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Hi all i want to generate 3D geometric random graph in r. In igraph there is no function of generating the graph in 3D. In 3D geometric random graph i found the euclidean distance between of the uniformly distributed points in 3D space and considered an edge if the distance is less than or equal to some threshold. Tried the following.

 ##Code to generate random geometric graph in 3D
    ##To generate geometric random graph in 3D I have placed points in 3D space in uniform distribution the number of points placed in 3D space would be equal to N= total number of nodes.

    ##function to calculate euclidean distance of the random points placed in 3D
    get.dist = function(x)
    {
      sqrt(x[1]^2 + x[2]^2)
    }

    ##Generate matrix with total number of possible edges N(N-1)/2 
    get.pairs = function(N)
    {
      M = matrix(0, nrow = N * (N - 1)/2, ncol = 2)
      x = 1:N
      k = 1

      for (i in head(x, -1))
      {
        for (j in (i + 1):(length(x)))
        {
          M[k, ] = c(i, j)
          k = k +1
        }
      }
      M
    }
    ##Create a graph object and associate calculated euclidien distance to   each pair of edge
    create.graph = function(N = 100, d = 0.3)
    {
      ##random points in 3D with uniform distribution
      rnd.points = matrix(runif(3 * N), ncol = 3)
      perms = get.pairs(N)

       ###Caculate the difference between the points to calculate euclidien   distance between each pair
      Edges = apply(perms, 1, FUN = function(x){
        vec.diff = rnd.points[x[1], ] - rnd.points[x[2], ]
        get.dist(vec.diff)
      })

      res = cbind(Edges, perms)
      colnames(res) = c('E', 'V1', 'V2')
      list(M = res, N = N, d = d, pts = rnd.points)  
    }

Now I have achieved M with all the associated distance value. 

##Create graph with provided number of nodes and threshold
cg <- create.graph(10,0.5)
mat <- cg$M

Now I will fetch only those from matrix mat's column E which are less than or equal to provided threshold which is here 0.5. And that would be my final graph object.

nd[nd[, 'E'] <= 0.5,]

Is it a proper way of generation of geometric graph in 3D.?

seema aswani
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    A proper way of doing .... "it"? Unfortunately you have not described what _it_ is with anything other than uncommented code so it's going to be difficult if not impossible to make any suggestions. – IRTFM May 31 '16 at 17:29
  • @42- I have added comments and description of each and every function. Please provide some light. This is what geometric graphs stand for. [link](https://en.wikipedia.org/wiki/Random_geometric_graph) – seema aswani May 31 '16 at 18:39
  • @42- Can you provide some suggestions whether code is right or not. – seema aswani May 31 '16 at 19:32
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    The method you used appears to implement the definition in your Wikipedia link. – IRTFM May 31 '16 at 19:51

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