R/getBackbone_function.R

Defines functions get.backbone

Documented in get.backbone

#' @title get.backbone
#'
#' @description This function extracts the backbone of a network
#' @param G igraph network
#' @param alpha Significance level
#' @param directed Default is TRUE
#' @export
#' @return Backbone of the network
#' @references Serrano, M. Á., Boguñá, M. and Vespignani, A. (2009) Extracting the multiscale backbone of complex weighted networks, Proceedings of the National Academy of Sciences, 106(16), pp. 6483–6488.
#' @examples
#' require(igraph)
#'
#' ##Create a random (directed) network
#' gs<-erdos.renyi.game(50,0.2,directed = TRUE)
#'
#' ##Add edge weights to the network
#' E(gs)$weight<-runif(ecount(gs), 0, 1)
#'
#' ##Extract backbone at 0.05 significance level
#' backbone<-get.backbone(gs,0.1)
#'

get.backbone<-function(G, alpha, directed = TRUE){
  # get edgelist
  edgelist<-igraph::get.data.frame(G)
  colnames(edgelist) <- c("from","to","weight")

  # get nodes list
  nodes<- unique(c(edgelist[,1], edgelist[,2]))
  N <-length(nodes)

  # initialize backbone dataframe
  backbone <-NULL

  cat("Disparity Filter\n")
  cat("alpha =", alpha, "\n")
  cat("\nOriginal graph\n")

  for (i in 1:N) # for each node
  {
    # get neighbors
    nei <- edgelist[edgelist$from == nodes[i],]
    nei <- rbind(nei, edgelist[edgelist$to == nodes[i],])

    # get degree for node i
    k_i <- length(edgelist$to[edgelist$to == nodes[i]]) + length(edgelist$to[edgelist$from == nodes[i]])

    if (k_i>1)
    {
      for (j in 1:k_i) # for each neighbor
      {
        # compute weighted edge
        p_ij <- as.numeric(nei$weight[j]) / sum(as.numeric(nei$weight))

        # VIA INTEGRATION
        #integrand_i = function(x){(1-x)^(k_i-2)}
        #integration = integrate(integrand_i, lower = 0, upper = p_ij)
        #alpha_ij = 1 - (k_i - 1) * integration$value

        alpha_ij <- (1 - p_ij)^(k_i - 1)

        if (alpha_ij < alpha)
        {
          backbone <- rbind(backbone, c(nei$from[j], nei$to[j], nei$weight[j]))
        }
      }
    }
  }

  colnames(backbone) <- c("from","to","weight")
  backbone <- unique(backbone[,c('from','to','weight')])
  G_backbone <- igraph::graph.data.frame(backbone, directed = directed)

  return(G_backbone)
}

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ITNr documentation built on May 2, 2019, 3:27 a.m.