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gee in S-Plus and R?

To: "S-news" <s-news@lists.biostat.wustl.edu>
Subject: gee in S-Plus and R?
From: "Fredrik Lundgren" <fredrik.lundgren@norrkoping.mail.telia.com>
Date: Wed, 12 Dec 2001 01:06:53 +0100
Hello,
I recently updated gee in R 1.3.1 (windows 98 SE)

I happended to compare S-plus and R and found rather large differences in 
coefficients.
How come?

Fredrik Lundgren
Norrköping, Sweden

S-Plus 6 rel3 gives

> summary(gee(breaks ~ tension, id = wool, data = warpbreaks, corstr = 
> "exchangeable"), correlation = F)
[1] "Beginning Cgee S-function, @(#) geeformula.q 5.2 99/06/03"
[1] "running glm to get initial regression estimate"
[1]  28.15   7.36  -0.88

 GEE:  GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
 gee S-function, version 5.2 modified 99/06/03 (1998) 

Model:
 Link:                      Identity 
 Variance to Mean Relation: Gaussian 
 Correlation Structure:     Exchangeable 

Call:
gee(formula = breaks ~ tension, id = wool, data = warpbreaks, corstr = 
"exchangeable")

Summary of Residuals:
   Min    1Q Median   3Q  Max 
 -22.4 -8.14  -2.67 6.33 33.6


Coefficients:
            Estimate Naive S.E. Naive z Robust S.E. Robust z 
(Intercept)    28.15       2.08  13.534        2.04   13.780
   tension1     7.36       1.96   3.765        1.87    3.945
   tension2    -0.88       1.13  -0.779        1.87   -0.471

Estimated Scale Parameter:  141
Number of Iterations:  1

....

R 1.3.1 gives
> summary(gee(breaks ~ tension, id=wool, data=warpbreaks, 
> corstr="exchangeable"))
summary(gee(breaks ~ tension, id=wool, data=warpbreaks, corstr="exchangeable"))
[1] "Beginning Cgee S-function, @(#) geeformula.q 4.13 98/01/27"
[1] "running glm to get initial regression estimate"
[1]  36.38889 -10.00000 -14.72222

 GEE:  GENERALIZED LINEAR MODELS FOR DEPENDENT DATA
 gee S-function, version 4.13 modified 98/01/27 (1998) 

Model:
 Link:                      Identity 
 Variance to Mean Relation: Gaussian 
 Correlation Structure:     Exchangeable 

Call:
gee(formula = breaks ~ tension, id = wool, data = warpbreaks, 
    corstr = "exchangeable")

Summary of Residuals:
       Min         1Q     Median         3Q        Max 
-22.388889  -8.138889  -2.666667   6.333333  33.611111 


Coefficients:
             Estimate Naive S.E.   Naive z Robust S.E.  Robust z
(Intercept)  36.38889   3.069434 11.855246    5.774705  6.301428
tensionM    -10.00000   3.910008 -2.557539    7.463905 -1.339781
tensionH    -14.72222   3.910008 -3.765266    3.731952 -3.944912

Estimated Scale Parameter:  141.1481
Number of Iterations:  1



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