[R] coxph means not equal to means of model matrix

[Therneau, Terry M., Ph.D.]

See ?coxph, in particular the new "nocenter" option.

Basically, the "mean" component is used to center later computations.� This can be 
critical for continuous variables, avoiding overflow in the exp function, but is not 
necessary for 0/1 covariates.�� The fact that the default survival curve would be for a 
sex of .453, say, was off-putting to many.

Terry T.


On 9/3/21 11:01 AM, Bond, Stephen wrote:
>
> Hi,
>
> Please, help me understand what is happening with the means of a Cox model?
>
> I have:
>
> R version 4.0.2 (2020-06-22) -- "Taking Off Again"
>
> Copyright (C) 2020 The R Foundation for Statistical Computing
>
> Platform: x86_64-w64-mingw32/x64 (64-bit)
>
> getOption("contrasts")
>
> ������� unordered���������� ordered
>
> "contr.treatment"����� "contr.poly"
>
> According to the help �coxph.object has a component holding the means of the X 
> (model.matrix). This does not hold any more.
>
> ```
>
> library(survival)
>
> test1 <- list(time=c(4,3,1,1,2,2,3),
>
> �������������������status=c(1,1,1,0,1,1,0),
>
> �������������������x=c(0,2,1,1,1,0,0),
>
> �������������������sex=factor(c(0,0,0,0,1,1,1)))
>
> m1 <- coxph(Surv(time, status) ~ x + sex, test1)
>
> m1$means
>
> ##������� x����� sex1
>
> ## 0.7142857 0.0000000
>
> colMeans(model.matrix(m1))
>
> ##�������� x����� sex1
>
> ## 0.7142857 0.4285714
>
> ```
>
> Will new observations be scored using the zero mean from the object?? Is this just a 
> reporting change where $means shows the reference level and no longer the mean of the 
> model matrix??
>
> Thanks everybody
>


	[[alternative HTML version deleted]]