[R] listing nodes in paths

[Federico Calboli]

Hi All,

I found a solution for my question:

> I have the following adjacency matrix for a directed graph:
>
>      [,1] [,2] [,3] [,4] [,5] [,6] [,7] [,8]
> [1,]    0    0    0    0    0    0    0    0
> [2,]    0    0    0    0    0    0    0    0
> [3,]    1    0    0    0    0    0    0    0
> [4,]    0    0    1    0    0    0    0    0
> [5,]    0    0    1    0    0    0    0    0
> [6,]    1    1    0    0    0    0    0    0
> [7,]    0    0    0    1    1    0    0    0
> [8,]    0    0    0    0    0    1    1    0
>
> My interest is the numberof path between (8) and (1). Using a  
> standard matrix moltiplication I can see I have one pathe of length  
> 2 and two paths of length 4.
>
> Is there already a function in R (whatever the library) that will  
> list the nodes touched in all those three paths (i.e. 8 -> 6 -> 1;  
> 8 -> 7 -> 4 -> 3 -> 1; 8 -> 7 -> 5 -> 3 -> 1)?

The function is an elaboration of 'findPath' in library 'ggm'. The  
original code was written in Python by Guido van Rossum and  
translated into R by Giovanni Marchetti... I translated the Python  
code for the list_all_paths in the same page:

http://www.python.org/doc/essays/graphs.html

The function is:

"paths" <- function (amat, st, en, path = c()){
   indices = 1:nrow(amat)
   if(st == en) # st is 'node' in recursive calls
     return(c(path, st))
   if(sum(amat[st,]) == 0 )
     return(NULL)
   paths = c()
   ne = indices[amat[st,]==1] # Boundary of x. Assumes that amat is  
symmetric
   for(node in ne){
     if(!is.element(node, c(path, st))){
       newpaths = paths(amat, node, en, c(path, st))
       for(newpath in newpaths){
         paths = c(paths,newpath)
       }
     }
   }
   return(paths)
}

and if I do:

 >paths(ad, 8, 1)
[1] 8 6 1 8 7 4 3 1 8 7 5 3 1

Which I can then slice to my heart content.

Best,

Federico

--
Federico C. F. Calboli
Department of Epidemiology and Public Health
Imperial College, St. Mary's Campus
Norfolk Place, London W2 1PG

Tel +44 (0)20 75941602   Fax +44 (0)20 75943193

f.calboli [.a.t] imperial.ac.uk
f.calboli [.a.t] gmail.com