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.
[[alternative HTML version deleted]]
______________________________________________
R-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/r-devel
