Networks / Pajek
Package for Large Network Analysis

How to
analyse networks and vectors sent from Pajek to program R

Suppose, that vectors v1, v2, v3 and networks n1, n2, n3 were sent from Pajek to R. In the following some simple commands in R using these vectors and networks (matrices) are listed.

Vector operations

v1+v2
vsum <- v1+v2
v1sq <- v1^2
a <- sqrt(v1*v2)
...

Basic statistics

var - variance, cov - covariance, cor - correlation 
 sum(v1)
 length(v1)
 mean(v1)
 summary(v1)
 var(v1)
 cov(v1,v2)
 cor(v1,v2)

Graphics (charts)

 plot(v1)
 plot(v1,v2)
 boxplot(v1,v2)
 hist(v1)
if vector values are integers, (e.g. from interval 1..10) it is sometimes better to provide breaks among classes: 
 hist(v1,br=0:10)
or 
 hist(v1, br=-1:10)

Exporting graphics

to pdf file 
 pdf("c:/temp/test.pdf")
 hist(v1)
 dev.off()
to ps file 
 postscript("c:/temp/test.ps")
 hist(v1)
 dev.off()
to windows meta file 
> win.metafile("c:/temp/test.wmf")
> hist(v1)
> dev.off()

Bivariate and multivariate analysis

  • cross-tabulation 
     table(v1,v2)
    to get chi-square test 
     tabl <- table(v1,v2)
 summary(tabl)
  • comparing means (t-test) 
     t.test(v1,v2)
  • comparing variances 
     var.test(v1, v2)
  • regression
    linear model 
    linm <- lm(v1 ~ v2)
summary(linm)
    with more variables 
    linm <- lm(v1 ~ v2 + v3)
summary(linm)
    nonlinear regression 
    nlm <- lm(v1 ~ v2 + v3^2)
summary(linm)

Saving vector from R to Pajek input file 

savevector <- function(v,direct){
  write(c(paste("*Vertices",length(v)),v),file=direct,ncolumns=1)}
Sample call 
savevector(v1,"c:/temp/test.vec")

Loading vector(s) to R from Pajek input file 

loadvector <- function(direct){
  vv<-read.table(file=direct,skip=1)
  if (dim(vv)[2]==1)
     vv<-vv[[1]]
  vv
  }
Sample call 
 v9<-loadvector("c:/temp/test.vec")
If there is only one vector in test.vec, result is vector v9 otherwise first vector is v9[[1]], second v9[[2]],...

Matrix operations

  • Transpose network 
    t(n1)
  • Eigenvalues/eigenvectors 
    eigen(n1)
  • Hubs and authorities 
     hubs <- eigen(n1 %*% t(n1)) $ vec[,1]
 auth <- eigen(t(n1) %*% n1) $ vec[,1]
  • function that saves ordinary or 2-mode matrix from R to Pajek input file (*Matrix) 
    savematrix <- function(n,direct,twomode=1){
    if ((dim(n)[1] == dim(n)[2]) & (twomode!=2))
      { write(paste("*Vertices",dim(n)[1]), file = direct);
            write(paste(seq(1,length=dim(n)[1]),' "',rownames(n),
                  '"',sep=""), file = direct,append=TRUE);
            write("*Matrix", file = direct,append=TRUE);
            write(t(n),file = direct,ncolumns=dim(n)[1],
                  append=TRUE) }
    else
      { write(paste("*Vertices",sum(dim(n)),dim(n)[1]),
              file = direct);
            write(paste(1:dim(n)[1],' "',rownames(n),'"',sep=""),
                  file = direct,append=TRUE);
            write(paste(seq(dim(n)[1]+1,length=dim(n)[2]),' "',
                  colnames(n),'"',sep=""), file = direct,append=TRUE);
            write("*Matrix", file = direct, append=TRUE);
            write(t(n),file = direct, ncolumns=dim(n)[2],append=TRUE)}
      }
    Sample call 
    savematrix(n1,"c:/temp/test.mat")
    To request a 2-mode matrix (in the case that number of rows and columns is the same): 
    savematrix(n1,"c:/temp/test.mat",2)
  • function that saves ordinary or 2-mode matrix from R to Pajek input file (*Arcs, *Edges) 
    savenetwork <- function(n,direct,twomode=1){
   if ((dim(n)[1] == dim(n)[2]) & (twomode!=2)) {
      write(paste("*Vertices",dim(n)[1]), file = direct);
      write(paste(seq(1,length=dim(n)[1]),' "',rownames(n),
            '"',sep=""), file = direct,append=TRUE);
      write("*Arcs", file = direct,append=TRUE);
      for (i in 1:dim(n)[1]) {
        for (j in 1:dim(n)[2]) {
          if (n[i,j]!=0) {write(paste(i,j,n[i,j]),
             file = direct,append=TRUE)}
        }
      }
   } else {
      write(paste("*Vertices",sum(dim(n)),dim(n)[1]),
        file = direct);
      write(paste(1:dim(n)[1],' "',rownames(n),'"',sep=""),
            file = direct,append=TRUE);
      write(paste(seq(dim(n)[1]+1,length=dim(n)[2]),' "',
            colnames(n),'"',sep=""), file = direct,append=TRUE);
      write("*Edges", file = direct, append=TRUE);
      for (i in 1:dim(n)[1]) {
        for (j in 1:dim(n)[2]) {
          if (n[i,j]!=0) {write(paste(i,j+dim(n)[1],n[i,j]),
             file = direct,append=TRUE)}
        }
      }
   }
}
    Sample call 
    savenetwork(n1,"c:/temp/test.mat")
    To request a 2-mode network (in the case that number of rows and columns is the same): 
    savenetwork(n1,"c:/temp/test.mat",2)
  • function that loads ordinary or 2-mode matrix to R from Pajek input file (*Matrix) 
    loadmatrix <- function(direct){
  nn<-read.table(file=direct,nrows=1)
  if (length(nn) == 2)
    { xx<-read.table(file=direct,skip=1,nrows=nn[[2]],fill=TRUE)
      n<-read.table(file=direct,skip=nn[[2]]+2)
      rownames(n)<-xx[[2]]
      colnames(n)<-xx[[2]] }
  else
    {xxrow<-read.table(file=direct,skip=1,nrows=nn[[3]],fill=TRUE)
     xxcol<-read.table(file=direct,skip=nn[[3]]+1,
                       nrows=nn[[2]]-nn[[3]],fill=TRUE)
     n<-read.table(file=direct,skip=nn[[2]]+2)
     rownames(n)<-xxrow[[2]]
     colnames(n)<-xxcol[[2]] }
  as.matrix(n)
  }
    Sample call 
    n9<-loadmatrix("c:/temp/test.mat")
How to?; Pajek; Vlado/Networks