[R] Confusion about coxph and Helmert contrasts

[Christian Lederer]

Hi,

perhaps this is a stupid question, but i need some help about
Helmert contrasts in the Cox model.


I have a survival data frame with an unordered factor `group'
with levels 0 ... 5.
Calculating the Cox model with Helmert contrasts, i expected that
the first coefficient would be the same as if i had used treatment 
contrasts, but this is not true.
I this a error in reasoning, or is it possible, that both contrasts use
a different ordering of the levels?
I am confused about the fact, that coefficients for different levels are 
calculated, depending on weather i include level 0 or not:

If level 0 is included, with both contrasts coxph calculates 
coefficients for group 1 ... group 5.
But if i exclude level 0, coxph calculates coeffficients for
group 2 ... 5 with treatment and coefficients for group 1 ... 4 using
helmert:

 > options(contrasts = c("contr.treatment", "contr.poly"))
 > cox.t <- coxph(Surv(time,cens) ~ as.factor(group), data=data)
 > options(contrasts = c("contr.helmert", "contr.poly"))
 > cox.h <- coxph(Surv(time,cens) ~ as.factor(group), data=data)
 > cox.t$coefficients
as.factor(group)1 as.factor(group)2 as.factor(group)3 as.factor(group)4
        -0.4301351         0.2078431        -0.0694138         0.3442058
as.factor(group)5
         0.1368716
 > cox.h$coefficients
as.factor(group)1 as.factor(group)2 as.factor(group)3 as.factor(group)4
      -0.215067529       0.140970216       0.001170877       0.083426449
as.factor(group)5
       0.021061935

 > data <- data[data$group > 0,]
 > options(contrasts = c("contr.treatment", "contr.poly"))
 > cox.t <- coxph(Surv(time,cens) ~ as.factor(group), data=data)
 > options(contrasts = c("contr.helmert", "contr.poly"))
 > cox.h <- coxph(Surv(time,cens) ~ as.factor(group), data=data)
 > cox.t$coefficients
as.factor(group)2 as.factor(group)3 as.factor(group)4 as.factor(group)5
         0.6399999         0.3612753         0.7762236         0.5688559
 > cox.h$coefficients
as.factor(group)1 as.factor(group)2 as.factor(group)3 as.factor(group)4
        0.31999997        0.01375844        0.11061629        0.02489624

A am absolutely confused; any help is welcome.

Christian :-)