[R] glm models with more than one response

[Gavin Simpson]

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
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_Friedman at nps.gov
> Office (305) 224 - 4282
> Fax     (305) 224 - 4147
> 
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