Thank you very much. I'll look into the r project listserv you suggested.
Unrelated: Ecological Models and Data in R is one of my favorite
mathematical ecology textbooks and a fantastic resource.


On Tue, Jan 24, 2012 at 9:30 PM, bbolker [via R] <
ml-node+s789695n4326186h74@n4.nabble.com> wrote:

> Dallas <tad.dallas <at> drakeresearchlab.com> writes:
>
> > I am currently testing species co-occurrence patterns using null models
> and
> > the oecosimu() function within the vegan() package. My issue is that
> none of
> > the methods appear to be the ones that I want. The methods listed are
> r0,
> > r1, r2, r2dtable, swap, tswap. However, I want to know how to go about
> > implementing fixed row algorithms, as suggested in Gotelli 2000 in
> Ecology.
> >
> > Also, the null models created seem to be incredibly dependent on the 1)
> > burnin and 2) thin values. These are the 1) Number of null communities
> > discarded before proper analysis in sequential methods "swap" and
> "tswap"
> > and 2) Number of discarded null communities between two evaluations of
> > nestedness statistic in sequential methods "swap" and "tswap". What are
> the
> > significance of these values?
>
>   You will probably have better luck with this question on the
> r-sig-ecology
> <at> r-project.org list.
>   I haven't looked at this stuff in a little while.  It sounds from the
> ?oecosimu description as though there are some fixed row algorithms (?)
>
> Methods ‘r0’, ‘r1’ and ‘r2’ maintain the site (row)
>      frequencies. Method ‘r0’ fills presences anywhere on the row with
>      no respect to species (column) frequencies, ‘r1’ uses column
>      marginal frequencies as probabilities, and ‘r2’ uses squared
>      column sums. Methods ‘r1’ and ‘r2’ try to simulate original
>      species frequencies, but they are not strictly constrained. All
>      these methods are reviewed by Wright et al. (1998).
>
> It might help in your e-mail to r-sig-ecology if you briefly
> describe Gotelli 2000's algorithm, so readers don't necessarily
> have to go back to the original source to know (at least approximately)
> what you want.
>
>   Ben Bolker
>
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