an issue with otopred function, which cannot handle sliding semi-landmarks yet and hence it is recommended that all semi-landmarks should be fixed if the user intend to use the otopred function (6 May 2014).

See Also

which this function wraps: procSym, sprdist

jinyung/otolith documentation built on May 19, 2019, 10:36 a.m.