Calculate covariance matrix between individual landmark coordinates

Description

Calculate covariance matrix between individual landmark coordinates. Skips any missing values in computation of covariance matrix.

Usage

1
covar(A)

Arguments

A

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

Details

This function does not guarantee that the returned matrix is positive definite. If the covariance matrix is not positive definite a warning is given and the matrix can be bent to create the closest positive definite matrix with as.matrix(Matrix::nearPD(mat)$mat).

Value

3N x 3N covariance matrix

Examples

1
2
A <- array(rnorm(4 * 2 * 3), dim = c(2, 3, 4)) 
A.cov <- covar(A)