rGPA: Generalized Procrustes analysis routine

Description Usage Arguments Value Note See Also

View source: R/rGPA.R

Description

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

Usage

1

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.