[igraph] Using external software for community detection in R

[Fabio Daolio]

First of all, thanks again for the great work on the library.

I'd like to share with you what I'm doing: possibly there's a
better way to do it, maybe this could be useful to somebody
else.
I need to use the MCL algorithm, and I'd also like to try the
InfoMap algorithm in the near future, using the R interface.

Let's say that my network is stored in the variable "df", that
I'd like to pass it to MCL as a list of weighed edge, and that,
finally, I'd like to assign a membership value to its vertices
as a result of the community detection.

Here's what I came up with:

outfile<-"tmp.txt"
cmd<-paste("mcl - --abc -o - >",outfile,sep="")
pw<-pipe(cmd,open="wb")
write.graph(df,file=pw,format="ncol")
close(pw)

pr<-pipe(paste("cat ",outfile,sep=""),open="r")
lines<-readLines(pr)
comms<-strsplit(split="\t", lines)
close(pr)

for(i in 1:length(comms)){
        for(n in comms[[i]]){
                V(df)[which(V(df)$name==n)-1]$memb<-i-1
        }
}

modularity(df,V(df)$memb)


Basically I set up a pipe for writing the network to MCL,
whose output is redirected to a temporary file, from which
I read through another pipe. It works.

Is there a way to avoid even the creation of that tmp file?
And is there a quicker way to assign memberships?
 
Sincerely,
--
Fabio Daolio

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UNIL    University of Lausanne
HEC     École des Hautes Études Commerciales
ISI             Institut des Systèmes d'Information

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