[R] Permutation of a distance matrix

[Duncan Murdoch]

On 16/11/2007 6:42 PM, 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.

I don't think for loops should slow down.  What you may be doing is 
gradually growing a result vector; that does slow down over time.

For example, this is slow:

result <- c()
for (i in 1:100000) result <- c(result, i)

but this is very quick:

result <- numeric(100000)
for (i in 1:100000) result[i] <- i

Duncan Murdoch

> 
> 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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