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+s789695n4326186...@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 âr0â, âr1â and âr2â maintain the site (row) > frequencies. Method âr0â fills presences anywhere on the row with > no respect to species (column) frequencies, âr1â uses column > marginal frequencies as probabilities, and âr2â uses squared > column sums. Methods âr1â and âr2â 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 > > ______________________________________________ > [hidden email] <http://user/SendEmail.jtp?type=node&node=4326186&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-tp4325097p4326186.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-tp4325097p4326236.html Sent from the R help mailing list archive at Nabble.com. [[alternative HTML version deleted]]
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