R/NE_dn.R

In twesleyb/neten: R Implementation of Network Enhancement

#' NE_dn
#'
#' R implementation of Network Enhancement
#'
#' @param w - input weighted N x N adjacency matrix
#'
#' @param type - normalization method to be used, defaults to 'avg' for average (aka 'ave')
#'
#' @return normalized adjacency matrix
#'
#' @author Bo Wang, \href{https://github.com/wangboyunze}{github}
#' @author microbma, \href{https://github.com/microbma}{github}
#' @author Tyler Bradshaw, \href{https://github.com/twesleyb}{github}
#'
#' @references \href{https://bit.ly/2RS5pLX}{Wang, Pourshafeie, Zitnik, et al., 2018}

NE_dn <- function(w, type="avg") {
  eps <- 2e-16
  w <- w * Length(w)
  D <- rowSums(abs(w)) + eps
  if (type == "ave" | type == "avg") {
    D <- 1 / D
    D <- diag(D)
    wn <- D %*% w
  } else if (type == "gph") {
    D <- 1 / sqrt(D)
    D <- diag(D)
    wn <- D %*% w %*% D
  }
  return(wn)
}