Hi Jane, I think someone may have asked something similar on the r-sig-eco email list (which is a good resource in general: https://stat.ethz.ch/mailman/listinfo/r-sig-ecology)
I think the answer may have been there there's a function in the vegan package for R (http://cran.r-project.org/web/packages/vegan/index.html). But it would be pretty simple to write something up in R. Here's one way of doing it (if I'm correct in my interpretation of a co-occurrence matrix!). The actual function (called `spp.cooc') is really only 2 lines long--the code just looks longer from making up example data and adding in the comments. Hope this might do the trick for you! Note that in it's current form you would have to give the function a matrix or data.frame of ONLY NUMBERS in which species are columns and sites are rows. This could be changed by manipulating the MARGIN argument of the apply command below, i.e., site.list <- apply(matrx,1,...) Hope this helps-- Andy # make some example data sppXsite <- matrix(rpois(15,0.5),nrow=3) colnames(sppXsite) <- paste("spp",1:5,sep="") rownames(sppXsite) <- paste("site",1:3,sep="") sppXsite # here's what it looks like # now make a function to compute the co-occurrence matrix spp.cooc <- function(matrx) { # first we make a list of all the sites where each spp is found site.list <- apply(matrx,2,function(x) which(x > 0)) # then we see which spp are found at the same sites sapply(site.list,function(x1) { sapply(site.list,function(x2) 1*any(x2 %in% x1)) }) # the result is returned in a symmetrical matrix of dimension # equal to the number of spp } # here's how it works co.matrix <- spp.cooc(sppXsite) co.matrix On Fri, Aug 27, 2010 at 12:46 AM, Jane Shevtsov <[email protected]> wrote: > Is there a fast way to make a species co-occurrence matrix given a > site-species matrix or lists of species found at each site? I'm > looking for a spreadsheet or database method (preferably OpenOffice) > or R function. > > Thanks, > Jane > > -- > ------------- > Jane Shevtsov > Ecology Ph.D. candidate, University of Georgia > co-founder, <www.worldbeyondborders.org> > Check out my blog, <http://perceivingwholes.blogspot.com>Perceiving Wholes > > "The whole person must have both the humility to nurture the > Earth and the pride to go to Mars." --Wyn Wachhorst, The Dream > of Spaceflight >
