[R] Null models of species co-occurrence

[Jari Oksanen]

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