[R] glm models with more than one response
gavin.simpson at ucl.ac.uk
Fri Feb 5 19:28:58 CET 2010
On Fri, 2010-02-05 at 13:10 -0500, Steve_Friedman at 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$Total_Mg, family = poisson)
By the way, you aren't really using the power of formulas with the
Typha.glm <- glm(fwc$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
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:
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?
> 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 Friedman Ph. D.
> Spatial Statistical Analyst
> Everglades and Dry Tortugas National Park
> 950 N Krome Ave (3rd Floor)
> Homestead, Florida 33034
> Steve_Friedman at nps.gov
> Office (305) 224 - 4282
> Fax (305) 224 - 4147
> R-help at r-project.org mailing list
> 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
More information about the R-help