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]]
______________________________________________ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.