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 )
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:
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 :)
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.