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

In geomorphR/geomorph: Geometric Morphometric Analyses of 2D and 3D Landmark Data

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.1,
  angle.pts.2,
  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.1	A vector or single value specifying the angle point of one subset. If more that one value is provided, the centroid of the landmarks described by the vector will be used; a single value identifies a specific landmark to use.
angle.pts.2	A vector or single value specifying the angle point of the second subset. This could be the entire set of points of an articulated structure to be rotated.
rot.pts	A vector containing numbers specifying which landmarks are in the subset to be rotated. If NULL, it is assumed that the points to be rotated are the same as those in angle.pts.2.
angle	An optional value specifying the additional amount by which the rotation should be augmented (in radians). It might be essential to use a negative angle if centroids from multiple points are used for angle points. It should be clear if this is the case, upon plotting results.
degrees	A logical value specifying whether the additional rotation angle is expressed in degrees or radians (radians is default)

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. To quantify the angle, users may specify a single landmark in each subset as angle endpoints, or may specify a set of landmarks. If the latter, the centroid of those points is used.

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

Value

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

Author(s)

Dean Adams and Michael Collyer

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) 
# Using specific points:
newLM1 <- fixed.angle(plethspecies$land,
art.pt = 1, angle.pts.1 = 5, 
angle.pts.2 = 6, rot.pts = c(2,3,4,5))
Y.gpa1 <- gpagen(newLM1)
plot(Y.gpa1, mean = FALSE)

# Using centroids from subsets
newLM2 <- fixed.angle(plethspecies$land, art.pt = 1, 
angle.pts.1 = c(1, 6:11), 
angle.pts.2 = 2:5, 
rot.pts = NULL, angle = 20, 
degrees = TRUE) # rotated points same as second partition
Y.gpa2 <- gpagen(newLM2)
plot(Y.gpa2, mean = FALSE)

## End(Not run)

geomorphR/geomorph documentation built on April 18, 2024, 6:41 p.m.