[R] Randomising matrices

[Finny Kuruvilla]

Hi Nick,

This way isn't the most elegant but works well, especially if the
matrices aren't too large:

# This function works on 2x2 arrays, randomizing them, but
# preserving row and column totals
shuffle_matrix <- function(x) {
   nrow = dim(x)[1]
   ncol = dim(x)[2]
   rmargins <- apply(x,1,sum)
   cmargins <- apply(x,2,sum)

   while(1) {
     shuffled <- array(sample(x,length(x),replace=TRUE),dim=c(nrow,ncol))
     if(all(apply(shuffled,1,sum) == rmargins)) {
       if(all(apply(shuffled,2,sum) == cmargins)) {
         break
       }
     }
   }
   shuffled
}

Example:

> a=array(sample(c(0,1),10,replace=TRUE),dim=c(5,2))
> a
      [,1] [,2]
[1,]    0    1
[2,]    1    1
[3,]    0    1
[4,]    0    1
[5,]    1    0
> shuffle_matrix(a)
      [,1] [,2]
[1,]    0    1
[2,]    1    1
[3,]    1    0
[4,]    0    1
[5,]    0    1

Best,
Finny Kuruvilla

*****************************************************************
Finny Kuruvilla, MD, PhD
Harvard Medical School Fellowship Program in Transfusion Medicine
Broad Institute of MIT and Harvard
Homepage: http://www.people.fas.harvard.edu/~kuruvill/home/


On Fri, 27 Apr 2007, Nick Cutler wrote:

> I would like to be able to randomise presence-absence (i.e. binary)
> matrices whilst keeping both the row and column totals constant. Is
> there a function in R that would allow me to do this?
>
> I'm working with vegetation presence-absence matrices based on field
> observations. The matrices are formatted to have sites as rows and
> species as columns. The presence of a species on a site is indicated
> with a 1 (absence is obviously indicated with a 0).
>
> I would like to randomise the matrices many times in order to construct
> null models. However, I cannot identify a function in R to do this, and
> the programming looks tricky for someone of my limited skills.
>
> Can anybody help me out?
>
> Many thanks,
>
> Nick Cutler
>
> Institute of Geography
> School of Geosciences
> University of Edinburgh
> Drummond Street
> Edinburgh EH8 9XP
> United Kingdom
>
> Tel: 0131 650 2532
> Web: http://www.geos.ed.ac.uk/homes/s0455078
>
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