Andy,
Sorry, my first response was a little hasty. I see you're trying
to preserve the distance of a sample to itself along the diagonal and
the symmetry of the matrix. This is actually simpler.
> library(labdsv)
> dis.bc <- dsvdis(bryceveg,'bray') # bray/curtis dissimilarity matrix
> dis.mat <- as.matrix(dis.bc)
> size <- nrow(dis.mat)
> for (i in 1:999) {
> z <- sample(1:size,size,replace=FALSE)
> tmp <- dis.mat[z,]
> tmp <- tmp[,z]
> # calculate mantel or other
> }
In this case we use the same permuted vector for both the row and column
and preserve the symmetry.
Dave Roberts
Andrew Park wrote:
>
> Hi there,
>
> I would like to find a more efficient way of permuting the rows and columns
> of a symmetrical matrix that represents ecological or actual distances
> between objects in space. The permutation is of the type used in a Mantel
> test.
>
> Specifically, the permutation has to accomplish something like this:
>
>
> Original matrix addresses:
>
> a11 a12 a13
>
> a21 a22 a23
>
> a31 a32 a33
>
>
> Example permutation
>
> a22 a23 a21
>
> a32 a33 a31
>
> a12 a13 a11
>
> that is relative positions of rows and columns are conserved in the
> permutation.
>
> Basically, I have been doing this in a "for" loop by (1) permuting the raw
> data vector using "sample", (2) generating a lower triangular distance matrix
> from the permuted raw data using the "distance" function from "ecodist', and
> (3) calculating a bunch of statistics including the Mantel correlation and
> multiple regression statistics, which are then stored in blank matrices that
> were declared prior to beginning the loop. The whole procedure needs to
> repeat at least 999 times but 1999 times would be better and 9999 times would
> be ideal.
>
> The problem is, R-users will know, is that using "for" loops like this is
> slow, and gets slower the further into the loop you get.
>
> However, I am not a sophisticated programmer, and cannot think of a more
> efficient way to do this.
>
> Thanks in advance,
>
> Andy Park (University of Winnipeg).
>
> ______________________________________________
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>
>
--
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
David W. Roberts office 406-994-4548
Professor and Head FAX 406-994-3190
Department of Ecology email [EMAIL PROTECTED]
Montana State University
Bozeman, MT 59717-3460
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