Clarify naming and fix defaults: `epix_slide` is over versions

[brookslogan]

• [x] ~Make ref_time_values default to something involving versions, not all time values; full_seq up to observed_versions_end with period determined using tsibble::guess_frequency or an alternative to avoid potential licensing complications~ the default value setting is now https://github.com/cmu-delphi/epiprocess/issues/153; the renaming will be part of a different discussion/issue
• [x] ~Rename ref_time_values to something involving "version"~ part of separate discussion
• [x] ~Rename n to something that doesn't imply it's counting something~ replace with before (+add issue about dot prefixes)
• [x] Remove any n default value (e.g., 7 doesn't make sense; we won't get 7 time values in typical data sources)
• [x] ~Rename time_value column in output to version~ part of separate discussion
• [x] ~Consider making output an epi_archive... but we might need to invent geo and time columns...~ part of larger discussion
• [x] Fix up documentation, examples, vignettes, etc. to make sense and work with the above

[brookslogan]

Another thought: do we want to rename epix_slide to epix_version_slide?

[brookslogan]

We should try to avoid using tsibble::guess_frequency if possible for now. Another issue with the full_seq suggestion is that it could be altered by compactify; we'd at least want to document this, by making sure compactify descriptions don't promise full compatibility and noting specifically for the ref_time_values/new-name documentation. This might also lead us to think of a different post-compactify format that records other versions that had updates reported. (This also hints at making epi_archive provide a different interpretation: the current setup is as if we continuously and perfectly monitored some data source for updates within some time range; an alternative setup is to say that we only observed a certain set of versions. It even more hassle for a user to provide this version set explicitly, but we could default to something like the default I was describing. This alternative interpretation would mean that as_of should not allow us to ask for versions that weren't measured or should return NAs. It's a bit more complex, but also more precise/realistic.)

[ryantibs]

Thanks for raising these! I'd like to talk some of these through before you guys get too far along to understand what the problems are.

I tried to design epix_slide() to be as close as possible to epi_slide(), thinking this was a feature, rather than a bug. Thus the way I see it is that the name of the function itself, and all its argument names, being close is a good thing.

Hence I like items 1 and 4 in your todo list, but I'm not sure I like the others which are suggesting we rename things (items 2, 3, 5).

Thinking back again about the output type for epix_slide() (item 6) is a good idea, though I'm not sure we'll arrive at any obvious solutions. I'd be happy to be wrong though.

Should we discuss on a call or here on GitHub? Call might be more fluid. We could combine it with discussing #64 #67 whenever you're ready.

[brookslogan]

We can discuss on call.

Recording a couple vague thoughts to hash out then:

• An alternative to n is to try to make it "true", and change the code to given them n time values... but that will be at some varying lag from the queried version, so the user will then need to be aware of and watch out for that...
• fill_through_version(archive, fill_versions_end, how="na") will also mess up the states version default if the spacing is not the smallest possible for a given class. This could be changed to involve frequency guessing, but then its behavior would also be affected by compactify. (If we had a /set/ (not a clopen range) of observed versions + said that things were unobserved between those, then this could be a no op.)
• time_value -> version thing: see existing bug, dev misinterpretation, forecasting&nowcasting&backcasting-output ahead/lag consistency. Archive transformers will be part of any metamodeling framework. Having geo and time value columns enforced is a little nuisance. Whether we want to compute the entire result at once, vs. previews, is a question. (Reminds of lazy merge idea as well. And early sketches of combined lazy archive merge-slide.) Think dbplyr might have a relevant interface.

[kenmawer]

How would item 6 even work though? I don't see this happening, unless we also the time_value feature along with the version feature.

Also, for item 1, ref_time_values should actually be ref_versions.

Finally, epix_slide won't grab the latest version; however, this is a bug beyond the scope of this update.

[ryantibs]

I'll leave it up to you Logan to schedule a call whenever you feel is the right time. We can discuss on the call since I think that's the most fluid, given that see some of these ideas differently (and maybe we'll clarify some confusion along the way, from either side).

[brookslogan]

Summary from call:

• Agreed-upon changes: clean up the n problem:
  • Remove the default n value, in both epix_slide and epi_slide
  • Replace n with [before in epix_slide and] before and after in ~epix_slide and~ epi_slide. n=7 would act like before=6, after=0. [before should have no default in either function. after should have a default of 0 in epi_slide (and doesn't exist in epix_slide).] [Edits: corrections to match Ryan's description below.]
• Separate discussion: should we rename ref_time_values and time_value output column to something involving version [--- or as_of, to match epi_df metadata?], or keep the former and have the latter turn into two duplicate columns with both names? Should we output an epi_archive?
• Separate discussion: should we rename max_version parameter of epix_slide to version [or as_of, to match epi_df metadata?]?
• Separate issue: dot-prefixing args in functions with user-"controlled" ... args (their own functions' parameter names or their own column names)

I don't think many of the tasks in this issue still apply. Closing this and opening other issues.

[ryantibs]

Thanks for the summary. That all sounds right except for one detail:

Default after should be 0 in epi_slide() and I think after shouldn't even be present as an arg in epix_slide().

(Subtleties for forecast data can be discussed and possible modifications made later, as part of the time vs version discussion)