Hi Moses,
> 1. Is there a way to get all geodesics together at once, instead of
> running get.shortest.paths(g, i, 1:n) separately n times?
You can use a for loop, which is what get.shortest.paths would do internally
anyway:
result <- list()
for (i in 1:n) { result <- c(result, get.shortest.paths(g, i, 1:n)) }
It could be the case that there is a more efficient solution but I'm not an
expert in R. Also, note that you might be interested in get.all.shortest.paths
instead of get.shortest.paths -- the former returns only a single path for any
vertex pair v1-v2 even if there are multiple geodesics between v1 and v2 with
the same length. If you use get.all.shortest.paths, you will need only the $res
component of the result:
for (i in 1:n) { result <- c(result, get.all.shortest.paths(g, i, 1:n)$res) }
> 2. Since, in my data, vertices have an attribute (say, taking values
> 1, 2, 3, ...), is it possible to filter out from the outcome of the
> previous computations only those geodesics which contain at least one
> intermediary vertex taking a particular value of the attribute? And
> how can I do this?
# Construct a list containing the acceptable intermediate vertices
acceptable.vertices <- which(V(g)$attribute == X)
# Get the shortest paths from a particular vertex
paths <- get.shortest.paths(g, v, 1:n)
# Filter on those that contain at least one acceptable vertex in the path
paths <- paths[acceptable.vertices %in% paths]
Best,
T.
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