geomorph (version 3.0.7)

fixed.angle: Rotate a subset of 2D landmarks to common articulation angle

Description

A function for rotating a subset of landmarks so that the articulation angle between subsets is constant

Usage

fixed.angle(A, art.pt = NULL, angle.pts = NULL, rot.pts = NULL,
  angle = 0, degrees = FALSE)

Arguments

A

A 3D array (p x k x n) containing landmark coordinates for a set of specimens

art.pt

A number specifying which landmark is the articulation point between the two landmark subsets

angle.pts

A vector containing numbers specifying which two points used to define the angle (one per subset)

rot.pts

A vector containing numbers specifying which landmarks are in the subset to be rotated

angle

An optional value specifying the additional amount by which the rotation should be augmented (in radians)

degrees

A logical value specifying whether the additional rotation angle is expressed in degrees or radians (radians is default)

Value

Function returns a (p x k x n) array of landmark coordinates.

Details

This function standardizes the angle between two subsets of landmarks for a set of specimens. The approach assumes a simple hinge-point articulation between the two subsets, and rotates all specimens such that the angle between landmark subsets is equal across specimens (see Adams 1999). As a default, the mean angle is used, though the user may specify an additional amount by which this may be augmented.

Presently, the function is only implemented for two-dimensional landmark data.

References

Adams, D. C. 1999. Methods for shape analysis of landmark data from articulated structures. Evolutionary Ecology Research. 1:959-970.

Examples

# NOT RUN {
#Example using Plethodon
#Articulation point is landmark 1, rotate mandibular landmarks (2-5) relative to cranium

data(plethspecies) 
fixed.angle(plethspecies$land,art.pt=1,angle.pts=c(5,6),rot.pts=c(2,3,4,5))
# }