Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Move epipredict vignette datasets to epidatasets #5

Merged
merged 59 commits into from
Oct 14, 2024
Merged

Move epipredict vignette datasets to epidatasets #5

merged 59 commits into from
Oct 14, 2024

Conversation

nmdefries
Copy link
Collaborator

@nmdefries nmdefries commented Sep 26, 2024 •
edited
Loading

Adds several new datasets that are currently either exported by epipredict or are used in its vignettes (but not exported). The datasets are:

  • archive_cases_dv_subset_all_states
  • case_death_rate_archive_tbl
  • county_smoothed_cli_comparison
  • (a few others were already added in Update data attributions #2)

Saves data to disk using version 2 of save, for compatibility with older versions of R. Changes data variables in data-raw scripts from *_dt to *_tbl. Change the covid_case_death_rates as_of date to match epipredict test expectations. Convert ctis_covid_behaviours to an epi_df.

brookslogan and others added 30 commits June 14, 2023 10:46
@brookslogan
Change to just file LICENSE, add @source for CTIS data
01b71e3
@nmdefries
describe format for all datasets; unify doc section naming format
4dc2306
@nmdefries
documentation wording
0bfcc1e
@nmdefries
move data dictionary docs to separate section to ensure heritability
e8d975a
@nmdefries
build docs
9ea783c
@nmdefries
add data contributors as authors
d98b829
@nmdefries
remove dangling partial attribution for CTIS data
2b00f03
@nmdefries
remove copyright holder info for CTIS. Resolve in issue cmu-delphi/ep…
403e890 
…iprocess#348
@nmdefries
note use in epiprocess vignettes
b9cab85
@nmdefries
build docs
a66ebd1
@nmdefries
Merge branch 'lcb/activate-roxygen-markdown' into lcb/adjust-attribution
aec5488
@nmdefries
archive, cases_deaths doc wording
09abc23
@nmdefries
county and outlier doc line wrapping
854401b
@nmdefries
add description tag to keep external use in top-level description
653fd18
@nmdefries
outlier dataset uses nj, not ca data
4226ecc
@nmdefries
add nat as maintainer
af635dc
@nmdefries @brookslogan
title suggestions
d4a1a42 
Co-authored-by: brookslogan <[email protected]>
@nmdefries
attribute COVID Canada working group
4e8119e
@nmdefries
match wording between data attributions
a9ad878
@nmdefries
build docs with new data titles
bca6556
@nmdefries
convert archive..._dt to archive
89d8bd6
@nmdefries
generate all datasets with explicit as_of
0017d3a
@nmdefries
document all as_ofs
20a0142
@nmdefries
check if epiprocess installed on load
adccc93
@nmdefries
remove on-load error
aacbe27
@nmdefries
on data load, convert to epiprocess object if epiprocess installed
18c7a60 
rename all the underlying data to *_dt

move dates into `local` and use :::
@nmdefries
describe archive format of can_prov_cases
0cf2d69
@nmdefries
use helper to modify rather than overwrite sysdata.rda
04339e3
@nmdefries
warn on data load if epiprocess not installed
49b622c
@nmdefries
update links and types in docs
046ac65
@nmdefries nmdefries force-pushed the ndefries/epipredict-support branch from 849b65f to a42a262 Compare September 26, 2024 22:14
@nmdefries nmdefries marked this pull request as ready for review September 30, 2024 17:12
Base automatically changed from lcb/adjust-attribution to main October 1, 2024 22:08
@nmdefries nmdefries requested a review from brookslogan October 2, 2024 15:12
@nmdefries nmdefries mentioned this pull request Oct 2, 2024
Merged
5 tasks
@nmdefries
Copy link
Collaborator Author

nmdefries commented Oct 2, 2024 •
edited
Loading

Not sure why so much commit history is showing up here. Edit: this seems to be an annoying issue with squash merges. This branch was off of another feature branch. Squash-merging that one to main automatically switched this one to be merged into main, but after the squash merge, it doesn't recognize all of the old commits as shared history.

@nmdefries
Copy link
Collaborator Author

nmdefries commented Oct 3, 2024 •
edited
Loading

Rebasing this is getting really messy, so I'm going to leave the commit history as-is. Commits that aren't on main start from ~c129398

@nmdefries nmdefries mentioned this pull request Oct 7, 2024
Merged
4 tasks
@brookslogan
Replace .before = 365000L
47b3ca0 
with `.before = Inf`, though simply omitting & relying on default would work as well.
brookslogan
brookslogan approved these changes Oct 14, 2024
View reviewed changes
Copy link
Collaborator

@brookslogan brookslogan left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Made a very minor tweak and files an issue about 7dav and prop signal history off into #9.

@brookslogan brookslogan merged commit 3bb5a82 into main Oct 14, 2024
2 checks passed
@brookslogan brookslogan deleted the ndefries/epipredict-support branch October 14, 2024 19:01
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@brookslogan brookslogan brookslogan approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@nmdefries @brookslogan