R/metric.distance.effdia.R

Defines functions metric.distance.effdia

Documented in metric.distance.effdia

#' Effective Diameter
#'
#' @description Calculate the effective diameter of a graph.
#' @param Network The input network.
#' @param probability The confidence level probability
#' @param error The sampling error
#' @param effective_rate The effective rate (by default it is set to be 0.9)
#' @param Cores Number of cores to use in the computations. By default uses \emph{parallel} function \code{detecCores()}.
#' @param full It will calculate the popular full version by default.
#' If it is set to FALSE, the estimated diameter will be calculated.
#' @details The diameter is the largest shortest path lengths of all pairs of nodes in
#' graph \emph{Network}. \code{metric.distance.diameter} calculates the (estimated)
#' diameter of graph \emph{Network} with a justified error.
#' @return A real value.
#' @author Luis Castro, Nazrul Shaikh.
#' @examples \dontrun{
#' ##Default function
#' x <-  net.erdos.renyi.gnp(1000,0.01)
#' metric.distance.effdia(x)
#' ##Population APL
#' metric.distance.effdia(x, full=TRUE)
#' ##Sampling at 99% level with an error of 10% using 5 cores
#' metric.distance.effdia(Network = x, probability=0.99, error=0.1, Cores=5)
#'}
#'
#' @import parallel
#' @import doParallel
#' @import foreach
#' @export
#' @references Dijkstra EW. A note on two problems in connexion with
#' graphs:(numerische mathematik, _1 (1959), p 269-271). 1959.
#' @references Castro L, Shaikh N. Estimation of Average Path Lengths of Social
#' Networks via Random Node Pair Sampling. Department of Industrial Engineering, University of Miami. 2016.

metric.distance.effdia <-  function(Network,probability=0.95, error=0.03, effective_rate=0.9,
                                      Cores=detectCores(), full=TRUE){
  if (!is.list(Network)) stop("Parameter 'Network' must be a list", call. = FALSE)
  if (probability>=1 | probability<=0) stop("Parameter 'probability' must be in (0,1)", call. = FALSE)
  if (error>=1 | error<=0) stop("Parameter 'error' must be in (0,1)", call. = FALSE)
  if (Cores <= 0 | Cores > detectCores() | Cores%%1!=0) stop("Parameter 'Cores' must be a positive integer greater than one and less than available cores", call. = FALSE)
  if (!is.logical(full)) stop("Parameter 'full' must be logical", call. = FALSE)
  if (0 %in% lengths(Network)) stop("The network object contains isolated nodes", call = FALSE)

  ##//Inner function SPL by edeges

  Shortest.path.big <- function(matrix.edges,network){

    ##Parameters
    #matrix.edges <- edges by rows, first element source, second element destination - for apply use!!
    #network in list representation


    Shortest.path.int <- function(edge,Network){

      ##//Parameters
      #orig  - source node
      #dest  - final destination node
      #Network - egocentric representation of the network

      ##Computation
      sp <- 1
      r1 <- 0
      #edge <- unlist(edge)
      orig <- edge[1]
      dest <- edge[2]



      ##Correcting same origen and destination
      if (orig==dest){
        #print("Si")
        x <- setdiff(seq(length(Network)),orig)
        #print(length(x))
        dest <- sample(x,1)
        #print(dest)
      }


      ##Loop of SP
      while (r1==0){

        if (sp==1){
          neig <- unlist(Network[orig])
          r1 <- which(neig==dest)
          r1 <- length(r1)
        }

        if (r1==0){
          neig <- unlist(Network[neig])
          r1 <- which(neig==dest)
          r1 <- length(r1)
          sp <- sp+1
        }
      }
      sp
    }

    output <- apply(matrix.edges,1,Shortest.path.int,Network=network)
    #output <- lapply(list.edges,Shortest.path.int,Network=network)

    output

  }


  ##//Sample nodes

  #Get 1000 of SP for st dev calculation for sampling
  N <- length(Network)
  #s <- round(min(N*(N-1)*0.001)/Cores,N)*Cores
  s <- round(1000/Cores)*Cores
  x= array(seq(N))
  S1 <- matrix(nrow=s,ncol=2)
  s1 <- sample(x,s,replace=TRUE); S1[,1] <- s1
  s1 <- sample(x,s,replace=TRUE); S1[,2] <- s1
  s1 <- c(seq(1,length(s1),length(s1)/Cores),length(s1)+1)
  S <- list()
  for (i in 1:(length(s1)-1)){
    S[[i]] <- S1[s1[i]:(s1[i+1]-1),]
  }
  cl <- makeCluster(Cores)
  registerDoParallel(cl, cores = Cores)
  v <- parLapply(cl=cl,S,Shortest.path.big,network=Network)
  stopCluster(cl)
  v <- stats::sd(unlist(v))

  #Final sample size

  #/Sample
  if (full==FALSE){
    d <- 1-probability
    Z <- stats::qnorm(1-d/2)
    s <- round((min(N,(Z*v/error)**2)/Cores))*Cores
    #print(s)
    #print(N)
    #print(length(x))
    S1 <- matrix(nrow=s,ncol=2)
    s1 <- sample(x,s,replace=TRUE); S1[,1] <- s1
    s1 <- sample(x,s,replace=TRUE); S1[,2] <- s1
    s1 <- c(seq(1,length(s1),length(s1)/Cores),length(s1)+1)
    S <- list()
    for (i in 1:(length(s1)-1)){
      S[[i]] <- S1[s1[i]:(s1[i+1]-1),]
    }
  }

  #/Full
  if (full==TRUE){
    s <- round((N/Cores))*Cores
    #print(s)
    #print(N)
    #print(length(x))
    S1 <- matrix(nrow=s,ncol=2)
    s1 <- sample(x,s,replace=FALSE); S1[,1] <- s1
    s1 <- sample(x,s,replace=FALSE); S1[,2] <- s1
    s1 <- c(seq(1,length(s1),length(s1)/Cores),length(s1)+1)
    S <- list()
    for (i in 1:(length(s1)-1)){
      S[[i]] <- S1[s1[i]:(s1[i+1]-1),]
    }
  }

  ##/Parallel processing
  cl <- makeCluster(Cores)
  registerDoParallel(cl, cores = Cores)
  Paths <- parLapply(cl=cl,S,Shortest.path.big,network=Network)
  stopCluster(cl)

  ##/Calculate Diameter
  Paths <- stats::quantile(unlist(Paths),effective_rate)[[1]]
  ##/Return final output
  return(Paths)

}
networkgroupR/fastnet documentation built on June 6, 2017, 10:20 a.m.