Hello,
> ### Which works fine, but for comparing the community structures I use this
> for loop:
>
> nmi <- rep(NA, 45)
> for (i in 1:10) {for (n in (i+1):10) { for (j in 1:45) {
> nmi[j] <- compare(info[[i]], info[[n]], method="nmi")
> }}}
>
> which just gives me 1's.
Okay, there's one thing I don't understand here. Why do you have an inner for
loop for the j variable? This will just run the comparison for the same pair of
communities 45 times, and fill the result of the nmi vector with this. Then the
outer two loops will move on to the next community pair, compare the pair 45
times, and fill the result of the nmi vector. So you are essentially
overwriting the nmi vector whenever you start to evaluate a new pair. What you
need is probably this:
j <- 1
for (i in 1:10) {
for (n in (i+1):10) {
nmi[j] <- compare(info[[i]], info[[n]], method="nmi")
j <- j+1
}
}
In this case you can still get a vector containing 1's only, but this will only
indicate that your communities are identical.
For what it's worth, you can get all the possible pairings of the community
structures with t(combn(info, 2)) -- this gives you a 2D array with two columns
where each row corresponds to one possible pairing. You can then use apply() to
apply the comparison function for each row:
pairs <- t(combn(info, 2))
nmi <- apply(pairs, 1, function (row) { compare(row[[1]], row[[2]],
method="nmi") })
--
T.
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