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 ______________________________________________ R-help@r-project.org 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.
