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+s789695n4326620...@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 > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4326620&i=0>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. > > > ------------------------------ > If you reply to this email, your message will be added to the discussion > below: > > http://r.789695.n4.nabble.com/Null-models-of-species-co-occurrence-tp4325097p4326620.html > To unsubscribe from Null models of species co-occurrence, click > here<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=unsubscribe_by_code&node=4325097&code=dGFkLmRhbGxhc0BkcmFrZXJlc2VhcmNobGFiLmNvbXw0MzI1MDk3fDE3ODk2NDQxNzA=> > . > NAML<http://r.789695.n4.nabble.com/template/NamlServlet.jtp?macro=macro_viewer&id=instant_html%21nabble%3Aemail.naml&base=nabble.naml.namespaces.BasicNamespace-nabble.view.web.template.NabbleNamespace-nabble.view.web.template.InstantMailNamespace&breadcrumbs=instant+emails%21nabble%3Aemail.naml-instant_emails%21nabble%3Aemail.naml-send_instant_email%21nabble%3Aemail.naml> > -- View this message in context: http://r.789695.n4.nabble.com/Null-models-of-species-co-occurrence-tp4325097p4327474.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]] ______________________________________________ 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.
