Re: [R] COMPAR.GEE Output

From: Ben Bolker <bolker_at_ufl.edu>
Date: Sun, 02 Mar 2008 17:13:00 +0000 (UTC)

Charles Willis <willis.charlie <at> gmail.com> writes:

>
> Hello,
>
> I am running the program COMPAR.GEE within the package APE. My dependent
> variable is binomial, while my independent variable is a multi-state
> categorical variable. The output reports an estimate for each state of the
> independent variable except the first one. For example, for the variable X
> with 3 states, the output is:
>
> intercept (estimate)
> X2 (estimate)
> X3 (estimate)
>
> I have two questions: 1) Why does it not give me an intercept for the first
> variable and how do i get it; 2) can a get a general estimate of
> correlation, like a wald's statistic for the variable?

  1. It's useful to provide a small self-contained example, as recommended by the posting guide (referred to after every r-help message).
  2. I would suggest asking this kind of question on the r-sig-phylo mailing list, which is devoted to phylogenetic and comparative analyses in R.
  3. In order to understand the output, you have to understand the way in which R parameterizes statistical models. I'm guessing that you specified family=binomial in your compar.gee call, which would mean by default assuming binomial error structure and a logit link (if you don't know what that means, you should probably read up on generalized linear models a bit ...). X1 is then the estimated logit-probability for state 1, X2 is the estimated *difference* in logit-prob between states 1 and 2, similarly for X3. If you just want the estimated probabilities for the three groups you can fit a model without an intercept using something like "response~predictor-1" as your formula.
  4. When you print the model object (e.g. c1=compar.gee(...); c1) it gives you standard errors and t statistics for each parameter which are (I believe) essentially Wald statistics, although you should certainly check the reference given in ?compar.gee ...

  good luck,
    Ben Bolker



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