From: Ben Bolker <bolker_at_ufl.edu>

Date: Sun, 02 Mar 2008 17:13:00 +0000 (UTC)

R-help_at_r-project.org mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sun 02 Mar 2008 - 17:17:24 GMT

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?
*

- It's useful to provide a small self-contained example, as recommended by the posting guide (referred to after every r-help message).
- 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.
- 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.
- 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

R-help_at_r-project.org mailing list

https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code. Received on Sun 02 Mar 2008 - 17:17:24 GMT

Archive maintained by Robert King, hosted by
the discipline of
statistics at the
University of Newcastle,
Australia.

Archive generated by hypermail 2.2.0, at Sun 02 Mar 2008 - 18:30:18 GMT.

*
Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help.
Please read the posting
guide before posting to the list.
*