On Fri, 2010-02-05 at 13:10 -0500, steve_fried...@nps.gov wrote: > Hi everyone, > > I am trying to construct a glm and am running into a couple of questions. > > The data set I am using consists of 6 categories for the response and 6 > independent predictors representing nutrient concentrations at sample point > locations. Ultimately I'd like to use the probabilities for each response > category in a simulation model such that these probabilities are used to > define a realized ecological niche. > > When I try the following it works for a single response. > > Typha.glm <- glm(fwc$VegType == "Cattail" ~ fwc$TP + fwc$TC + fwc$TN + > fwc$BD + fwc$LOI + fwc$Total_Mg, family = poisson)
By the way, you aren't really using the power of formulas with the above: Typha.glm <- glm(fwc$VegType == "Cattail" ~ TP + TC + TN + BD + LOI + Total_Mg, data = fwc, family = poisson) Depending on what model you are actually fitting, you could probably simplify the LHS of that formula too. Is that model appropriate with binary data --- the response is now 0/1 TRUE/FALSE? This sounds more like a multinomial type model to me. You might want to look at this recent paper in J Statistical Software by Thomas Yee: http://www.jstatsoft.org/v32/i10 The paper covers his VGAM software but does, IIRC, comment on R packages for fitting a wide range of categorical models. This isn't really my field, but you probably need to think about the nature of the response a bit more. May be follow up on R-SIG-Ecology? HTH G > > But if I try this without specifying a specific VegType it fails. > > plants.glm <- glm(fwc$VegType ~ fwc$TP + fwc$TC + fwc$TN + fwc$BD + > fwc$LOI + fwc$Total_Mg, family = poisson) > > Error in y + 0.1 : non-numeric argument to binary operator > In addition: Warning message: > In model.matrix.default(mt, mf, contrasts) : > variable 'fwc$VegType' converted to a factor > > My questions are: > > 1. How can I extract the probability of the VegType for different > concentrations of each of the independent parameters? > > 2. Do I need to run this model extracting for a specific VegType each time > or is there a way to run the glm for each VegType in one statement? > > 3. I've experimented with binning each of the nutrient values to establish > frequency values for each VegType, but am uncertain how to reconstruct that > data into a common data set that can be submitted to the glm. Is this step > even necessary ? > > Running on Windows XP > R 2.10.1 > > Thanks and Much Appreciated > > Steve > > Steve Friedman Ph. D. > Spatial Statistical Analyst > Everglades and Dry Tortugas National Park > 950 N Krome Ave (3rd Floor) > Homestead, Florida 33034 > > steve_fried...@nps.gov > Office (305) 224 - 4282 > Fax (305) 224 - 4147 > > ______________________________________________ > 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. -- %~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~%~% 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-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.