[R-sig-eco] Removing from least- to most-connected in bipartite second.extinct?

[Drew Tyre]

Hi Scott,

I've not used package bipartite, but a quick look suggests it would be
easy to modify the extinction function to do what you want. in
extinction() simply replace max() in the following code with min(),
and it will go from least to most connected when method='degree'.

    if (meths.match == 3) {
        if (partis.match == 1) {
            sequ <- rowSums(web > 0)
            which.ex <- which(sequ == max(sequ))   ## change max to min
            if (length(which.ex) > 1)
                ex <- sample(which.ex, size = 1)
            else ex <- which.ex
            web[ex, ] <- 0
        }
        if (partis.match == 2) {
            sequ <- colSums(web > 0)
            which.ex <- which(sequ == max(sequ))  ## change max to min
            if (length(which.ex) > 1)
                ex <- sample(which.ex, size = 1)
            else ex <- which.ex
            web[, ex] <- 0
        }
    }

On Thu, Jul 12, 2012 at 11:24 PM, Scott Chamberlain
<myrmecocystus at gmail.com> wrote:
> Hello,
>
> I am interested in calculating the consequences of removing species from a bipartite network, specifically removing species from the least-connected to the most-connected. The bipartite package in R has the second.extinct and robustness functions which allows investigation of secondary extinctions but does not allow for removing species from least-connected to the most-connected. The only removal options are: 1) random, 2) least-abundant to most-abundant 3) most-connected to least-connected. I am wondering if there are any other programs in which I could run the extinction series that I desire.
>
> Thanks,
> Scott Chamberlain
>
>
>
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Drew Tyre

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