You could use either a 'for' loop or the '*apply' family. You can also use
lists for your variables for indexing, e.g.
for (i in 1:NumGroups) {
subv.group[[i]] <- c(as.numeric(as.vector(subv[i, ])))
etc.
etc.
}
Do something similar with the other variables. I don't know how fast/slow
this will be. I'm sure it can be optimized.
Not sure why you have "c" with "as.numeric" and "as.vector"; the "c" should
be unnecessary I think. Also, why convert "subv1" to type character?
On Tue, Dec 16, 2014 at 1:45 PM, Dimitri Marschall <
[email protected]> wrote:
>
> 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.
>
> _______________________________________________
> igraph-help mailing list
> [email protected]
> https://lists.nongnu.org/mailman/listinfo/igraph-help
>
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