# File NetStatsTest.R
# Purpose: Open a file
#          Read contents of a NN matrix (counts)
#          Calculate Network statistics
#			Density
#			Bewteenness
#			Centralization (various)
#			Closeness
#			Degree
# Date: June 29, 2006
#       modified July 5th, 2006

# Author: Cuau Vital
# 	

#opens up libraries neede to run the script
library(igraph)
library(sna)


#read all files in the given directory
#change tempMyDir as needed
myfiles <-list.files("c:/tempMyDir")

#create table, that will display results
bigMatrix <- matrix(c(0, 0), nrow=12, ncol=100)
i <- 0

# loop through files
for(f in myfiles[-1]) {
 
  i=i+1
  #modify C:/tempMyDir for your own path
  c <- paste("c:/tempMyDir/", f, sep="") 

  #read file, read it as table
  netMatW <- read.table( c, sep="\t" )
  # change it into a matrix form
  netMatW <-as.matrix(netMatW)
  # dichotomize into 0's and 1's
  netMat <- event2dichot(netMatW, "absolute", 0)
  # create a graph to work with igraph libraries
  g1 <-graph.adjacency(netMat, mode="undirected")


  #calculate stats using sna library
  gden(netMat)->density
  centralization(netMat, degree) -> Gdegree
  centralization(netMat, betweenness) -> Gbetweenness
  centralization(netMat, mode="graph", closeness) -> Gcloseness 
  degree(netMatW, cmode="indegree") ->deg
  range(deg) ->rgDegree
  closeness(netMat) ->close
  range(close) ->rgCloseness
  betweenness(netMat) -> bc
  bc <- bc/342
  range(bc) ->rgBC

  #use Information Centrality from igraph library
  infocent(netMatW, gmode=graph) ->inforC
  centralization(netMatW, infocent) ->Ginfo
  var(inforC) ->varInfo

  geodist(netMat)->dist
  max(dist$gdist)->diam 
  transitivity(g1) ->trans

  #write output into a table 
  bigMatrix[1,i]<-density
  bigMatrix[2,i]<- trans
  bigMatrix[3,i]<- Gdegree 
  bigMatrix[4,i] <- Gbetweenness
  bigMatrix[5,i]<- Gcloseness
  bigMatrix[6,i] <- Ginfo 
  bigMatrix[7,i]<-  varInfo
  
  bigMatrix[8,i]<- diam
  bigMatrix[9,i] <- mean(deg) 
  bigMatrix[10,i] <- mean(bc)  
  bigMatrix[11,i] <- mean(close)
  bigMatrix[12,i]<- mean(inforC)
 
 }
# format table
out <- file("c:/tempMyDir/NetStatsOut.xls", "w")
cat("Network Measures\n", file=out)
cat("\n", file =out)
cat("Dn\tT\tC_D\tC_B\tC_C\tC_I\tS2_I\tDi\tµ C_D(ni)\tµ C_B(ni)\tµ C_C(ni)\tµ C_I(ni)\n", file=out)

#write table into file NetStatsOut.xls
write(bigMatrix, out, ncolumns=12, sep="\t")
close(out)