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Closes #1755 tbl_strata(.quiet) fix #1757

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merged 1 commit into from
Jun 24, 2024
Merged

Closes #1755 tbl_strata(.quiet) fix #1757

merged 1 commit into from
Jun 24, 2024

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ddsjoberg
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What changes are proposed in this pull request?
Quiet argument no longer passed to tbl_stack()

If there is an GitHub issue associated with this pull request, please provide link.
closes #1755

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.
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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).
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  • Approve Pull Request
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@ddsjoberg ddsjoberg requested a review from Melkiades June 23, 2024 05:06
@ddsjoberg ddsjoberg marked this pull request as ready for review June 23, 2024 05:07
Melkiades
Melkiades approved these changes Jun 24, 2024
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Lgtm!! Thanks for the fix :)

@ddsjoberg ddsjoberg merged commit 8372139 into v2.0 Jun 24, 2024
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@ddsjoberg ddsjoberg deleted the 1755-quiet-bug branch June 24, 2024 13:45
@ddsjoberg ddsjoberg mentioned this pull request Jun 24, 2024
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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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@ddsjoberg @Melkiades