R/ang.pdist.R

In Hong-Seungki/routine: The Clustering Methods on the Surface of Torus

#' Pairwise L2 angular distance
#'
#' \code{ang.pdist()} computes pairwise distances matrix.
#'
#' @param data n x d angular data on \eqn{[-\pi, \pi)^d}
#' @return \code{ang.pdist} returns an object of class \code{dist}.
#' @export
#' @examples
#' \dontrun{
#' data <- matrix(c(pi/3, -pi/3, pi/2,
#'                  -pi, -pi/4, pi/2,
#'                  0, -pi/3, -pi/6),
#'                ncol = 3, byrow = TRUE)
#'
#' ang.pdist(data)
#' }
ang.pdist <- function(data){
  # assuming that data are n x d angular data on [-pi,pi)^d
  # computes L2 angular distance

  n <- nrow(data)
  d <- ncol(data)
  pdistmat <- matrix(0, ncol = n, nrow = n)

  for (i in 1:n-1){
    ad <- 0
    for (dd in 1:d){
      ad <- ad + ( ang.dist(data[i,dd], data[(i+1):n, dd]) )^2
    }
    ad <- sqrt(ad)
    pdistmat[i, (i+1):n] <- ad
    pdistmat[(i+1):n, i] <- ad
  }
  as.dist(pdistmat)
}