Hi all!

I've got this error while running 

example(Glm)



library("rms")
> example(Glm)

Glm> ## Dobson (1990) Page 93: Randomized Controlled Trial :
Glm> counts <- c(18,17,15,20,10,20,25,13,12)

Glm> outcome <- gl(3,1,9)

Glm> treatment <- gl(3,3)

Glm> f <- glm(counts ~ outcome + treatment, family=poisson())

Glm> f

Call:  glm(formula = counts ~ outcome + treatment, family = poisson())

Coefficients:
(Intercept)     outcome2     outcome3   treatment2   treatment3  
  3.045e+00   -4.543e-01   -2.930e-01   -4.210e-16   -3.997e-16  

Degrees of Freedom: 8 Total (i.e. Null);  4 Residual
Null Deviance:    10.58 
Residual Deviance: 5.129 AIC: 56.76 

Glm> anova(f)
Analysis of Deviance Table

Model: poisson, link: log

Response: counts

Terms added sequentially (first to last)


          Df Deviance Resid. Df Resid. Dev
NULL                          8    10.5814
outcome    2   5.4523         6     5.1291
treatment  2   0.0000         4     5.1291

Glm> summary(f)

Call:
glm(formula = counts ~ outcome + treatment, family = poisson())

Deviance Residuals: 
       1         2         3         4         5         6         7         8  
-0.67125   0.96272  -0.16965  -0.21999  -0.95552   1.04939   0.84715  -0.09167  
       9  
-0.96656  

Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
(Intercept)  3.045e+00  1.709e-01  17.815   <2e-16 ***
outcome2    -4.543e-01  2.022e-01  -2.247   0.0246 *  
outcome3    -2.930e-01  1.927e-01  -1.520   0.1285    
treatment2  -4.210e-16  2.000e-01   0.000   1.0000    
treatment3  -3.997e-16  2.000e-01   0.000   1.0000    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 10.5814  on 8  degrees of freedom
Residual deviance:  5.1291  on 4  degrees of freedom
AIC: 56.761

Number of Fisher Scoring iterations: 4


Glm> f <- Glm(counts ~ outcome + treatment, family=poisson())
Error in Design(eval(mf, parent.frame())) : 
  dataset dd not found for options(datadist=)




 
My session Info


sessionInfo()
R version 2.12.1 Patched (2011-01-08 r53945)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
 [1] tcltk     tools     splines   stats     graphics  grDevices utils    
 [8] datasets  methods   base     

other attached packages:
[1] lattice_0.19-17 debug_1.2.4     mvbutils_2.5.4  rms_3.1-0      
[5] mgcv_1.7-2      Hmisc_3.8-3     survival_2.36-2 foreign_0.8-41 

loaded via a namespace (and not attached):
[1] cluster_1.13.2     grid_2.12.1        Matrix_0.999375-46 nlme_3.1-97       

While I don't have this issue on  another R-machine


> library(rms)
> example(Glm)

Glm> ## Dobson (1990) Page 93: Randomized Controlled Trial :
Glm> counts <- c(18,17,15,20,10,20,25,13,12)

Glm> outcome <- gl(3,1,9)

Glm> treatment <- gl(3,3)

Glm> f <- glm(counts ~ outcome + treatment, family=poisson())

Glm> f

Call:  glm(formula = counts ~ outcome + treatment, family = poisson())

Coefficients:
(Intercept)     outcome2     outcome3   treatment2   treatment3  
  3.045e+00   -4.543e-01   -2.930e-01    8.717e-16    4.557e-16  

Degrees of Freedom: 8 Total (i.e. Null);  4 Residual
Null Deviance:    10.58 
Residual Deviance: 5.129 AIC: 56.76 

Glm> anova(f)
Analysis of Deviance Table

Model: poisson, link: log

Response: counts

Terms added sequentially (first to last)


          Df Deviance Resid. Df Resid. Dev
NULL                          8    10.5814
outcome    2   5.4523         6     5.1291
treatment  2   0.0000         4     5.1291

Glm> summary(f)

Call:
glm(formula = counts ~ outcome + treatment, family = poisson())

Deviance Residuals: 
       1         2         3         4         5         6         7         8  
-0.67125   0.96272  -0.16965  -0.21999  -0.95552   1.04939   0.84715  -0.09167  
       9  
-0.96656  

Coefficients:
              Estimate Std. Error z value Pr(>|z|)    
(Intercept)  3.045e+00  1.709e-01  17.815   <2e-16 ***
outcome2    -4.543e-01  2.022e-01  -2.247   0.0246 *  
outcome3    -2.930e-01  1.927e-01  -1.520   0.1285    
treatment2   8.717e-16  2.000e-01   0.000   1.0000    
treatment3   4.557e-16  2.000e-01   0.000   1.0000    
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1 

(Dispersion parameter for poisson family taken to be 1)

    Null deviance: 10.5814  on 8  degrees of freedom
Residual deviance:  5.1291  on 4  degrees of freedom
AIC: 56.761

Number of Fisher Scoring iterations: 4


Glm> f <- Glm(counts ~ outcome + treatment, family=poisson())

Glm> # could have had rcs( ) etc. if there were continuous predictors
Glm> f

General Linear Model

Glm(formula = counts ~ outcome + treatment, family = poisson())

                   Model Likelihood     
                      Ratio Test        

Obs           9    LR chi2      5.45    
Residual d.f. 4    d.f.            4    
g         0.227    Pr(> chi2) 0.2440    


           Coef    S.E.   Wald Z Pr(>|Z|)
Intercept   3.0445 0.1709 17.81  <0.0001 
outcome2   -0.4543 0.2022 -2.25  0.0246  
outcome3   -0.2930 0.1927 -1.52  0.1285  
treatment2  0.0000 0.2000  0.00  1.0000  
treatment3  0.0000 0.2000  0.00  1.0000  



Glm> anova(f)
                Wald Statistics          Response: counts 

 Factor     Chi-Square d.f. P     
 outcome    5.49       2    0.0643
 treatment  0.00       2    1.0000
 TOTAL      5.49       4    0.2409

Glm> summary(f, outcome=c('1','2','3'), treatment=c('1','2','3'))
             Effects              Response : counts 

 Factor          Low High Diff. Effect S.E. Lower 0.95 Upper 0.95
 outcome - 1:2   2   1    NA    0.45   0.20  0.06      0.85      
 outcome - 3:2   2   3    NA    0.16   0.22 -0.26      0.58      
 treatment - 1:2 2   1    NA    0.00   0.20 -0.39      0.39      
 treatment - 3:2 2   3    NA    0.00   0.20 -0.39      0.39      
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=C              LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] splines   stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] rms_3.1-0       Hmisc_3.8-3     survival_2.36-2

loaded via a namespace (and not attached):
[1] cluster_1.13.2  grid_2.12.1     lattice_0.19-13 tools_2.12.1 
Many thanks

Anna



Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.


      
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