Hi, > I therefore used transitivity function in igraph, and for my graph I've got > the value: 0.5493 (global), 0.42 (average). > Reading the previous mail called "Small worlds in igraph", I think the > "global" is best for what I want to show. > I also compared my results using 2 others softwares Gephi and networkx in > python. > If I use this 2 way I have a average clustering coefficient of 0.2625 for > networkx and 0.262 for Gephi. The most common source of difference between different implementations of the average local clustering coefficient (which is I guess what you are calculating with NetworkX) is that it is not well-defined for nodes with degree zero or degree one. Since these nodes have only one neighbor, they cannot participate in any triangles. There are at least two possible ways to deal with it; one is to exclude these vertices completely from the average, the other is to assume that they have a local transitivity of zero (which is, strictly speaking, not true, since their local transitivity is zero over zero, which is undefined).
In the R interface of igraph, you can switch between the two possibilities with the "isolates" keyword argument. transitivity(g, type="average", isolates="zero") will assume that these vertices have zero transitivity, while transitivity(g, type="average", isolates="NaN") will exclude these vertices from the calculation. The count_zeros switch in NetworkX seems to be similar, but the documentation worries me a bit. It says that "If False include only the nodes with nonzero clustering in the average". This means that count_zeros=True will make the function equivalent to isolates="zero" in the R interface of igraph, but count_zeros=False will exclude nodes with zero triangles around it even if the degree of the node is larger than one! I'm not sure whether this is just an error in the documentation or an error in the implementation itself (or they really meant it this way). Anyway, I would compare the result of igraph using isolates="zero" with the result of NetworkX using count_zeros=True (which is the default). Please shout if the results still differ. Best, Tamas _______________________________________________ igraph-help mailing list [email protected] https://lists.nongnu.org/mailman/listinfo/igraph-help
