Re: [igraph] triad census

[Chris Watson]

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 <address@hidden> 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 <address@hidden> 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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