[Rd] survival package

From: Terry Therneau <therneau_at_mayo.edu>
Date: Tue, 10 Feb 2009 15:32:04 -0600 (CST)

R core team -
  It took far, far longer than I anticipated, but I have finally finished the next release of the survival code. Primary changes

  1. The source has been migrated to Rforge. This will now be the primary source. I've used SCCS -> rcs -> cvs and now svn. Further changes will be someone else's problem. I expect that maintaince will now begin to migrate to a larger group and my role diminish; I hope to focus more energy on coxme. I tried to carry forward the entire history of the package. In the current US software copyright mess we might one day have to use that long history. I think I started the SCCS tree in around 1987. I expect to have survival, date, coxme, and bdsmatrix as separate packages within the package tree.
  2. I have merged in a large number of changes/updates that had occured at Mayo, along with all the changes I found in the R source (version 2.32 - when I started this task, 2.34 when I finished). Major changes Complete rewrite of the survfit function(s); most of the work is now done in S instead of C. Added Turnbull's method for general censoring and also competing risk estimates. There are no longer any dependencies on the 'date' library, and it has been removed to a separate branch. The expected survival routines now work with any of Date, posix, timeDate, or date. Survreg was re-written to use R.h style instead of S.h. Common code now works with both packages. It's a big improvement in several ways: easier to code, much easier to read, less clunky. Aalen's additive regression model The survival rate tables have been updated -- the 2000 US rate tables were finally released in Aug 2008. There are 20-30 other small upgrades and fixes that had accrued over time. The file Changelog.09 has more details.
  3. I've tried very hard to make all the code work in both Splus and R. Our group still uses Splus more than R so I have to support both. However, I think that with the recent change in Splus, which will focus them more on vertical markets, and the uptake of R here due to the genetics libraries, that this dual support will no longer be needed within 2-3 years. A year ago I would have defended the extra work necessary to make code work in both dialects much more vigorously. It isn't all that much work if you think ahead. Splus still has a presence in certain markets, and code that works in both is good evangelism. But -- said gain in utility keeps shrinking. In the R directory files that work with both are named whatever.S, those tested only in R are .R. If you think they should all be named .R, then now is the time to do it.
  4. I am very impressed with the package system and R CMD check. I had a cozy Splus/Unix enviroment with a custom makefile that made things very easy and delayed my changeover. This was a significant learning curve, but knowing what I know now I should have started earlier. Kudos to you all.
  5. Known issues:
  6. An additional test suit (book5/book6) corresponding to the not-yet-published extension of my book's appendix of validity tests was added. It found an issue with "stderr of expected survival/Cox model with noninteger case weights/Efron approximation". Not yet addressed, of a 1/n vs 1/(n-1) size. ii. The stderr of terms/survreg/penalized model is different between Splus and R by 50% or more. I haven't yet figured out which formula is correct. iii. The CMD check script still complains about some of my .Rd files; almost all involve imperfect documentation of weights, subset, or ... options. I've been working on this very hard for the last month, and just can't raise any excitment about these last few warnings at the moment.

 Both i and ii exist in the current R code, so there is no loss in updating before working them out.

        Terry T

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