[igraph] missing links of subgraphs

[Matteo Orrù]

Hello everybody,

In my research I am working on networks community structure and I am
interested in investigating the relationship between community
structure and missing links.

Thus I applied hrg.consensus and hrg.predict to subgraph representing
network communities (found using fastgreedy.community).

In order to extract the subgraph I used induced.subgraph (initially
without specifing an implementation).

Here it is the instructions I used:

sub_graph <- induced.subgraph(graph=g_n1, v=unlist(fg_communities[k]))

g_n1_hrg_con <- hrg.consensus(sub_graph)

g_n1_miss_link <- hrg.predict(graph = sub_graph, hrg = g_n1_hrg_con)

As reported in the help in this case induced.subgraph choose
heuristically what implementation to use.
As a result I obtain that the $edge matrix, element of the list
returned by hrg.predict, stores vertices that don't belong to the
subgraph.
I am working with several networks of different size and from my tests
I found that it doesn't happen every time.

My supposition is that in sometimes induced.subgraph use
"copy_and_delete" and some others "create_from_scratch".
WHEN it choose "copy_and_delete" it store somewhere the information
about the vertices of the main graph, SO when I use subgraph as
argument for hrg.consensus and hrg.predict it considers the "external"
vertices too (those not belonging to the subgraph).

I have some evidences that using "create_from_scratch" this issue doesn't occur.

I would like to know if this assumption is correct and if I can avoid
vertices not belonging to a subgraph to show in $edges matrix using
"create_from_scratch" as a imp value in induced.subgraph.

Thank you very much in advance.

Matteo Orrù

I think to have found a strange behaviour of hrg.consensus and
hrg.predict while using the