[Rd] survival changes
Therneau, Terry M., Ph.D.
therne@u @end|ng |rom m@yo@edu
Sat Jun 1 12:22:33 CEST 2019
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
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
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.
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