My guess is that this combination of variables produces separation in the data: Too many (all?) of the response 1's are in at level of VAR3, and the 0's are at the other level (or vice versa).
HTH, Simon. On Sat, 2007-12-29 at 18:39 -0500, Charles Willis wrote: > Hello, > > I am trying to run the APE program COMPAR.GEE with a model containing a > categorical response variable and a mixture of continuous and categorical > independent variables. The model runs when I have categorical (binary) > response and two continuous independent variables (VAR1 and VAR2), but when > I include a categorical (binary) independent variable (VAR3), I receive the > following output with an error: > > Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27 > running glm to get initial regression estimate > (Intercept) VAR1 VAR2 VAR3 > -2.656607e+01 -3.110687e-15 -1.582172e-16 5.313214e+01 > "Error in gee(RESPONSE ~ VAR1 + VAR2 + VAR3, c(1, 1, 1, 1, 1, : > Cgee: error: logistic model for probability has fitted value very close to > 1. > estimates diverging; iteration terminated. > In addition: Warning message: > In glm.fit(x = X, y = Y, weights = weights, start = start, etastart = > etastart, : > algorithm did not converge" > > The input is the following model: > > compar.gee(RESPONSE ~ VAR1 + VAR2 + VAR3, data = subset1, family = > "binomial", phy = prunedtree1) > > I have set all of the categorical data as factors and designated the family > as "binomial". I don't know what else to do and the error message is not > clear to me. If anyone can interpret this error message and/or knows how to > run a compar.gee with a mixed set of categorical and continuous variable, I > would be greatly appreciative for your advice. > > Thank you, > Charlie > > > > -- Simon Blomberg, BSc (Hons), PhD, MAppStat. Lecturer and Consultant Statistician Faculty of Biological and Chemical Sciences The University of Queensland St. Lucia Queensland 4072 Australia Room 320 Goddard Building (8) T: +61 7 3365 2506 email: S.Blomberg1_at_uq.edu.au Policies: 1. I will NOT analyse your data for you. 2. Your deadline is your problem. The combination of some data and an aching desire for an answer does not ensure that a reasonable answer can be extracted from a given body of data. - John Tukey. ______________________________________________ [email protected] 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.
