Read pairwise network data into igraph, then do permutation.

#continental US demo, permutation of pariwse interaction network, igraph usage

require(RCurl)
URL = "https://docs.google.com/spreadsheet/pub?key=0ArLJZixvTlU7dDI5c3dnTzdRX1dndzBORUk1UC0wYlE&single=true&gid=0&output=csv"
states = read.csv(textConnection(getURL(URL)), colClass = c("character", "character"))

g = graph.data.frame(states, directed=F)
g.degree = degree(g)
g.degree [g.degree == max(g.degree)] #TN and MO have 8 bordering states

g.shortestpath.m = shortest.paths(g)
str(g.shortestpath.m)
sorted.names = sort( rownames(g.shortestpath.m) )
gsm = g.shortestpath.m[, sorted.names]
gsm = gsm[sorted.names, ]

URL2 = "https://docs.google.com/spreadsheet/pub?key=0ArLJZixvTlU7dC1rTlRhTkw5UlY0eWZGT1JOVUVCWGc&single=true&gid=0&output=csv"
state.year.tb = read.csv(textConnection(getURL(URL2)), colClass = c("character", NA))


permute.pairs.wo.selfpairs = function( inpairs,  ncycles=10, debug=1 ) {
  if (ncycles >= 1 ) {
    if(debug) {
      print(paste('ncycles=', ncycles))
    }
    longids = c(as.character(inpairs[,1]), as.character(inpairs[,2]) )
    longids = sample(longids)
    len = length(inpairs[,1])
    newpairs = data.frame( cbind( longids[1:len], longids[(len+1): (2*len)]) )
    names(newpairs) = c('id1', 'id2')
    newpairs$id1 = as.character( newpairs$id1)
    newpairs$id2 = as.character( newpairs$id2)   
    newpairs$selfpairs = ifelse( newpairs$id1 == newpairs$id2, 1, 0 )
    self.tb = newpairs[ newpairs$selfpairs==1, ]
    nonself.tb = newpairs[newpairs$selfpairs==0, ]
    if(debug) {
      print(self.tb)
    }
    if( length(self.tb[,1])>0 ) {
      if ( ncycles == 0) { return (c(NA,NA, NA) )
      } else {
        ncycles = ncycles - 1
        selectedpairs = rbind(self.tb,  nonself.tb[1: (length(self.tb[,1])*2), ] )
        restpairs = nonself.tb[ (length(self.tb[,1])*2+1): length(nonself.tb[,1]), ]
        return( rbind(restpairs, permute.pairs.wo.selfpairs(selectedpairs, ncycles)))
      }
    } else { 
      return (newpairs)
    }
  } else {
    return( c(NA,NA,NA ))
  }
}

#test
x = permute.pairs.wo.selfpairs(states)
x2 = permute.pairs.wo.selfpairs(states)