Procrustes superimposition of landmark datasets with some missing values

Description

This function carries out a generalized procrustes superimposition on all fully complete specimens and produces a consensus confirguration (using "Shapes" procGPA). Each incomplete specimen is then individually rotated and aligned with the consensus configuration based on any landmarks are available (using "Shapes" procOPA). Landmarks are returned in the same shape space as the original dataset. Both 2D and 3D coordinates can be accommodated.

Usage

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align.missing(X, nlandmarks)

Arguments

X

A n* l X 2 (or 3) matrix of coordinate data, where n is the number of specimens and l is the number of landmarks. All landmarks from one specimen should be grouped together.

nlandmarks

The number of landmarks per specimen

Value

Returns and n*l X 2 (or 3) matrix of aligned landmarks

Author(s)

J. Arbour

References

Arbour, J. and Brown, C. 2014. Incomplete specimens in Geometric Morphometric Analyses. Methods in Ecology and Evolution 5(1):16-26.

See Also

MissingGeoMorph

Examples

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data(dacrya)

## make some specimens incomplete
dac.miss<-missing.specimens(dacrya,10,c(1,2,3,4,5,6),16)
dac.miss

## align all specimens
dac.aligned<-align.missing(dac.miss,16)

## compare original and aligned
plot(dacrya,col="blue")
points(dac.aligned,col="red")