How about calling the assortativity.degree function? http://igraph.org/r/doc/assortativity.html
Gabor On Wed, Jan 28, 2015 at 3:57 PM, Alexander Semenov <[email protected]> wrote: > Hi, all! > > I've tried 3 different versions of code to calculate assortativity via > degree correlation and two of them returned NA, while the third gave some > reasonable numbers. My quistion is: can I trust it and why could 2 other > receipts fail? > > 1) First variant, which returned NA was taken from here: > http://www.isk.kth.se/~shahabm/WSAnalysis/networks/NetworkAnalysis.r > deg <- degree(g) > es <- get.edges(g, E(g)) + 1 > dc <- cor(deg[es[,1] ], deg[es[,2] ]) > > 2) The second one was from igraph wiki: > http://igraph.wikidot.com/r-recipes#toc7 > > assortativity <- function(graph){ > deg <- degree(graph) > deg.sq <- deg^2 > m <- ecount(graph) > num1 <- 0; num2 <- 0; den <- 0 > edges <- get.edgelist(graph, names=FALSE)+1 > > num1 <- sum(deg[edges[,1]] * deg[edges[,2]]) / m > num2 <- (sum(deg[edges[,1]] + deg[edges[,2]]) / (2 * m))^2 > den <- sum(deg.sq[edges[,1]] + deg.sq[edges[,2]]) / (2 * m) > > return((num1-num2)/(den-num2)) > } > > 3) And only this receipt gave me some reasonable numbers: > correlation <- function(g, m="pearson") { > el <- get.edgelist(g) > d1 <- degree(g,el[,1]) > d2 <- degree(g,el[,2]) > if (sd(d1,d2)==0) return(1) > co <- cor(d1,d2,method=m) > return(co) > } > > I found it in this book: > https://books.google.ru/books?id=Bdc1VFp7OZMC&pg=PA37&lpg=PA37&dq=igraph+degree+correlation&source=bl&ots=mJ6ivAJupU&sig=pYWtaE533vAbXUfKTwWLq8AmLaQ&hl=en&sa=X&ei=FCvJVIWdDsvcywPd9oDACA&redir_esc=y#v=onepage&q=igraph%20degree%20correlation&f=false > > It also showed me this warning: > Warning message: > In if (na.rm) "na.or.complete" else "everything" : > the condition has length > 1 and only the first element will be used > > So I basically want to know if I can trust the numbers, that were returned > by the receipt #3. Of course it would be nice to know, why the first two > receipts didn't work, but I'm not sure if I can send you the data I was > working on to reproduce my results. > > Thanks in advance, > Alex. > > (Social | Network | Data) Analyst > > Junior Research Fellow at the International Laboratory of Applied Network > Research > National Research University Higher School of Economics > http://anr.hse.ru/en/ > > http://jarens.ru > ru.linkedin.com/in/semenoffalex/ > https://www.facebook.com/semenoffalex > https://twitter.com/jarens > > skype: semenoffalex > tel: +7 926 602 25 51 > > > _______________________________________________ > igraph-help mailing list > [email protected] > https://lists.nongnu.org/mailman/listinfo/igraph-help > >
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