[EXTERNAL] Re: survival changes

On Jun 1, 2019, at 12:59 PM, Peter Langfelder <peter.langfelder at gmail.com> wrote:

On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel
<r-devel at r-project.org> wrote:

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.

A more "clean break" solution would be to start a whole new package
(call it survival2) that would make these changes, and deprecate the
current survival. You could add warnings about deprecation and urging
users to switch in existing survival functions. You could continue
bugfixes for survival but only add new features to survival2. The new
survival2 and the current survival could live side by side on CRAN for
quite some time, giving maintainers of dependent packages (and just
plain users) enough time to switch. This could allow you to
change/clean up other parts of the package that you could perhaps also
use a rethink/rewrite, without too much concern for backward
compatibility.

Peter

Hi,

I would be cautious in going in that direction, bearing in mind that survival is a Recommended package, therefore included in the default R distribution from the R Foundation and other parties. To have two versions can/will result in substantial confusion, and I would argue against that approach.

There is language in the CRAN submission policy that covers API changes, which strictly speaking, may or may not be the case here, depending upon which direction Terry elects to go:

"If an update will change the package?s API and hence affect packages depending on it, it is expected that you will contact the maintainers of affected packages and suggest changes, and give them time (at least 2 weeks, ideally more) to prepare updates before submitting your updated package. Do mention in the submission email which packages are affected and that their maintainers have been informed. In order to derive the reverse dependencies of a package including the addresses of maintainers who have to be notified upon changes, the function reverse_dependencies_with_maintainers is available from the developer website."


Given the potential extent and impact of the changes being considered, it would seem reasonable to:

1. Post a note to R-Devel (possibly R-Help to cover a larger useR base) regarding whatever changes are finalized and formally announce them. The changes are likely to affect end useRs as well as package maintainers.

2. Send communications directly via e-mail to the relevant package maintainers that have dependencies on survival.

3. Consider a longer deprecation time frame for relevant functions, to raise awareness and allow for changes to be made by package maintainers and useRs as may be apropos. Perhaps post reminders to R-Help at relevant time points in advance as you approach the formal deprecation and release of the updated package.


Terry, if you have not used it yet and/or are not aware of it, take a look at ?Deprecated in base:

   https://stat.ethz.ch/R-manual/R-devel/library/base/html/Deprecated.html

which is helpful in setting up a deprecation process. If you Google "deprecating functions in R", there are numerous examples/flows of use and the associated processes, since the help page does not contain any examples at present.

Regards,

Marc Schwartz