[Top][All Lists]

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [igraph] Walktrap / Community / Modularity

From: Amanda Schierz
Subject: Re: [igraph] Walktrap / Community / Modularity
Date: Tue, 17 Jul 2012 16:32:04 +0100
User-agent: Microsoft-MacOutlook/

Just letting you know I applied this code successfully. I had to make a
slight amendment as igraph starts numbering from 0 (this effects the
contents of the adjlist) so I have added 1 to the adjlist contents before
doing the match,

sapply(1:vcount(g), function(v) { sum(membership[adjlist[[v]]+1] ==
membership[v]) / length(adjlist[[v]]) })

Many thanks

On 06/07/2012 14:40, "Tamás Nepusz" <address@hidden> wrote:

>> Thanks for your reply. Do you know if there is a way I can calculate
>>vertex modularity? I want to know how modular a vertex is - ie. does its
>>edges stay within the community or cross communities - is it a hub of
>>the community or is it the community/rest of graph communicator.
>I am not aware of any formal definition for "vertex modularity", but an
>informal measure that some people have used is to count what fraction of
>the edges incident on the vertex stay inside the community. This can be
>calculated relatively easily.
>Suppose that you have a membership vector called "membership", and your
>graph is in "g". Then first we get the adjacency list of the graph:
>adjlist <- get.adjlist(g)
>and then apply the following (pretty convoluted) expression:
>sapply(1:vcount(g), function(v) { sum(membership[adjlist[[v]]] ==
>membership[v]) / length(adjlist[[v]]) })
>Let's dissect the above expression a bit. sapply() takes two arguments;
>the first is a list, the second is a function. sapply() will call the
>function with each element of the list and store the values in a vector.
>The list we pass here is simply the list of vertex identifiers (from 1 to
>the number of vertices), and the function itself calculates the "vertex
>modularity" for a single vertex. In the function, we do the following.
>First, we take the neighbors of vertex v by calling adjlist[[v]] (note
>the double brackets), then fetch the community ids for each vertex:
>Then we compare each element of this vector with the community id of v
>membership[adjlist[[v]]] == membership[v]
>The result is a binary vector where TRUE means that a given neighbor is
>in the same community as v itself and FALSE means that it is not.
>Applying sum() to this vector gives us the number of neighbors that are
>in the same community as v, and dividing it by the number of neighbors
>gives us the number you are looking for.
>igraph-help mailing list

The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company 
Limited by Guarantee, Registered in England under Company No. 534147 with its 
Registered Office at 123 Old Brompton Road, London SW7 3RP.

This e-mail message is confidential and for use by the addressee only.  If the 
message is received by anyone other than the addressee, please return the 
message to the sender by replying to it and then delete the message from your 
computer and network.

reply via email to

[Prev in Thread] Current Thread [Next in Thread]