align.angle: Align a subset of landmarks by rotation from one point

In aphanotus/borealis: Tools for reproducible geometric morphometric analysis

Align a subset of landmarks by rotation from one point

Description

Joints can introduce nuisance variation in landmark-based geometric morphometrics. This function rotates a subset of landmarks about a pivot point, such that all specimens will align to a designated reference specimen(s). This step should be run before Procrustes alignment, and it is robust to differences in the relative position, orientation and size of specimens.

Usage

align.angle(
  A,
  art.pt = NULL,
  angle.pts.1,
  angle.pts.2 = NULL,
  rot.pts = NULL,
  angle = 0,
  degrees = TRUE,
  reference.specimen = "all",
  show.plot = TRUE
)

Arguments

A	A 3-dimensional array containing XY shape coordinates for multiple specimens, or a list containing such as an array and data provenance.
art.pt	A number or numeric vector specifying the landmark that define the articulation point between the two landmark subsets.
angle.pts.1	A number or numeric vector of landmarks 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 number or numeric vector of landmarks specifying the angle point of the second subset. This could be the entire set of points of an articulated structure to be rotated. If angle.pts.2 = NULL, then all points other than angle.pts.1 and art.pt are used.
rot.pts	A vector containing numbers specifying which landmarks to rotate. 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 (degrees is the default).
reference.specimen	A number or numeric vector specifying which specimens should be taken as the reference for the angle defined by angle.pts.1, art.pt, and angle.pts.2 or provided in angle. The default is "all", which uses the mean angle of all specimens.
show.plot	A logical argument specifying whether to display a plot comparing the distributions of variance in landmark distances, corrected for centroid size, before and after alignment to the fixed angle.

Details

The input array should contain landmark coordinates with p, 2, and n dimensions, where n is the number of specimens and p is the number of landmarks). Dimension 2 must have two columns that contain X and Y locations of the landmark. The function will pass extra arguments to landmark.plot, including links. Plotting the landmarks can be useful to ensure that the reference specimen and pivot point result in sensible alignments.

Value

Returns a list with coords, provenance, and any other potential list elements from the input.

Source

Dave Angelini [e-mail] [aut, cre]

References

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

Examples

data("mantis", package = "borealis")

# Define mantis.lines
{
  x <- 1:16
  mantis.lines <- matrix(c(x[-length(x)],x[-1]), ncol = 2)
  mantis.lines[10,] <- c(10,1)
  mantis.lines[15,] <- c(15,6)
  mantis.lines <- rbind(mantis.lines,
                        matrix(c(5,11, 6,11, 13,16, 14,16), ncol = 2, byrow = TRUE))
}

# angle.pts.1, art.pt (the vertex), and angle.pts.2 define the angle to enforce
# rot.pts defines the landmarks to actually rotate
x <- align.angle(mantis,
                 art.pt = 11,
                 angle.pts.1 = 1:10,
                 angle.pts.2 = 12:15,
                 rot.pts = 12:16)

landmark.plot(mantis, specimen.number = 1:4, links = mantis.lines)
landmark.plot(x, specimen.number = 1:4, links = mantis.lines)

# By default the average of all specimens defines the reference angle
# However reference.specimen can specify one of more specimens to use.
x <- align.angle(mantis,
                 art.pt = 11,
                 angle.pts.1 = 1:10,
                 angle.pts.2 = 12:15,
                 rot.pts = 12:16,
                 reference.specimen = c(1,7) )

landmark.plot(x, specimen.number = 1:4, links = mantis.lines)

aphanotus/borealis documentation built on Nov. 4, 2022, 8:44 p.m.