Hi Brant I have not got Fitzmaurice etal but from their web site it seems that you are trying to do ordinal GEE
With GEE models particularly ordinal models you MUST get your data structure correct otherwise it can fail or even R can crash try f1 = ordgee(ordered(y) ~ factor(gender) + cage + cage2 + factor(gender):cage + factor(gender):cage2, id = id, data = muscatine2, waves=muscatine2$occasion, mean.link="logit", corstr=("unstructured")) > summary(f1) Call: ordgee(formula = ordered(y) ~ factor(gender) + cage + cage2 + factor(gender):cage + factor(gender):cage2, id = id, waves = muscatine2$occasion, data = muscatine2, mean.link = "logit", corstr = ("unstructured")) Mean Model: Mean Link: logit Variance to Mean Relation: binomial Coefficients: estimate san.se wald p Inter:0 -1.214613103 0.050571150 576.8597850 0.000000e+00 factor(gender)1 0.115330450 0.071158497 2.6268450 1.050703e-01 cage 0.037419375 0.013263832 7.9589357 4.785054e-03 cage2 -0.017437692 0.003378786 26.6352422 2.457205e-07 factor(gender)1:cage 0.007510802 0.018268075 0.1690390 6.809673e-01 factor(gender)1:cage2 0.003860069 0.004632095 0.6944407 4.046580e-01 Scale is fixed. Correlation Model: Correlation Structure: unstructured Correlation Link: log Estimated Correlation Parameters: estimate san.se wald p alpha.1 3.130702 0.1535950 415.4599 0 alpha.2 2.408103 0.1455606 273.6921 0 alpha.3 2.793549 0.1351264 427.3978 0 Returned Error Value: 0 Number of clusters: 4856 Maximum cluster size: 3 I presume that you may have a dataset in mind to work on later you may want to check out the repolr and multgee packages as well Duncan Duncan Mackay Department of Agronomy and Soil Science University of New England Armidale NSW 2351 Email: home: mac...@northnet.com.au -----Original Message----- From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On Behalf Of Brant Inman Sent: Sunday, 2 March 2014 03:52 To: r-help@r-project.org Subject: [R] geeglm error NA/NaN/Inf in 'y' R-helpers: I am getting an error when trying to fit a GEE model. Below is code reproducing the error. ### library(foreign) muscatine <- read.dta('http://www.hsph.harvard.edu/fitzmaur/ala2e/muscatine.dta') muscatine$gender <- as.factor(muscatine$gender) muscatine$y <- as.factor(muscatine$y) muscatine$cage <- muscatine$age - 12 muscatine$cage2 <- muscatine$cage^2 head(muscatine); summary(muscatine) muscatine2 <- na.omit(muscatine); summary(muscatine2) # Remove missing data # GEE model to reproduce example in Fitzmaurice, Laird, Ware book library(geepack) f1 <- geeglm(y ~ gender*cage + gender*cage2, id=id, data=muscatine2, family=binomial(link=logit), waves=occasion, corstr='unstructured') ### This gives me the following error > f1 <- geeglm(y ~ gender*cage + gender*cage2, id=id, data=muscatine2, + family=binomial(link=logit), + waves=occasion, corstr='unstructured') Error in lm.fit(zsca, qlf(pr2), offset = soffset) : NA/NaN/Inf in 'y' In addition: Warning messages: 1: In model.response(mf, "numeric") : using type = "numeric" with a factor response will be ignored 2: In Ops.factor(y, mu) : - not meaningful for factors ### I would tremendously appreciate any help that could explain why I am getting this error as I am not understanding this. Brant ______________________________________________ R-help@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. ______________________________________________ R-help@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.