Re: [igraph] clustering coefficient in bipartite network

[Gábor Csárdi]

Hi Simone,

the latest is from last week,
http://code.google.com/p/igraph/downloads/detail?name=igraph_nightly_0.6-2221-20101122.tar.gz

But be careful, because this one has the one-based indexing already.
Alternatively I can rewrite the code to work with 0.5.

Gabor

On Sat, Nov 27, 2010 at 11:31 AM, Simone Gabbriellini
<address@hidden> wrote:
> Hi Gabor,
>
> thanks again for this piece of code...
>
> I have to admit I am still trying to figure out what this function does in 
> the details, because of my lack of R expertise... so many things are unclear 
> but I am going to figure them out... ;)
>
> the only thing I can say now is that I have this error:
>
>> ccBip(g)
> Errore in E(x)[subs]$weight/mapply(f, neib[el[subs, 1]], neib[el[subs,  :
>        non-numeric argument transformed in binary operator
>
> my version of igraph is, I guess, the last nightly source, 
> igraph_nightly_0.6-2030-20100726.tar.gz
>
> best,
> Simone
>
>
> Il giorno 27/nov/2010, alle ore 00.30, Gábor Csárdi ha scritto:
>
>> Hi Simone,
>>
>> On Fri, Nov 26, 2010 at 12:10 PM, Simone Gabbriellini
>> <address@hidden> wrote:
>>> HI Gabor,
>>>
>>> thanks very much, yes that is the right direction for me!
>>>
>>> what I have to reproduce is, according to Latapy:
>>>
>>> for each bottom node v:
>>>        for each bottom node u, 2-dist-neighbor of v:
>>>                 find the number of (shared top nodes of u and v) / (total 
>>> top nodes neighbors of u AND v)
>>
>> ccBip <- function(g) {
>>  if (! "name" %in% list.vertex.attributes(g)) {
>>    V(g)$name <- seq_len(vcount(g))
>>  }
>>  neib <- get.adjlist(g)
>>  names(neib) <- V(g)$name
>>  proj <- bipartite.projection(g)
>>  lapply(proj, function(x) {
>>    el <- get.edgelist(x)
>>    sapply(V(x)$name, function(v) {
>>      subs <- el[,1]==v | el[,2]==v
>>      f <- function(un, vn) length(union(un, vn))
>>      vals <- E(x)[subs]$weight /
>>        mapply(f, neib[el[subs,1]], neib[el[subs,2]])
>>      mean(vals)
>>    })
>>  })
>> }
>>
>> I think this does exactly what you want, assuming I understood the
>> definition correctly. I have only tested it with igraph 0.6, for which
>> the nightly builds are available again at
>> http://code.google.com/p/igraph/downloads/list
>>
>> Please tell me if something is not clear.
>>
>> Best,
>> Gabor
>>
>>> then to find the local clustering of v, I have to average the list of 
>>> values obtained.
>>>
>>> and conversely for top nodes... it's a bit tricky for me with R...
>>>
>>> thanks a lot,
>>> simone
>>>
>>> Il giorno 26/nov/2010, alle ore 11.34, Gábor Csárdi ha scritto:
>>>
>>>> Hi Simone,
>>>>
>>>> a couple of comments.
>>>>
>>>> On Thu, Nov 25, 2010 at 5:22 PM, Simone Gabbriellini
>>>> <address@hidden> wrote:
>>>>> Hello List,
>>>>>
>>>>> I am trying to reproduce the clustering measures detailed in Latapy et 
>>>>> al. Social Networks, 30 (2008).
>>>>>
>>>>> I attempted successfully to reproduce the ccN(G) clustering, which is 
>>>>> basically an extension for bipartite networks of the global transitivity 
>>>>> measure.
>>>>>
>>>>> I am stuck with the cc. measure of clustering coefficient, an extension 
>>>>> of local transitivity for bipartite network - a reprise of what Borgatti 
>>>>> and Everett have already suggested in 1997.
>>>>>
>>>>> I have to find, for each distance-2 neighbors of a node (which are still 
>>>>> nodes of the same set), how many nodes of the other set they have in 
>>>>> common.
>>>>>
>>>>> This is not all of what is needed to implement this measure, but it would 
>>>>> be a great step for me...
>>>>>
>>>>> In order to find distance-2 neighbors for each node, I can use a 
>>>>> partition, as Tamas suggested in a previous thread.
>>>>>
>>>>> V(g)[type==FALSE]$neibi<-neighborhood(bipartite.projection(g)[[1]], 1)
>>>>>
>>>>> V(g)[type==TRUE]$neibi<-neighborhood(bipartite.projection(g)[[2]], 1)
>>>>
>>>> it is actually better to use vertex names to be sure that you assign
>>>> the second neighbors to the right vertices. While your solution works
>>>> if the order of the vertices is kept in the projections, this is not
>>>> documented for bipartite.projection, so you cannot take it for
>>>> granted.
>>>>
>>>> Anyway, I think an easier way to get the second neighbors is to simply
>>>> subtract the 1-neighborhood from the 1-2-neighborhood, this works for
>>>> bipartite graphs.
>>>>
>>>> nei12 <- neighborhood(g, 2)
>>>> nei1 <- neighborhood(g, 1)
>>>> nei2 <- mapply(setdiff, nei12, nei1)
>>>>
>>>>> While in order to find neighbors in the bipartite, I can simply use:
>>>>>
>>>>> V(g)$nei<-neighborhood(g, 1)
>>>>>
>>>>> now, how can I confront a node with every nodes listed in its neibi 
>>>>> attribute in order to find if there are duplicates in each nei 
>>>>> attributes? this is the hardest part I cannot solve.
>>>>
>>>> If you have two numeric or character vectors, 'v1' and 'v2', then
>>>> 'intersection(v1, v2)' treats them as sets and gives a vector that is
>>>> their intersection. Is this what you need?
>>>>
>>>> G.
>>>>
>>>>> any help more than welcome!
>>>>>
>>>>> thanks in advance,
>>>>> Simone
>>>>> _______________________________________________
>>>>> igraph-help mailing list
>>>>> address@hidden
>>>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Gabor Csardi <address@hidden>     UNIL DGM
>>>>
>>>> _______________________________________________
>>>> igraph-help mailing list
>>>> address@hidden
>>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>>
>>> _______________________________________________
>>> igraph-help mailing list
>>> address@hidden
>>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>>>
>>
>>
>>
>> --
>> Gabor Csardi <address@hidden>     UNIL DGM
>>
>> _______________________________________________
>> igraph-help mailing list
>> address@hidden
>> http://lists.nongnu.org/mailman/listinfo/igraph-help
>
>
> _______________________________________________
> igraph-help mailing list
> address@hidden
> http://lists.nongnu.org/mailman/listinfo/igraph-help
>



-- 
Gabor Csardi <address@hidden>     UNIL DGM