mirrorfill {paleomorph}

Fill missing symmetrical landmarks for all specimens in an array using mirrored values from other side of a bilaterally symmetrical object where present

Description

Given an N x 3 x M matrix, where N is the number of landmarks, 3 is the number of dimensions, and M is the number of specimens, fill in missing landmarks using their mirrored counterpart.

Usage

mirrorfill(A, l1, l2)

Arguments

A

An N x 3 x M matrix where N is the number of landmarks, 3 is the number of dimensions, and M is the number of specimens.

l1

Vector of indices for which landmarks to use to make a specimen midline

l2

Vector or matrix of pairs of symmetrical landmarks

Details

l2 should be either

• An even length vector containing pairs of landmarks on either side of the specimen. i.e. l2[1] and l2[2] are paired, l2[3] and l2[4] are paired etc.

• A two column matrix with each row giving a pair of symmetrical landmarks.

l2 should be an even number length containing pairs of landmarks on either side of the specimen.

Examples

 # Create array
 A <- array(rep(1:36, by = 4), dim = c(12, 3, 4))

 # Make it symmetrical
 A[7:12, 1:2, ] <- A[1:6, 1:2, ]
 A[7:12, 3, ] <- -A[1:6, 3, ]

 # Remove some data points
 missinga <- A
 missinga[1:2, , 1:3] <- NA

 mirrorA <- mirrorfill(missinga, l1 = c(3:6, 9:12), l2 = c(1, 7, 2, 8))