I constructed a graph from a data-frame using the igraph graph_from_data_frame function. My two first column represent the edge list, and i have another column named "weight". There is several other attributes columns.
I then tried to find a community structure within my graph using cluster_fast_greedy.
data <- data %>% rename(weight = TH_LIEN_2)
graph <- graph_from_data_frame(data,directed=FALSE)
is_weighted(graph)
cluster_1 <- cluster_fast_greedy(graph, weights = NULL)
The output is a list of three (merges, modularity, membership), each containing some of my vertices.
However, the following returns "NULL":
cluster_1[["merges"]]
cluster_1[["modularity"]]
cluster_1[["membership"]]
(I believe cluster_1[["membership"]] is supposed to be a list of integer indicating the cluster the vertices belong to?)
I have tried different method of clustering (cluster_fast_greedy, cluster_label_prop, cluster_leading_eigen, cluster_spinglass, cluster_walktrap) and with a weighted and non weighted graph and the output looks the same every time. (The number of element on the list varying from 1 to 4)
Does anyone have an idea of why it does that?
Thank you and have a nice day!
Cassandra
>Solution :
You should use the dollar sign $ to access the cluster object. For example
g <- make_full_graph(5) %du% make_full_graph(5) %du% make_full_graph(5)
g <- add_edges(g, c(1, 6, 1, 11, 6, 11))
fc <- cluster_fast_greedy(g)
and you will see
> str(fc)
Class 'communities' hidden list of 5
$ merges : num [1:14, 1:2] 3 4 5 1 12 13 15 11 7 8 ...
$ modularity: num [1:15] -6.89e-02 -4.59e-02 6.94e-18 6.89e-02 1.46e-01 ...
$ membership: num [1:15] 3 3 3 3 3 1 1 1 1 1 ...
$ algorithm : chr "fast greedy"
$ vcount : int 15
> fc$merges
[,1] [,2]
[1,] 3 2
[2,] 4 16
[3,] 5 17
[4,] 1 18
[5,] 12 14
[6,] 13 20
[7,] 15 21
[8,] 11 22
[9,] 7 9
[10,] 8 24
[11,] 10 25
[12,] 6 26
[13,] 27 19
[14,] 23 28
> fc$modularity
[1] -6.887052e-02 -4.591368e-02 6.938894e-18 6.887052e-02 1.460055e-01
[6] 1.689624e-01 2.148760e-01 2.837466e-01 3.608815e-01 3.838384e-01
[11] 4.297521e-01 4.986226e-01 5.757576e-01 3.838384e-01 -1.110223e-16
> fc$membership
[1] 3 3 3 3 3 1 1 1 1 1 2 2 2 2 2
> fc$algorithm
[1] "fast greedy"
> fc$vcount
[1] 15