[Rd] survival changes

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

In the next version of the survival package I intend to make a non-upwardly compatable 
change to the survfit object.  With over 600 dependent packages this is not something to 
take lightly, and I am currently undecided about the best way to go about it.  I'm looking 
for advice.

The change: 20+ years ago I had decided not to include the initial x=0,y=1 data point in 
the survfit object itself.  It was not formally an estimand and the plot/points/lines etc 
routines could add this on themselves.  That turns out to have been a mistake, and has led 
to a steady proliferation of extra bits as I realized that the time axis doesn't always 
start at 0, and later (with multi state) that y does not always start at 1 (though the 
states sum to 1), and later the the error doesn't always start at 0, and another 
realization with cumulative hazard, and ...
The new survfit method for multi-state coxph models was going to add yet another special 
case.  Basically every component is turning into a duplicate of "row 1" vs "all the 
others".  (And inconsistently named.)

Three possible solutions
1. Current working draft of survival_3.0.3:  Add a 'version' element to the survfit object 
and a 'survfit2.3' function that converts old to new.  All my downstream functions (print, 
plot,...) start with an "if (old) update to new" line.  This has allowed me to stage 
updates to the functions that create survfit objects -- I expect it to happen slowly.  
There will also be a survfit3.2 function to go backwards. Both the forward and backwards 
functions leave objects alone if they are currently in the desired format.

2. Make a new class "survfit3" and the necessary 'as' functions. The package would contain 
plot.survfit and plot.survfit3 methods, the former a two line "convert and call the 
second" function.

3. Something I haven't thought of.

Number 2 has a cleanness about it, but there is a long term nuisance about it wrt 
documentation.  Users, not unreasonably, expect the survfit function to produce a survfit 
object, and that is what they look for in the help pages.

I plan to have 3.0-x on github before userR so that users can begin to play with it (and 
to get feeback before pushing to CRAN), so need to make a decision.

Terry T.



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