[R] Help with contrast settings in glm and lm

[Jesús María Frías Celayeta]

Hi!

	I am trying to validate some R code that we have been porting from
S (ellipse library) and now we are on the step of trying with some
examples to see if the code gives the same results as in S. I have
received some results from S-PLUS 4.5 help examples and I have some
trouble reproducing them. Apparently S+ uses helbert contrasts in
categorical variables as a default and R uses contrasts based in
orthogonal polynomials. However, in R there exists contr.helmert and I
would like to actually set R in a way that a regression procedure will use
helmert type contrasts (as in S+), in order to have the same results. 

	Is there a way to change the default contrasts used in regression
(lm and glm) so that after it the regression uses those contrasts? I have
tried options() with no too much sucess. I am probably loosing some page
in the manual, so just in the case I excuse myself in advance. 


This is the detailed thing.

1.-My fit with cntr.poly (the default) is
> glmfit.R

Call:  glm(formula = skips ~ ., family = poisson, data = solder.balance) 

Coefficients:
(Intercept)    Opening.L    Opening.Q     Solder.L       MaskA3 MaskB3  
   -0.06267     -1.33890      0.56194     -0.77763      0.42819 1.20225  
     MaskB6    PadTypeD4    PadTypeL4    PadTypeD6    PadTypeL6 PadTypeD7  
    1.86648      0.11000      0.37237     -0.25865     -0.55845 0.01156  
  PadTypeL7    PadTypeL8    PadTypeW9    PadTypeL9       Panel2 Panel3  
   -0.38021     -0.16115     -1.32758     -0.52645      0.33352 0.25440  

Degrees of Freedom: 719 Total (i.e. Null);  702 Residual
Null Deviance:      6856 
Residual Deviance: 1130         AIC: 2749 

2.-When I change the options for the contrasts for contr.helmert to try to
emulate S+ results.

> options(contrasts=c("contr.treatment", "contr.helmert"))
> glmfit.R.2<- glm(formula = skips ~ ., family = poisson, data =
solder.balance) 
> glmfit.R.2

Call:  glm(formula = skips ~ ., family = poisson, data = solder.balance) 

Coefficients:
(Intercept)     Opening1     Opening2      Solder1       MaskA3 MaskB3  
   -0.06267     -0.81749     -0.35867     -0.54987      0.42819 1.20225  
     MaskB6    PadTypeD4    PadTypeL4    PadTypeD6    PadTypeL6 PadTypeD7  
    1.86648      0.11000      0.37237     -0.25865     -0.55845 0.01156  
  PadTypeL7    PadTypeL8    PadTypeW9    PadTypeL9       Panel2 Panel3  
   -0.38021     -0.16115     -1.32758     -0.52645      0.33352 0.25440  

Degrees of Freedom: 719 Total (i.e. Null);  702 Residual
Null Deviance:      6856 
Residual Deviance: 1130         AIC: 2749 

> options("contrasts") 
$contrasts
[1] "contr.treatment" "contr.helmert"  

	which is the same as in 1 

3.- This result does quite differ from the glm in S+ using helmert
contrasts: 

> glmfit
Call:
glm(formula = skips ~ ., family = poisson, data = solder.balance)

Coefficients:
 (Intercept) Opening.L Opening.Q     Solder     Mask1     Mask2 Mask3   PadType1  PadType2 
   0.7356797 -1.338898 0.5619403 -0.7776274 0.2140968 0.3293834 0.3307507 0.05500044 0.1057882
   PadType3   PadType4   PadType5    PadType6     PadType7   PadType8 PadType9    Panel1 
 -0.1048597 -0.1228765 0.01308473 -0.04662037 -0.007583584 -0.1355021 -0.02828819 0.1667612
     Panel2 
 0.02921374

Degrees of Freedom: 720 Total; 702 Residual
Residual Deviance: 1130.48 


Thanks in advance for any help,


IOsu

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