Re: [igraph] closeness and average path length in terms of the harmonic distance between vertices

[Bob Pap]

Many thanks, dear Tamás.

On 7 March 2013 12:22, Tamás Nepusz <address@hidden> wrote:

Hi Bob,

> Sorry I only come back to you only now.  shortest.paths does not seem to indicate the vertices that have been traversed in the shortest paths - just a matrix of those shortest paths.

Yup, but you can use get.shortest.paths() to get _one_ shortest path per vertex pair, or get.all.shortest.paths() to get _all_ possible shortest paths between vertices. Of course the output of the latter function can be huge, especially if the graph has a regular structure (like a lattice) and there are many shortest paths between the same pair of vertices.

> Having looked at closeness(), is seems that closeness is currently done as:
> res <- .Call("R_igraph_closeness", graph, vids - 1, mode,  weights, PACKAGE = "igraph")
>
> How do I learn more of what is being done by this function? Many thanks.

It goes down to the C core of igraph, where it eventually ends up in a function named igraph_closeness:

http://igraph.sourceforge.net/doc/html/ch13s06.html#igraph_closeness

The source code is here:

https://github.com/igraph/igraph/blob/master/src/centrality.c#L2565

However, this function requires extensive knowledge of the C layer of igraph, so I don't know how useful it will be to you in the end. It boils down to doing a breadth first search on the graph and recording the distances in a vector.

--
T.

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Kindly,

Bob Pap