On Sun, 2011-03-27 at 20:18 +0100, Gavin Simpson wrote: <snip /> > > I think you are confusing the error structure with the model or > systematic structure? Yes, Poisson errors are expected with count > abundance data, or if there is more dispersion than expected under the > Poisson, then a negative binomial error might be appropriate or failing > that ZIP, ZINB or burdle models.
LOL - I meant a "hurdle" model! [If the OP is interested in those, then they could do a lot worse than look at the pscl package.] Thanks Roman. G > To fit a bell shaped response curve, you need to fit a quadratic > equation in the response; say no3 + no3^2. The Guassian model of species > abundance is IIRC correctly specified if a Possion error distribution > with a log link is specified. > > Say you have species abundances and you wish to model them using a > Gaussian response model, then in R you could do: > > mod <- glm(abund ~ no3 + I(no3^2), data = dat, family = poisson) > > where `mod` will contain the fitted model, `abund` is the variable with > the single species counts, `dat` is the data frame containing `abund` > and `no3`. > > This is fine if you want to use this model to extract the optimum, max > fitted abundance and tolerance of the response, but if you are just > interested in the fitting the response curve then using orthogonal > polynomials should be more computationally robust. > > You can test whether the bell shaped response is a better fit to a > sigmoid (monotonic) increasing or decreasing response (say where you > have only sampled a part of the gradient of relevance to a particular > species or the gradient space/environment is truncated in some way), by > comparing the quadratic model with one that includes the no3 term, eg: > > mod2 <- glm(abund ~ no3, data = dat, family = poisson) > > then > > anova(mod2, mod, test = "Chisq"). > > HTH > > G -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% Dr. Gavin Simpson [t] +44 (0)20 7679 0522 ECRC, UCL Geography, [f] +44 (0)20 7679 0565 Pearson Building, [e] gavin.simpsonATNOSPAMucl.ac.uk Gower Street, London [w] http://www.ucl.ac.uk/~ucfagls/ UK. WC1E 6BT. [w] http://www.freshwaters.org.uk %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% _______________________________________________ R-sig-ecology mailing list R-sig-ecology@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-ecology