Problems with igraph, statnet and GEPHI?

Question

I'm working with some graph models in both Gephi, Python and R. Until by chance I decided to compare the results they gave me. So I had the following problem. When calculating the betweenness centrality with Gephi and R (using igraph and statnet), the three give me different results (igraph and statnet, not very different). Since I am working a very large network, I decided to take a small network and perform the calculation by hand, the figure shown below (taked from: enter link description here )

enter image description here

Using the adjacency list:

source  target
1   2
1   3
1   4
2   3
3   4
4   5
4   6
5   6
5   8
5   7
6   8
6   7
7   8
7   9

To then see what results I threw R and Gephi. I discovered that Gephi gives me the same results:

enter image description here

But R (both for igraph and statnet not).

> library('igraph')
> data <- read.csv(file.choose())
> set.seed(123456)
> graph_1<-graph.data.frame(data)
> summary(graph_1)
IGRAPH cfa51db DN-- 9 14 -- 
+ attr: name (v/c)

> graph_1
IGRAPH cfa51db DN-- 9 14 -- 
+ attr: name (v/c)
+ edges from cfa51db (vertex names):
 [1] 1->2 1->3 1->4 2->3 3->4 4->5 4->6 5->6 5->8 5->7 6->8 6->7 7->8 7->9

> betweenness(graph_1)
 1  2  3  4  5  6  7  8  9 
 0  0  6 15  6  6  6  0  0

> detach("package:igraph", unload=TRUE)
> library(statnet)
> library(intergraph)
> graph_2<-asNetwork(graph_1)

> betweenness(graph_2)
[1]  0  0  6 15  6  6  6  0  0

Am I doing something wrong by running my R code or is it using another algorithm to calculate the betweenness centrality? Thank you :)

Answer 1

You are computing two different things.

First, to make your example reproducible, here is code that all of us can use to make your example.

library(igraph)
EL = matrix(c(1,2, 1,3, 1,4, 2,3, 3,4, 4,5, 4,6, 5,6, 5,8, 
    5,7, 6,8, 6,7, 7,8, 7,9), ncol=2, byrow=T)
graph_1 = graph_from_edgelist(EL)

Now, using your code, I get the same result.

betweenness(graph_1)
[1]  0  0  6 15  6  6  6  0  0

However,

betweenness(graph_1, directed=F)
[1]  3  0  3 15  6  6  7  0  0

Gives the same result as you got from Gephi.

The help page ?betweenness says:

directed
Logical, whether directed paths should be considered while determining the shortest paths.

Clearly, Gephi has different defaults than R.