R help - Sep 2021 - coxph means not equal to means of model matrix

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



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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
>

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