[R] geeglm error NA/NaN/Inf in 'y'

[Duncan Mackay]

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: mackay at northnet.com.au



-----Original Message-----
From: r-help-bounces at r-project.org [mailto:r-help-bounces at r-project.org] On
Behalf Of Brant Inman
Sent: Sunday, 2 March 2014 03:52
To: r-help at 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 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.