Further to my previous e-mail, this is how I found the number of triangles:
conn <- array (dim = c(vcount(el.13), vcount(el.13), vcount(el.13)))
for (i in 1:length(Successor)){
for (j in 1:length(Successor[[i]])) {
for (k in (j+1):(length(Successor[[i]]))){
conn[i,j,(k-1)] <- ifelse(length(Successor[[i]]) < 2, NA,
ifelse(k > length(Successor[[i]]), NA,
ifelse(V(el.13)[Successor[[i]][j]]==V(el.13)[Successor[[i]][k]],NA,
are.connected(el.13, V(el.13)[Successor[[i]][j]],
V(el.13)[Successor[[i]][k]]))))
}}}
So transitivity, as defined previously would be:
trans <- sum(conn, na.rm = T)/triplets
Could someone more experienced tell me if this is ok and the reason of the
differences with triad.census in the number of triplets of the form B <- A
-> C ???
Thanks!
On Tue, May 26, 2015 at 10:41 AM, Tadaishi Yatabe-Rodriguez <
[email protected]> wrote:
> Hi all,
>
> I'm trying to calculate transitivity of the form B <- A -> C, where also
> B->C in a directed graph. For this I counted all the neighbors looping over
> each vertex using the function neighbors(graph[i], mode='out'). Then I
> counted the number of neighbors using the function length. Finally I get
> the number of possible triplets for each vertex using combinatorial, i.e.
> choose(number.neihgbors, 2) and I got the number of triplets of the form B
> <- A -> C for each vertex. When I added them all and then compare with the
> results from triad census for the same kind of triplets results didn't
> match. Any idea why? Here's the code
>
> ##Successors of A
> Successor=list()
> for (i in 1:vcount(el.13)){
>
> Successor[[i]] <- neighbors(el.13, v=V(el.13)[i], mode = "out")
>
> }
> ### Clustering of the form B <- A -> C, where also B->C
>
> n.succ <- sapply(Successor, FUN=length)
>
> trip <- choose(n.succ, 2)
> triplets <- sum(trip)
>
> Thanks!
>
> --
> *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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