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v2.0 add_overall.tbl summary() #1663

Merged
merged 3 commits into from
May 17, 2024
Merged

v2.0 add_overall.tbl summary() #1663

merged 3 commits into from
May 17, 2024

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What changes are proposed in this pull request?

If there is an GitHub issue associated with this pull request, please provide link.

Reviewer Checklist (if item does not apply, mark is as complete)

  • Ensure all package dependencies are installed by running renv::install()
  • PR branch has pulled the most recent updates from master branch. Ensure the pull request branch and your local version match and both have the latest updates from the master branch.
  • If an update was made to tbl_summary(), was the same change implemented for tbl_svysummary()?
  • If a new function was added, function included in _pkgdown.yml
  • If a bug was fixed, a unit test was added for the bug check
  • Run pkgdown::build_site(). Check the R console for errors, and review the rendered website.
  • Code coverage is suitable for any new functions/features. Review coverage with withr::with_envvar(new = c("NOT_CRAN" = "true"), covr::report()). Begin in a fresh R session without any packages loaded.
  • R CMD Check runs without errors, warnings, and notes
  • usethis::use_spell_check() runs with no spelling errors in documentation

When the branch is ready to be merged into master:

  • Update NEWS.md with the changes from this pull request under the heading "# gtsummary (development version)". If there is an issue associated with the pull request, reference it in parentheses at the end update (see NEWS.md for examples).
  • Increment the version number using usethis::use_version(which = "dev")
  • Run codemetar::write_codemeta()
  • Run usethis::use_spell_check() again
  • Approve Pull Request
  • Merge the PR. Please use "Squash and merge".

@ddsjoberg ddsjoberg changed the base branch from main to v2.0 May 17, 2024 00:22
@ddsjoberg ddsjoberg merged commit 930fa9f into v2.0 May 17, 2024
10 checks passed
@ddsjoberg ddsjoberg deleted the v2.0-add_overall.tbl_summary branch May 17, 2024 00:49
ddsjoberg added a commit that referenced this pull request Jun 29, 2024
@ddsjoberg @edelarua
@zdz2101 @Melkiades
v2.0 to main branch (#1778)
2596514 
* progress

* Bridge updates (#1570)

* progress

* Update NEWS.md

* Update NEWS.md

* small updates

* Selecting updates (#1573)

* in progress

* progress

* GH Action workflow updates (#1574)

* updates

* more updates

* Update test-coverage.yaml

* Update pull_request_template.md

* updates

* updates

* Update NEWS.md

* Assign digits (#1575)

* in progress

* progress

* Dynamic column headers (#1576)

* in progress

* progress

* progress

* Update DESCRIPTION

* progress

* Update tbl_summary.R

* Updating with the `tbl_summary(sort)` argument (#1583)

* in progress

* Update tbl_summary.R

* moving indentation to its own table styling enttry (#1584)

* moving indentation to its own table styling enttry

* Update NEWS.md

* check updates

* Update DESCRIPTION

* Adding `tbl_summary(percent)` argument (#1585)

* updates

* updates

* progress (#1595)

* doc updates

* adding default stat labels

* progress

* Update tbl_summary.R

* Update bridge_summary.R

* style

* Update README.Rmd

* dichotomous variable updates

* Update test-tbl_summary.R

* checks updates

* forcats shim update

* purrr shim update

* Update test-tbl_summary.R

* new checks file

* lil updates

* Adding more `tbl_summary()` tests and organizing snapshot tests (#1604)

* data arg update

* by arg update for snaps

* snap updates for label argument

* snaps sort arg

* more updates

* trucking along

* Update tbl_summary.md

* more testing

* doc update

* messaging update

* Update .Rbuildignore

* updates

* updates after cards rename

* adding ARDs as lists inside tbl_summary

* Create import-standalone-tibble.R

* selecting updates (#1611)

* rename column summary_type to var_type (#1612)

* Adding v2 `add_p.tbl_summary()` (#1615)

* in progress

* in progress

* Update style_sigfig.R

* in progress

* progress

* progress

* progress

* progress

* progress

* updates

* progress

* progress

* Update test-add_p.tbl_summary.R

* updates

* Update R-CMD-check.yaml

* Update R-CMD-check.yaml

* Update R-CMD-check.yaml

* Update R-CMD-check.yaml

* more updates

* Update test-coverage.yaml

* more updates

* progress

* Update R-CMD-check-as-cran.yaml

* Update R-CMD-check-as-cran.yaml

* progress

* updates

* Update R-CMD-check.yaml

* more updates

* Update add_p.R

* more updates

* Adding `add_difference.tbl_summary()` to v2 branch (#1634)

* more progress

* more updates

* Update DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION

* idk what's going on

* Update DESCRIPTION

* Update test-add_difference.tbl_summary.R

* Update DESCRIPTION

* emmeans updates

* emmeans updates

* Update DESCRIPTION

* updates

* Update utils-add_p_tests.R

* First draft of `card_summary()` (#1636)

* first draft of `card_summary()`

* Update card_summary.R

* adding some unit tests

* more tests

* styler

* Generalizing `brdg_summary()` and supporting `pier_*()` functions (#1642)

* brdg updates!

* updates

* v2.0 Adding `add_n.tbl summary()` (#1645)

* adding add_n.tbl_summary()

* Update add_n.R

* Update add_n.R

* lil updates

* progress

* Adding v2.0 `tbl_regression()` (#1648)

* progress

* doc updates

* updates

* Update DESCRIPTION

* Update test-tbl_regression.R

* bridge rename (#1661)

* Adding `add_q()` (#1662)

* v2.0 `add_overall.tbl summary()` (#1663)

* progress

* progress

* styler

* progress (#1664)

* V2.0 adding pkgdown (#1665)

* adding pkgdown yaml

* doc update

* doc updates related to pkgdown

* v2.0 Adding `add_stat()` (#1667)

* progress

* Update add_stat.md

* lil updates

* Update _pkgdown.yml

* v2.0 `add_stat_label.tbl_summary()` (#1669)

* progress

* progress

* doc updates

* Update add_stat_label.R

* v2.0 `modify_table_styling()` (#1672)

* progress

* progress

* progress (#1673)

* v2.0 `modify_header()`, `modify_spanning_header()`, `modify_footnote()`, `modify_caption()` (#1676)

* progress

* progress

* Create test-modify_spanning_header.R

* progress (#1677)

* v2.0 `modify_column_hide()`, `modify_column_unhide()`, `modify_column_alignment()`, `modify_column_indent()` (#1678)

* in progress

* progress

* progress

* v2.0 `modify_fmt_fun()` (#1679)

* progress

* Update DESCRIPTION

* Update DESCRIPTION

* v2.0 bold and italicize labels and levels (#1680)

* progress

* Update _pkgdown.yml

* v2.0 `bold_p()` (#1686)

* progress

* progress

* progress

* v2.0 Migrating themes (#1685)

* progress

* progress

* Update DESCRIPTION

* progress

* Update test-theme_gtsummary.R

* Update _pkgdown.yml

* v2.0 `style_*()` migration (#1688)

* in progress

* style updates

* progress

* v2.0 language translations (#1682)

* in progress

* Update sysdata.rda

* progress

* V2.0 `tbl_stack()` (#1694)

* adding function

* lil updates

* Update utils-add_p_tests.R

* v2.0 `tbl_uvregression()` (#1692)

* progress

* updates

* updates

* progress

* in progress

* progress

* progress

* Update tbl_uvregression.Rd

* progress

* Update DESCRIPTION

* V2.0 `separate_p_footnotes()` (#1695)

* progress

* progress

* updates

* Update _pkgdown.yml

* V2.0 `tbl_custom_summary()` (#1698)

* progress

* progress

* progress

* Update _pkgdown.yml

* progress (#1700)

* v2.0 regression tidiers + S3 methods (#1701)

* progress

* updates

* docs

* updates

* trying to get pkgdown to work

* updates

* v2.0 `add_global_p()` (#1706)

* progress

* Update R-CMD-check.yaml

* progress (#1707)

* V2.0 `add_vif()` (#1708)

* progress

* Update _pkgdown.yml

* Update _pkgdown.yml

* progress (#1709)

* V2.0 `tbl_butcher()` (#1711)

* progress

* Update NEWS.md

* progress (#1710)

* v2.0 Adding `add ci.tbl summary()` (#1666)

* in progress

* doc updates

* Update add_ci.R

* progress

* progress

* progress

* Update _pkgdown.yml

* Update NEWS.md

* Update NEWS.md

* Update DESCRIPTION

* doc update

* Update add_ci.R

* V2.0 `add_nevent.tbl uvregression()` (#1713)

* progress

* doc updates

* V2.0 `add_p.tbl continuous()` (#1717)

* progress

* Update _pkgdown.yml

* lil gt updates (#1718)

* V2.0 `as_tibble()` (#1719)

* progress

* redoc

* progress (#1721)

* V2.0 standalone updates (#1722)

* update standalone scripts

* Update tbl_summary.R

* v2.0 `tbl_merge()` (#1703)

* progress

* Update test-tbl_uvregression.R

* remove deps

* v2.0 `tbl_crosss()`, `add_p.tbl_cross()` (#1702)

* progress

* doc updates

* updates

* V2.0 `add_glance_*()` (#1724)

* in progress

* glancing

* V2.0 more selectors (#1726)

* adding selectors

* update

* V2.0 `tbl_survfit()` (#1728)

* in progress

* progress

* progress

* progress

* Update DESCRIPTION

* Update DESCRIPTION

* Update _pkgdown.yml

* v2.0 Add unit tests for `as_tibble` and `as.data.frame` (#1723)

* Add tests

* Add unit tests for as_tibble

* Remove comment

* Update tbl_stack.R

* Use base R pipe

* Add test for column grouping

* A bit of clean up

* Comment code

* Remove some snapshot tests

* Add test for as.data.frame

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* V2.0 `as_kable()` (#1729)

* progress

* Update import-standalone-stringr.R

* V2.0 add unit tests for `add_n` and `add_nevent` to `tbl_uvregression()`  (#1725)

* add test for add_n.tbl_uvregression()

* all tests added and styler

* forgot a skip_if_not

* adopt feedback

* adopt feedback

* V2.0 `as_flex_table()` (#1731)

* in progress

* in progress

* stringr updates

* Update add_q.R

* adding kabel extra output (#1732)

* V2.0 as kable extra (#1733)

* adding kabel extra output

* adding indent

* V2.0 `as_hux_table()` (#1735)

* in progress

* progress

* progress

* renaming label_style function (#1737)

* progress (#1738)

* data update

* progress (#1739)

* progress (#1742)

* adding a few tests

* V2.0 rename card functions (#1744)

* rename some functions

* Update _pkgdown.yml

* snap updates

* progress (#1745)

* progress (#1746)

* more tests

* progress (#1747)

* progress

* v2.0 Add unit tests for `as_gt` (#1727)

* Add tests for as_gt

* Fix

* Fix

* Fix

* Test

* Test

* Rearrange existing

* Add tests for as_gt

* Update footnotes test

* Simplify interpreter test

* Add footnotes test

* Clean up

* Add test for bold/italics

* Add test for missing symbols

* Add test for column merging

* Simplify tests

* Add test for missing values

* Add tests for formatting functions

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* v2.0 Add unit tests for  `as_flex_table` (#1752)

* Initialize

* Add tests

* Test for formatting functions

* Test for glance statistics

* Test tbl_merge

* Added explicit test for markdown syntax in headers

* V2.0 `tbl_wide_summary()` (#1749)

* progress

* Update NEWS.md

* Update _pkgdown.yml

* docs

* doc update

---------

Co-authored-by: Melkiades <davide.garolini@roche.com>

* V2.0 `tbl_ard_wide_summary()` (#1750)

* progress

* Update NEWS.md

* Update _pkgdown.yml

* docs

* doc update

* progress

---------

Co-authored-by: Melkiades <davide.garolini@roche.com>

* v2.0 Add unit tests for `tbl_merge` (#1754)

* Add tests for tbl_merge

* Add more tests

* Message test

* Update test-tbl_merge.R

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* V2.0 `inline_text()` (#1751)

* Update inline_text.R

* in progress

* in progress

* progress

* Update _pkgdown.yml

* Update NEWS.md

* closes #1755 (#1757)

* updates (#1761)

* adding tests (#1762)

* Create test-select_helpers.R (#1763)

* v2.0 Add unit tests for `tbl_stack` (#1756)

* Initialize

* Reorder

* Wrong file

* Add tests

* Add snapshot

* Fix pkg check

* Update tbl_stack.md

* Add test for mismatched number of columns error

* fix

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* Update print.R

* V2.0 add stat.tbl continuous tests (#1759)

* raise attention

* need at least this to get old tests working

* how to use include for formula formation?

* should work

* as a fun exercise

* add comments

* nvm found the issue

* DS review updates

* move the tests and take in feedback

* remove unncessary comments and return tbl_continuous back to original shape

* use native pipe only

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* Update DESCRIPTION

* adding show header fn

* website updates

* progress

* v2.0 Add unit tests for `as_kable` (#1760)

* init

* Add tests

* Updates after review

* Fix failing test

* Adding `tbl_svysummary()` (#1764)

* progress

* in progress

* in progress

* Update DESCRIPTION

* progress

* V2.0 `add_p.tbl_svysummary()` (#1766)

* progress

* progress

* Update _pkgdown.yml

* lil updates

* doc updates

* V2.0 `add_difference.tbl_svysummary()` (#1768)

* Create add_difference.tbl_svysummary.R

* progress

* Update _pkgdown.yml

* progress

* V2.0 `add_n.tbl_svysummary()` (#1769)

* progress

* progress

* progress

* v2.0 Add unit tests for `as_kable_extra` (#1770)

* Add tests

* Add test

* Clean up

* v2.0 additional tests for `tbl uvregression()` (#1730)

* there's preexisting add_global_p() tests?

* add basic plot test

* remove purrr dependencies

* swap in tests for each argument

* styler and fix errors

* adopt feedback

* accidentally pushed one

* add geepack

* new snap

* make sure p-values match properly

* avoid using example geepack uses

* adopt feedback

* forgot to push new snap

---------

Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com>

* progress (#1772)

* V2.0 vignettes (#1773)

* making progress

* progress

* updates

* V2.0 todo (#1776)

* doc updates

* snap updates

* progress

* progress

* V2.0 workflows (#1777)

* mostly workflow updates

* Update test-coverage.yaml

* Removing archive of old package version

---------

Co-authored-by: Emily de la Rua <59304861+edelarua@users.noreply.github.com>
Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>
Co-authored-by: Melkiades <davide.garolini@roche.com>
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