I've been trying to get this code running to get the agreement between
different runs of the Infomap algorithm
info <- list()
for (i in 1:10){
info[[i]]<-infomap.community(el.13, nb.trials=100)
}
### Which works fine, but for comparing the community structures I use this
for loop:
nmi <- rep(NA, 45)
for (i in 1:10) {for (n in (i+1):10) { for (j in 1:45) {
nmi[j] <- compare(info[[i]], info[[n]], method="nmi")
}}}
which just gives me 1's.
Can someone get this code running?
Thanks,
Tada
On Thu, Sep 11, 2014 at 1:09 PM, Tadaishi Yatabe-Rodriguez <
[email protected]> wrote:
> Hi,
>
> I'm running the Infomap algorithm, but since its random by nature, I'd
> like to get an idea of how alike community structures are between
> realizations of the algorithm. I''ve used community structure comparison
> algorithms such as nmi in the compare function, but I've noticed that I
> would need to do some sort of pairwise comparison of the community objects
> I've created, which I'm not quite sure how to code.
> Also, Tamas has pointed put to me that I could create a matrix that counts
> the number of times a pair of nodes is in the same cluster and use that as
> an indicator of the most likely clusters. Then again, I'm not quite sure
> how to do this.
>
> Thanks,
>
> Tada
>
> --
> *Tadaishi Yatabe*
> DVM, MPVM, PhD (C)
> Center for Animal Disease Modeling and Surveillance (CADMS)
> Department of Medicine and Epidemiology
> School of Veterinary Medicine
> University of California Davis
>
--
*Tadaishi Yatabe*
DVM, MPVM, PhD (C)
Center for Animal Disease Modeling and Surveillance (CADMS)
Department of Medicine and Epidemiology
School of Veterinary Medicine
University of California Davis
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