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Km compactify rectify#101

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brookslogan merged 114 commits intocmu-delphi:maincmu-delphi/epiprocess:mainfrom

dajmcdon:km-compactify_rectifydajmcdon/epiprocess:km-compactify_rectifyCopy head branch name to clipboard

Jul 29, 2022

Commits

Commits on May 13, 2022

• Added some details for compactify

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Commits on May 16, 2022

• Added compactify variable with check.

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• Updated function.

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• Put !!! to indicate incomplete part.

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• Shortened code

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Commits on May 17, 2022

• More code updates, including updates for vignette.

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• Put in new changes to vignette.

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• Merge branch 'main' of https://github.com/dajmcdon/epiprocess into km-compactify

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Commits on May 20, 2022

• Added function to remove LOCF. This was copy-pasted while working outside this project.

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

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

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Commits on May 21, 2022

• Changed some text and fixed a typo.

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• Add a comment about code

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Commits on May 31, 2022

• Put in a code stub for compactify testing.

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• Made tests and fixed a bug.

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

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• Fixed tests, LOCF rows still need to be printed.

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Commits on Jun 1, 2022

• Added warnings for LOCF.

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• Updated testing and warnings.

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• Updated testing.

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Commits on Jun 9, 2022

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

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

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• Added updates and changed some names.

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• Changed LOCF check

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Commits on Jun 10, 2022

• Updated archive code.

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Commits on Jun 11, 2022

• Improved LOCF filtering by treating NA's as if they are LOCF's due to being redundant.

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Commits on Jun 13, 2022

• Modified arrange function to also account for other_keys.

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• Update comment on RStudio.

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• Updated LOCF checking to take out redundancies.

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• Greatly improved as to actually test LOCF with more control over values as to check if it works.

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Commits on Jun 14, 2022

• Improved tests to account for multiple values.

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• Updated vignette with an example.

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Commits on Jun 16, 2022

• Updated a few changes based on pull request comments.

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• Cleared up ifelse, improved printing and updated descriptions.

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• Added a few more changes on the vignette and with the warning message.

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• Fixed as_epi_archive on covidcast to be more clear about what is does. Also, improved warning message

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• Updated.

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• Added a test (not finished yet) to test as_of.

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• Added test for testing as_of in conjunction with compactify.

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• Made test more descriptive.

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• Fixed error with if_else

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• Updated vignette.

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• Updated warning message to be more clear.

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• Updated comments.

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Commits on Jun 17, 2022

• Fixed spacing with tests.

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Commits on Jun 18, 2022

• Fix a missing `dplyr::`

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• Fix warnings&errors in examples&tests, keep archive_cases_dv in sync

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Commits on Jun 21, 2022

• Pulled from main.

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• Added a feature for time of compactify.

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• Basic template (not documented yet).

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• Updated broken <<<<< code.

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• Pulled from main, fixed changes.

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• Also need to commit this.

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• Fixed accidentally deleted comment.

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  8ec0b0b

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• Fixed formatting issue.

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  4ec8bbf

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• This new branch is for test rectification due to new datasets. I also noticed some call undefined datasets.

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  f93bd71

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• Updated test to use new dataset similar to old one.

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• Broke up the archive vignette to create a vignette for compactify, which includes performances with and without LOCF applied to data.

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• Updated incorrect code and vignette for more details.

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• Removed comment.

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• Replaced incorrect dataset.

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Commits on Jun 22, 2022

• Updated documentation.

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• Updated this to show a plot of times with and without LOCF.

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Commits on Jun 28, 2022

• Merged upstream; fixed DESCRIPTION conflict.

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• Resolved conflicts.

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Commits on Jun 29, 2022

• Merge branch 'cmu-delphi/main' into km-compactify_time

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• Committed changes for #118.

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• Added changes relating to PR #115.

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• km-compactifify_rectify withouot any errors.

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Commits on Jun 30, 2022

• Merge branch 'main' into km-compactify_rectify

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• Clarify compactify testing code

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Commits on Jul 4, 2022

• Fixed broken code.

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Commits on Jul 5, 2022

• Apply code formatting to an `epi_archive` example

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• Revise `compactify` warning text and assign it a(nother) class

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• Emit some help on `archive_cases_dv` eval errors during `unregister`

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• Merge branch 'main' into km-compactify_rectify

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• Add `clobberable_versions_start`, `observed_versions_end` params

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Commits on Jul 6, 2022

• Merge remote-tracking branch 'dajmcdon/km-compactify_rectify' into km-compactify_rectify

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• Add back explanation about reconstructing sample archive from stored DT

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• Go back to using NA to indicate no clobberable versions

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• Re-`document`

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Commits on Jul 11, 2022

• Merge branch 'main' into km-compactify_rectify

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• This still won't pass checks.

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Commits on Jul 21, 2022

• Add epix_fill_through_version, overhaul epix_merge; needs extra work

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• Merge remote-tracking branch 'dajmcdon/km-compactify_rectify' into km-compactify_rectify

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Commits on Jul 22, 2022

• Fix "always compactifies" epix_merge doc, be precise about mutation in docs

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• Fix example archive to match old val

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• Change "LOCF" to "LVCF" where it's referring to last version carried forward

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Commits on Jul 24, 2022

• Merge branch 'main' into km-compactify_rectify

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• Fix epix_fill_through_version bug from unique-aliasing edge case

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• Fill out tests for new epix_merge

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• Fix head -> utils::head

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• Fix some undoc'd archive params, base::invisible links

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• Merge in epix_slide quosure-passing fix + test

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• Fix tail -> utils::tail in epix_merge

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• Update examples, vignettes to use current merge (but keeping dead? code)

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• Fix compactify vignette rebuilding in `check()`

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• Avoid some check() NOTEs from data.table dotdot prefix

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Commits on Jul 25, 2022

• Remove improper and faulty tidyselect usage from group_by tests

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• Make epix_slide tidyselect tests tougher (not just default grping)

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Commits on Jul 27, 2022

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

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• Rename `observed_versions_end[_conflict]` -> `versions_end[_conflict]`

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

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• Merge branch 'main' into km-compactify_rectify

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• Updated km-compactify_rectify whilst dealing with conflicts.

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• Empty commit.

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Commits on Jul 28, 2022

• Fixup merge

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• Fixup formatting on merge fixup

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• Merge branch 'main' into km-compactify_rectify

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

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• Updated missing n.

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Commits on Jul 29, 2022

• Repair compactify vignette median slide

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

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

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