Re: [R] Direct adjusted survival?

From: Terry Therneau <therneau_at_mayo.edu>
Date: Thu, 31 Jan 2008 08:51:46 -0600 (CST)


> The lines that I hoped to be the survival probabilities for each edtrt-group
> adjusted for confounding by log(bili) are nearly identical to the KM-lines,
> and they certainly don't appear adjusted for the very strong confounding by
> log(bili). I'm not quite sure what they are, though.

   Yes, survexp will fit direct adjusted curves (and also the Hakulinen and conditional methods). For your example, I would expect that the ordinary Kaplan-Meier curves for treatment 1 vs 2 should be almost identical to the adjusted curves for treatment 1 vs 2. The PBC data is from a randomized trial, the two treatment arms are (not surprisingly) very well balanced with respect to bilirubin values, and so adjusting for imbalance makes no real change. This is exactly what the survexp code that you gave does.

   If you are expected the curves to change, then I guess I'm not sure what you mean by "strong confounding". Bilirubin is perhaps the most important clinical measure of severity for any of the cholestatic liver diseases, of which PBC is one; but being a strong predictor of mortality does not necessarily imply confounding.  

   Standard errors for the direct curve are daunting -- it is several pages of code in a Gail and Benichou (?) paper. I need to create an example for doing this with the bootstrap. One problem is the two sources of variation. The original Cox model's curves have variance of course, but do we consider the population of subjects being averaged over (for the DA curve) to be fixed or random?

   For a long explanation of expected survival I would refer you to chapter 10 of Therneau and Grambsch, "Modeling Survival Data". One of the more confusing aspects is that things get re-discovered and renamed, the "direct adjusted survival" curve for instance is Ederer's method (1961) brought forward to a Cox model. The ideas are not hard, but it does take a whole chapter.

        Terry Therneau



R-help_at_r-project.org mailing list
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. Received on Thu 31 Jan 2008 - 15:52:34 GMT

Archive maintained by Robert King, hosted by the discipline of statistics at the University of Newcastle, Australia.
Archive generated by hypermail 2.2.0, at Thu 31 Jan 2008 - 19:30:24 GMT.

Mailing list information is available at https://stat.ethz.ch/mailman/listinfo/r-help. Please read the posting guide before posting to the list.

list of date sections of archive