[R-sig-eco] mgcv:gam predicted class?

[Gavin Simpson]

On Thu, 2013-07-18 at 16:13 +0200, Per Bergström wrote:
> How to get prediction of classes in gam?
> I have a problem with getting predicted classes from a gam-model using 
> the gam function in the "mgcv"-package.
> I have a dataset where I have classified the response variable into 5 
> classes (i. e. 1, 2, 3, 4, 5) and I want to use a gam-model generated on 
> a training dataset (traindata) to predict the class beloning of data 
> from a test-dataset (testdata) but I can't get it to work.
> 
> I generated the gam-model using:
> model<-gam(growthclass~Vol+Expo+distance+......+temperature,family=binomial, 
> type="classification",data=traindata)

The binomial would presume two classes (0,1) and there is no `type`
argument in `mgcv::gam()`, so the model you are fitting seems ill-fitted
(sorry) to the problem.

What you describe could be a multinomial model, but I don't know how
that can be fitted with splines.

It seems *you* has discretised the response. Why not fit the model on on
the non-discrete response and then apply the classification to those
values rather than the other way round which is what you have done.

HTH

G

> When I then try to predict the class beloning of the test-dataset using:
> pred<-predict(model,newdata=testdata)
> I get results like this:
> 
>          2           4           6           7           9
> -1.93680872  2.28422570  0.99747563  0.03627236  0.74235160
> 
> But I really want the results to look like this:
> 
>          2           4           6           7           9
> 	1 	    3           2	    1 	        2
> 
> 
> i.e. the predicted classes for the new samples.
> 
> Obviously I am doing something wrong and it is probably very simple to solve but I've got stuck on it for a while and would appreciate some help solving it.
> 
> Thanks
> Per
> 
> 
> 
> 
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> 
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-- 
Gavin Simpson, PhD                          [t] +1 306 337 8863
Adjunct Professor, Department of Biology    [f] +1 306 337 2410
Institute of Environmental Change & Society [e] gavin.simpson at uregina.ca
523 Research and Innovation Centre          [tw] @ucfagls
University of Regina
Regina, SK S4S 0A2, Canada