Km compactify rectify by kenmawer · Pull Request #101 · cmu-delphi/epiprocess

kenmawer · 2022-06-14T01:25:13Z

I rectified compactify by overhauling it.

…-compactify

…side this project.

… being redundant.

…es as to check if it works.

brookslogan · 2022-07-25T09:58:02Z

Closes #111. Closes #136.

brookslogan · 2022-07-25T17:05:12Z

Closes #62.

kenmawer

Looks good to me. I'd say that on a separate PR, we can specify examples, etc. on vignettes about what things such as clobberable versions and the end version mean, if those aren't there.

brookslogan · 2022-07-25T18:18:00Z

Okay, discussing with Ryan, we might need to roll back some of my changes, at least.

kenmawer · 2022-07-25T18:53:21Z

The pull request is filled with random changes, which makes it hard to track down what had actually been changed within this pull request rather than outside of it. I may have overlooked something that should be updated/fixed, especially here with the clutter.

brookslogan · 2022-07-26T18:57:04Z

The Files changed helps with this, or using commit1..commit2 or commit1...commit2 with git commands. Of course, it probably would have been better if for some of these incidental bugfixes if I just made checks for the edge cases they addressed and complained and made the fixes in separate PRs. Then we'd be able to merge more quickly and have less changes from merge conflict resolution to deal with.

To try to prevent this from continuing to get out of hand, I'll try to do the minimal immediate edits from Ryan's feedback and file others in issues.

Always introduce version-wise LOCF as "last observation of each observation carried forward (LOCF)" or something quite similar. Clarify time-wise LOCF in one place.

kenmawer · 2022-07-27T16:36:32Z

It noticed that by fixing the conflicts, the tests fail. Did I wrongly use the bottom part rather than the top part of the conflict?

Merge branch 'main' of https://github.com/cmu-delphi/epiprocess into km-compactify_rectify # Conflicts: # R/archive.R # tests/testthat/test-methods-epi_archive.R

Merge branch 'km-compactify_rectify' of https://github.com/dajmcdon/epiprocess into km-compactify_rectify # Conflicts: # R/archive.R # tests/testthat/test-methods-epi_archive.R

brookslogan · 2022-07-28T16:19:06Z

I'm looking at git log --remerge-diff and some minor point did pop up. I'll push changes for what I notice, then you can double-check. After that, maybe I'll just file the remaining issues Ryan brought up in Issues and merge so we don't have to keep merging main in here.

- max(self$DT$time_value) -> max_time - merge updates to as_of test: both - test that doesn't mutate key - use custom test archive, not archive_cases_dv_subset

kenmawer added 30 commits May 13, 2022 16:08

Added some details for compactify

636f212

Added compactify variable with check.

05a4804

Updated function.

7760ce4

Put !!! to indicate incomplete part.

fe1f2d8

Shortened code

1268bb7

More code updates, including updates for vignette.

56859cb

Put in new changes to vignette.

bd4daf3

Merge branch 'main' of https://github.com/dajmcdon/epiprocess into km…

a6d6975

…-compactify

Added function to remove LOCF. This was copy-pasted while working out…

084bf8c

…side this project.

Still need to figure out how to get this to not give me a null dataset.

d6a5fed

Fixed a typo on the code. I still haven't finished it.

87c487d

Changed some text and fixed a typo.

22937ae

Add a comment about code

7310d22

Put in a code stub for compactify testing.

5eb4bdd

Made tests and fixed a bug.

82756d5

There's still work to do in ensuring the LOCF rows are printed properly!

97a2161

Fixed tests, LOCF rows still need to be printed.

21d3d55

Added warnings for LOCF.

ffb32fe

Updated testing and warnings.

fd1c26a

Updated testing.

cbdf9dd

Still needs updating so tests pass. No longer using delphi.epidata.

c417f56

Changed how LOCF checking will work. (Still needs work.)

fef7377

Added updates and changed some names.

b142442

Changed LOCF check

f7b353b

Updated archive code.

46628ca

Improved LOCF filtering by treating NA's as if they are LOCF's due to…

5479dd8

… being redundant.

Modified arrange function to also account for other_keys.

4f0ee0d

Update comment on RStudio.

5420261

Updated LOCF checking to take out redundancies.

c66cb4e

Greatly improved as to actually test LOCF with more control over valu…

0a924be

…es as to check if it works.

This was referenced Jul 25, 2022

Data variables don't store all the right values (at least archive_cases_dv_subset) #150

Closed

Consider adding join/merge between epi_archive and data frame #148

Open

kenmawer commented Jul 25, 2022

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kenmawer requested a review from brookslogan July 25, 2022 18:07

lcbrooks and others added 4 commits July 27, 2022 04:12

Change "LVCF" back to "LOCF", but with consistent intro text

8271a97

Always introduce version-wise LOCF as "last observation of each observation carried forward (LOCF)" or something quite similar. Clarify time-wise LOCF in one place.

Rename observed_versions_end[_conflict] -> versions_end[_conflict]

155ea73

Rename versions_end_conflict -> sync, "stop" -> "forbid"

a71c3fe

Merge branch 'main' into km-compactify_rectify

4c1f7c8

kenmawer added 2 commits July 27, 2022 11:01

Updated km-compactify_rectify whilst dealing with conflicts.

2ddc3d5

Merge branch 'main' of https://github.com/cmu-delphi/epiprocess into km-compactify_rectify # Conflicts: # R/archive.R # tests/testthat/test-methods-epi_archive.R

Empty commit.

c5eaf14

Merge branch 'km-compactify_rectify' of https://github.com/dajmcdon/epiprocess into km-compactify_rectify # Conflicts: # R/archive.R # tests/testthat/test-methods-epi_archive.R

brookslogan mentioned this pull request Jul 27, 2022

Ensure doc consistency about explicit/implicit versions in epi_archive #172

Open

lcbrooks and others added 8 commits July 28, 2022 10:07

Fixup merge

ef45cf1

- max(self$DT$time_value) -> max_time - merge updates to as_of test: both - test that doesn't mutate key - use custom test archive, not archive_cases_dv_subset

Fixup formatting on merge fixup

8bb37c4

Merge branch 'main' into km-compactify_rectify

ca37636

Changed n's default to be consistent with the rest of the branch.

174fecf

Updated missing n.

4eb7f11

Repair compactify vignette median slide

c1c61e4

Sync compactify.Rmd text with code: 1000 iterations of filter

bbd1c17

Fix incomplete change from "LVCF" back to "LOCF"

2a79c08

brookslogan approved these changes Jul 29, 2022

View reviewed changes

brookslogan merged commit b90916d into cmu-delphi:main Jul 29, 2022

This was referenced Aug 1, 2022

Change which epi_archive operations have reference semantics #67

Closed

Revise epix_merge to always fit in last-version-carried-forward framework, merge additional metadata #136

Closed

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Km compactify rectify - #101

Km compactify rectify#101
brookslogan merged 114 commits into
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