R/disparityfilter.R

In FilipeamTeixeira/dispfilter: Disparity Filter for Weighted Networks

#' Disparity Filter
#'
#'
#' Uses the Serrano's disparity filter (\url{http://www.pnas.org/content/106/16/6483.full})
#' to extract the backbone of the network in "Extracting the multiscale backbone of complex weighted networks"
#'
#' @param g igraph object
#' @param alpha Alpha value. Default 0.003
#'
#' @examples
#' \dontrun{
#' dispfilter(g, alpha = 0.003)
#' }
#' @export
#'
#' @import igraph
#' @importFrom dplyr %>% left_join mutate select

dispfilter <- function(g, alpha = 0.003){

  if (igraph::has.multiple(g))
    stop("This disparity filter does not support yet multiple edges")
  if (is.null(V(g)$name)){
    g <- set_vertex_attr(g, "name", value = as.character(1:vcount(g)))
    }

  e <- cbind(igraph::as_data_frame(g)[, 1:2 ], weight = E(g)$weight)

  # in
  w_in <- graph.strength(g, mode = "in")
  w_in <- data.frame(to = names(w_in), w_in, stringsAsFactors = FALSE)
  k_in <- degree(g, mode = "in")
  k_in <- data.frame(to = names(k_in), k_in, stringsAsFactors = FALSE)

  e_in <- e %>%
    left_join(w_in, by = "to") %>%
    left_join(k_in, by = "to") %>%
    mutate(alpha_in = (1-(weight/w_in))^(k_in-1))

  # out

  w_out <- graph.strength(g, mode = "out")
  w_out <- data.frame(from = names(w_out), w_out, stringsAsFactors = FALSE)
  k_out <- degree(g, mode = "out")
  k_out <- data.frame(from = names(k_out), k_out, stringsAsFactors = FALSE)

  e_out <- e %>%
    left_join(w_out, by = "from") %>%
    left_join(k_out, by = "from") %>%
    mutate(alpha_out = (1-(weight/w_out))^(k_out-1))

  e_full <- left_join(e_in, e_out, by = c("from", "to", "weight"))

  e_full <- e_full %>%
    mutate(alpha = ifelse(alpha_in < alpha_out, alpha_in, alpha_out)) %>%
    select(from, to, alpha)

  E(g)$alpha <- e_full$alpha

  g <- delete.edges(g, which(E(g)$alpha >= alpha))
  g <- delete.vertices(g, which(degree(g) == 0))

  return(g)

weight <- alpha_in <- alpha_out <- from <- to <- NULL

}