I don't know about the number of triads, but for number of triangles you can just do: graph.motifs(g)[4]
I have only used that for undirected graphs, though. On Tue, May 26, 2015 at 11:41 AM, Tadaishi Yatabe-Rodriguez < [email protected]> wrote: > 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 > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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