Re: [R] COMPAR.GEE Output

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

Charles Willis <willis.charlie <at>> 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 mailing list PLEASE do read the posting guide and provide commented, minimal, self-contained, reproducible code. Received on Sun 02 Mar 2008 - 17:17:24 GMT

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