[igraph] igraph r-interface basic operators

[Florian Klinglmueller]

Hi,

I have been playing around with igraph lately and think that it is a great package as it adds tremendous functionality to R. However, I continually get into trouble with basic edge and vertex operations, especially, adding and removing edges. I have added some examples of confusion at the end of this mail and attached the code.

I think that there is a certain lack of consistency in how they operate, to the degree that I would consider it a bug. Maybe I'm just wrong in expecting that the examples given below should work in some consistent way. However, it makes it extremely difficult to decide whether a certain way  to operate on some elements of a graph (e.g. get all edges via E(G) or get.edges(G,...)) will work for a certain problem or not (e.g. add them to a graph via + or add.edges, ...) when writing code. A major problem that I see is that it is essentially unclear how to write iterators over the nodes or edges of an igraph object (without resorting to exporting to other classes (eg via get.edgelist)).

Best,

Florian

R 2.15.1> require(igraph)
Loading required package: igraph
R 2.15.1> # Consider the following graphs
R 2.15.1>
R 2.15.1> G4 <- graph.full(4)
R 2.15.1> G <-  minimum.spanning.tree(G4)
R 2.15.1> g <-  G4 - G
R 2.15.1>
R 2.15.1> G[]
Loading required package: Matrix
Loading required package: lattice
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . 1 1 1
[2,] 1 . . .
[3,] 1 . . .
[4,] 1 . . .
R 2.15.1> g[]
4 x 4 sparse Matrix of class "dgCMatrix"
           

[1,] . . . .

[2,] . . 1 1
[3,] . 1 . 1
[4,] . 1 1 .
R 2.15.1>
R 2.15.1> # now here comes what confuses me
R 2.15.1>
R 2.15.1> for(e in E(G))
+   print(delete.edges(G,e)[])
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . . 1 1
[2,] . . . .
[3,] 1 . . .
[4,] 1 . . .
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . 1 . 1
[2,] 1 . . .
[3,] . . . .
[4,] 1 . . .
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . 1 1 .
[2,] 1 . . .
[3,] 1 . . .
[4,] . . . .
R 2.15.1>
R 2.15.1> # works
R 2.15.1>
R 2.15.1> for(e in E(G))
+   print(add.edges(g,e)[])
Error in print(add.edges(g, e)[]) :
  error in evaluating the argument 'x' in selecting a method for function 'print': Error in add.edges(g, e) :
  At type_indexededgelist.c:269 : invalid (odd) length of edges vector, Invalid edge vector
R 2.15.1>
R 2.15.1> # gives an error
R 2.15.1>
R 2.15.1> # next
R 2.15.1> e <- E(G)[1]
R 2.15.1> E <- get.edge(G,1)
R 2.15.1>
R 2.15.1> delete.edges(G,e)[]
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . . 1 1
[2,] . . . .
[3,] 1 . . .
[4,] 1 . . .
R 2.15.1> # removes one edge
R 2.15.1>
R 2.15.1> delete.edges(G,E)[]
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . . . 1
[2,] . . . .
[3,] . . . .
[4,] 1 . . .
R 2.15.1> # removes two edges
R 2.15.1>
R 2.15.1> (G - e)[]
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . . 1 1
[2,] . . . .
[3,] 1 . . .
[4,] 1 . . .
R 2.15.1> # works
R 2.15.1>
R 2.15.1> (G - E)[]
2 x 2 sparse Matrix of class "dgCMatrix"
       
[1,] . .
[2,] . .
R 2.15.1> # empty graph with 2 nodes
R 2.15.1>
R 2.15.1> add.edges(g,e)
Error in add.edges(g, e) :
  At type_indexededgelist.c:269 : invalid (odd) length of edges vector, Invalid edge vector
R 2.15.1> # error messag
R 2.15.1>
R 2.15.1> add.edges(g,E)[]
4 x 4 sparse Matrix of class "dgCMatrix"
           
[1,] . 1 . .
[2,] 1 . 1 1
[3,] . 1 . 1
[4,] . 1 1 .
R 2.15.1> # works
R 2.15.1>
R 2.15.1> g + E
Error in `+.igraph`(g, E) : Cannot add unknown type to igraph graph
R 2.15.1> # error
R 2.15.1>
R 2.15.1> (g + e)[]
5 x 5 sparse Matrix of class "dgCMatrix"
             
[1,] . . . . .
[2,] . . 1 1 .
[3,] . 1 . 1 .
[4,] . 1 1 . .
[5,] . . . . .
R 2.15.1> # adds a node ???
R 2.15.1>

bug.R
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