Fantastic! I'll avoid the sequential models and will look into the r0 and
r1 methods. Thank you.

Tad

On Wed, Jan 25, 2012 at 3:03 AM, Jari Oksanen [via R] <
ml-node+s789695n4326620h28@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.
> Dallas,
>
> What do you mean with "fixed row algorithms"? If you mean the the last row
> in
> Table 2 of Gotelli (Ecology 81, 2606-2621; 2000) labelled "Row sums
> fixed", then
> these all are in vegan: SIM2 == r0, SIM4 == r1, SIM9 == quasiswap. Not all
> cases
> of Gotelli's table are included, but could easily be added.
>
> >
> > 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?
> >
> The *sequential* models *are* dependent on burnin and thin: you change
> data very
> little in one step so that matrices are dependent in the sequence. The
> help page
> for null models contains information how to analyse this with R tools. The
> easiest solution is not to use sequential models, but to use
> non-sequential
> quasiswap.
>
> Like Ben Bolker wrote, you'd probably get better response in
> r-sig-ecology.
>
> Cheers, Jari Oksanen
>
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