On 6/1/19 1:32 PM, Marc Schwartz wrote:
On Jun 1, 2019, at 12:59 PM, Peter Langfelder <peter.langfel...@gmail.com>
wrote:
On Sat, Jun 1, 2019 at 3:22 AM Therneau, Terry M., Ph.D. via R-devel
<r-devel@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
Thanks for the comments thus far.
I think that a new package is out of the question, survival is just too deeply
embedded.
Note that my standard policy is to run R CMD check on ALL of the packages in CRAN that
depend, import, or suggest survival, before any update to CRAN. Well, almost all: I skip
the bioconductor ones, and there are a handful that want a GIS or some other addition not
on my test box. It usually takes a week or more to chase down everything. Then the CRAN
folks do the same, and often find one or two that I missed. I plan to make the github
version available well before pushing to CRAN. Any change to the package will be painful
to me as well.
Terry T.
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