bilat.align: Align a bilterally symmetric landmark configuration with a...

In LOST: Missing Morphometric Data Simulation and Estimation

Align a bilterally symmetric landmark configuration with a plane

Description

Aligns a bilaterally symmetric landmark dataset to a specific plane by minimized the sum of squared distances of one coordinate (x, y or z). Useful for averaging bilateral landmarks or in preparation for correcting for artifacts like bending.

Usage

bilat.align(coords, land.pairs, average = TRUE, restricted = NULL)

Arguments

coords	Either a matrix or array of landmark data with columns representing the x, y, z coordinates and rows representing landmarks. See details for how this is applied for a single vs. multiple specimens.
land.pairs	A 2 column matrix indicating bilaterally paired landmarks. All "left" landmarks should be in the same column (and likewise for "right landmarks")
average	An optional term indicating that bilaterally paired landmarks should be mirrored and averaged, leaving only one "side" and the midline landmarks.
restricted	A set of row numbers indicating which landmarks should be considered by "optim" when selecting the optimal rotation. Typically landmarks representing a rigid structure if some landmarks represent articulated/moveable features.

Details

If a matrix for a single specimen's landmarks is provided this is aligned to a plane, if an array of multiple specimens is provided, these should be previously aligned with Procrustes superimposition, and the entire configuration is optimized with a single rotation applied to all specimens. SS are minimized across the third axis (coords[,3] or coords[,3,]).

Value

A matrix or array giving the rotated landmark configuration

Author(s)

J.H. Arbour

References

Arbour,J.H. In Prep. Get Unbent! R Tools for the removal of arching and bending of fish specimens in geometric morphometric shape analysis

See Also

unbend.spine, unbend.tps.poly

Examples

library(rgl)
data(darters)
## align darter configuration by head landmarks (restricted)
aligned<-bilat.align(darters$coords[,,1],
darters$land.pairs,average=FALSE,darters$restricted)

plot3d(aligned, aspect=FALSE)

LOST documentation built on July 4, 2024, 9:06 a.m.