[igraph] R : Loop contract.vertices to calculate network measures for groups in a social network in Igraph

[Dimitri Marschall]

Hi,
I am trying to calculate different networks measures such as 
`betweenness()` and `constraint()`in my network using Igraph in R. My 
problem is that I am not looking at individuals but on groups of 
individuals in my network. Therefore I have to contract the vertices 
before I calculate the different network measures. Thus far I have been 
able to create a basic code to calculate the measures. But I have a 
total of ca. 900 groups (with up to 7 members per group) in a network of 
ca. 70.000 nodes and 250.000 edges. So I am trying to create a loop to 
automate the approach and make life a little bit easier.


Now I want to present my approach to calculate the `constrain()`.

    # load package
    library(igraph)

    # load data and create a weighted edgelist
    df <- data.frame(from=c(6, 9, 10, 1, 7, 8, 8, 4, 5, 2, 5, 10), 
to=c(3, 4, 2, 5, 10, 1, 9, 10, 6, 9, 3, 6), weight=c(4, 2, 1, 2, 3, 3, 
1, 1, 4, 5, 2, 2))
    g <- graph.data.frame(df, directed =FALSE)

    #import groups
    groups <- "
    1 5 8
    2
    10 7  "

    subv <- read.table(text = groups, fill = TRUE, header = FALSE)

I would like to loop the upcoming code , to calculate not each 
`constraint()` separately. But for all the three groups given in the 
reproducible example at once.

    #create a subvector of the first group and delete all the NA entries
    subv1 <- c(as.numeric(as.vector(subv[1,])))
    subv1 <- subv1[!is.na(subv1)]

    #save subvector as charcter
    subv1 <- as.character(subv1)

    #creat subgraph with the nodes of group 1 from graph and add their 
1st neighbors
    g2 <- induced.subgraph(graph=g ,vids=unlist(neighborhood(graph=g 
,order=1, nodes = subv1)))

    #identify the igraph IDs of the nodes in the first group
    match("1", V(g2)$name)
    match("5", V(g2)$name)
    match("8", V(g2)$name)

    #create a contract vector and contract the vertices from largest to 
smallest using the output from match
    convec1 <- c(1:(5-1), 3, 5:(vcount(g2)-1))
    g3 <- contract.vertices(g2, convec1, vertex.attr.comb=toString)
    convec2 <- c(1:(4-1), 3, 4:(vcount(g3)-1))
    g4 <- contract.vertices(g3, convec2, vertex.attr.comb=toString)

    #remove the selfloops and sum the weight attributes for the created 
graph
    g5  <- simplify(g4, remove.loops = TRUE, 
edge.attr.comb=list(weight="sum"))

    # calculate the constraint measure for the vertex 1, 5, 8
    constraint(g5, nodes=3, weights=NULL)

So now I have the constraint measure for the first group. For the second 
and third I would have to repeat my steps again. This would be feasible, 
but as I stated I have 900 groups. Is there any possibility to loop this?

Kind regards,
D.A.M.