Stephanie Dray's comments are absolutely correct. This method will
only work with small matrics. The below modification is much faster
than the first version that I wrote, but still slow on large
matrices.
shuffle_matrix <- function(x) {
nrow = dim(x)[1]
ncol = dim(x)[2]
cmargins <- apply(x,2,sum)
shuffled = array(length(x),dim=c(nrow,ncol))
while(1) {
for(k in 1:nrow) {
shuffled[k,] = sample(x[k,],ncol)
}
if(all(apply(shuffled,2,sum) == cmargins)) {
break
}
}
shuffled
}
On Fri, 27 Apr 2007, Stéphane Dray wrote:
Your solution is not suitable for quite large matrices.
There are several papers on the subject :
e.g. :
@ARTICLE{SD751,
author = {Gotelli, N.J. and Entsminger, G.L.},
title = {Swap and fill algorithms in null model analysis:rethinking the
knight's
tour},
journal = {Oecologia},
year = {2001},
volume = {129},
pages = {281-291},
endnotereftype = {Journal Article},
keywords = {null model},
pdf = {/home/stephane/Biblio/Articles/SD751.pdf},
shorttitle = {Swap and fill algorithms in null model analysis:rethinking the
knight's
tour}
}
There are different algorithms to solve the question but I am really not sure
that they are implemented in R.
Sincerely,
Finny Kuruvilla wrote:
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
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
--
Stéphane DRAY ([EMAIL PROTECTED] )
Laboratoire BBE-CNRS-UMR-5558, Univ. C. Bernard - Lyon I
43, Bd du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
Tel: 33 4 72 43 27 57 Fax: 33 4 72 43 13 88
http://biomserv.univ-lyon1.fr/~dray/
*****************************************************************
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/
______________________________________________
[email protected] mailing list
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
