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Moving out from old CI/CD to new one#51

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munoztd0 merged 2 commits intomainfrom
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Aug 12, 2025
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Moving out from old CI/CD to new one#51
munoztd0 merged 2 commits intomainfrom
main_ci_cd

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@munoztd0 munoztd0 commented Aug 11, 2025 •
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Only changes to github actions that need to be integrated in main. No actual "code" changes

@munoztd0 munoztd0 requested a review from jkovach2 August 11, 2025 15:13
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munoztd0 commented Aug 11, 2025 •
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This error is expected this is actually the purpose of this PR

Inspection 🛠 / Check URLs 🌐 / URL Checker 🔎 (pull_request)Failing after 43s
✖ Error: README.md:4:97 404: Not Found: https://johnsonandjohnson.github.io/junco/main/unit-test-report/

After this merge then the unit-test-reporter will be created and this URL will exist.

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github-actions bot commented Aug 11, 2025 •
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Unit Tests Summary

  1 files   49 suites   57s ⏱️
231 tests 178 ✅  53 💤 0 ❌
493 runs  388 ✅ 105 💤 0 ❌

Results for commit ed66d14.

♻️ This comment has been updated with latest results.

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github-actions bot commented Aug 11, 2025 •
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badge

Code Coverage Summary

Filename                                        Stmts    Miss  Cover    Missing
--------------------------------------------  -------  ------  -------  ------------------------------------------------------------------------------------------------------------------------------------------------------
R/a_eair_j.R                                      233      11  95.28%   33-35, 148, 174, 522, 604-607, 635
R/a_freq_combos_j.R                                80       1  98.75%   69
R/a_freq_j.R                                      339      56  83.48%   93, 99, 132-140, 153-157, 164-173, 279-287, 301-305, 311, 318-322, 650-653, 658, 664-666, 721, 755, 759-761, 784-788
R/a_freq_resp_var_j.R                              91      38  58.24%   65-70, 114-125, 153-178
R/a_freq_subcol_j.R                                76       3  96.05%   61-63
R/a_summarize_aval_chg_diff.R                     207      42  79.71%   27-34, 47, 101-102, 134, 138-140, 147, 152-154, 179, 198-204, 407, 411, 415, 430-433, 446, 449, 465, 488-494, 507
R/a_summarize_ex_j.R                              107      17  84.11%   80, 100-107, 213, 217, 221, 249-253, 281
R/analyze_values.R                                 11       0  100.00%
R/ancova_rbmi.R                                    70       0  100.00%
R/ancova.R                                         63       1  98.41%   74
R/blank_line.R                                     26       0  100.00%
R/cmp_functions.R                                  28       2  92.86%   59, 70
R/column_stats.R                                  139      40  71.22%   30-48, 89, 107-116, 123-125, 127-139
R/colwidths.R                                     304      96  68.42%   19, 33-102, 107, 131, 253, 260, 306, 324-343, 352-366, 370-376, 381, 392, 404-412, 442-453, 506, 513
R/count_denom_fraction.R                           28       7  75.00%   81, 86-89, 93, 115
R/coxph_hr.R                                       91       0  100.00%
R/coxreg_multivar.R                                58       0  100.00%
R/dps_markup_to_rtf.R                              31      10  67.74%   93-105
R/estimate_proportion_diff.R                       45       0  100.00%
R/event_free.R                                     44       0  100.00%
R/get_ref_info.R                                   14       0  100.00%
R/h_eair_funs.R                                    21       0  100.00%
R/h_freq_funs.R                                   303      51  83.17%   29, 124, 140, 210-219, 241-244, 247-250, 316-322, 362, 366, 370, 374, 378, 418, 431-432, 477, 496, 502, 611, 670, 672, 676, 680-681, 685-690, 710, 731
R/jjcs_num_formats.R                               48       0  100.00%
R/jjcsformats.R                                   238      81  65.97%   28-38, 38-39, 39-40, 40-50, 56-58, 58-62, 64-65, 70-92, 92-97, 99-105, 157, 169, 178, 181, 186, 191, 283, 293, 306, 308, 311, 314, 359
R/junco_utils_default_stats_formats_labels.R       48       0  100.00%
R/kaplan_meier.R                                   48       0  100.00%
R/lsmeans.R                                       128       7  94.53%   55-59, 76-77
R/mmrm_rbmi.R                                      61       0  100.00%
R/mmrm.R                                          104       4  96.15%   42, 64, 104, 155
R/odds_ratio.R                                    164      12  92.68%   118-128, 162-165
R/pool_rbmi.R                                      44      27  38.64%   8-40
R/proportions.R                                    60       1  98.33%   132
R/pruning_functions.R                             175       8  95.43%   169, 316, 319, 355, 365, 401, 442-443
R/rbmi.R                                          124      74  40.32%   125, 131, 375-468
R/relative_risk.R                                  97       5  94.85%   228, 242-245
R/remove_col_count.R                                4       0  100.00%
R/resp01_functions.R                              159      28  82.39%   143-151, 178, 341, 344-353, 355-361
R/s_functions.R                                    27       4  85.19%   4, 7, 16-17
R/sorting_functions.R                              49       2  95.92%   175, 189
R/span_var_map.R                                   15       0  100.00%
R/split_functions.R                               122      31  74.59%   62, 69, 77-95, 103, 106, 113, 116-120, 126, 134-139
R/summarize_ancova.R                              240      52  78.33%   34, 91, 94-117, 120, 124-132, 156-163, 230-233, 241-248
R/summarize_mmrm.R                                 79       0  100.00%
R/summarize_row_counts.R                            8       0  100.00%
R/tabulate_lsmeans_wide.R                         134       0  100.00%
R/tabulate_lsmeans.R                               68       4  94.12%   86-89
R/tabulate_rbmi.R                                 111       0  100.00%
R/tern_utils_default_stats_formats_labels.R       178      17  90.45%   61-68, 71-74, 215-216, 276-277, 326
R/test_proportion_diff.R                           77       1  98.70%   197
R/title_footers.R                                  53      10  81.13%   5, 19-25, 90, 98, 140, 144
R/tt_to_tblfile.R                                 480      49  89.79%   38, 41, 44, 81, 96, 99, 118, 146, 162-176, 198, 208-214, 321-325, 349, 355-357, 361-364, 458-463, 577, 676
R/unicodify.R                                       4       0  100.00%
R/visit_levels.R                                    8       0  100.00%
TOTAL                                            5564     792  85.77%

Diff against main

Filename      Stmts    Miss  Cover
----------  -------  ------  --------
TOTAL             0       0  +100.00%

Results for commit: ed66d14

Minimum allowed coverage is 80%

♻️ This comment has been updated with latest results

jkovach2
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@munoztd0 munoztd0 merged commit abe917e into main Aug 12, 2025
2 checks passed
@munoztd0 munoztd0 deleted the main_ci_cd branch August 12, 2025 14:14
munoztd0 added a commit that referenced this pull request Sep 12, 2025
@munoztd0 @gmbecker @rmao6
merge main (#72)
7e8c4af 
* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
munoztd0 added a commit that referenced this pull request Sep 16, 2025
@munoztd0 @gmbecker
@rmao6 @github-actions
Submitted to cran 0.1.1 (#75)
f5958ec 
* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
munoztd0 added a commit that referenced this pull request Dec 9, 2025
@munoztd0 @rmao6
@gmbecker @github-actions @danielinteractive
Release rbmi suggests (#112)
5c80b82 
* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

* Submitted to cran 0.1.1 (#75)

* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* update: move rbmi to suggest

* update: prepare to CRAN release

* update: add missing snapshot stats formats

* update: rbmi related snapshots

* update: rbmi example conditionned

* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* update: added suppressPackageStartupMessages(library(rbmi))

* update: remove comment in example

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* [skip style] [skip vbump] Restyle files

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: fix linting

* update: fix example

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* update: do_exclude_split

* fix: merge issues with .rd links

* fix: WORDLIST

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
munoztd0 added a commit that referenced this pull request Dec 11, 2025
@munoztd0 @wwojciech
@iaugusty @github-actions @rmao6 @gmbecker @danielinteractive @eanokian
116 tt to tbldf function behavior with invalid structures (#124)
fe9f7c3 
* a_maxlev fun update: `denom_df` argument replaced by `.alt_df_full`. (#114)

* replace denom_df arg with .alt_df_full filled by the rtables machinery

* changelog update

---------

Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org>

* Added `a_two_tier()` analysis function (#122)

* first commit. just new add.

* new commit - two_tier_afun.

* added a_two_tier + unit tests

* new unit tests + CHANGELOG update

* _pkgdown.yml update

* spellcheck update

* update: add _pkgdown.yml a_two_tier

---------

Co-authored-by: munoztd0 <david.munoztord@mailbox.org>

* address bug #120: a_freq_j() - risk diff. Suspected results in the presence of upper row-split and no alt_counts_df (#123)

* resolve bug and add test

* [skip style] [skip vbump] Restyle files

* Trigger CI: empty commit

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Release rbmi suggests (#112)

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

* Submitted to cran 0.1.1 (#75)

* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* update: move rbmi to suggest

* update: prepare to CRAN release

* update: add missing snapshot stats formats

* update: rbmi related snapshots

* update: rbmi example conditionned

* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* update: added suppressPackageStartupMessages(library(rbmi))

* update: remove comment in example

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* [skip style] [skip vbump] Restyle files

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: fix linting

* update: fix example

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* update: do_exclude_split

* fix: merge issues with .rd links

* fix: WORDLIST

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

* update: remotes

* update: Consistent `tt_to_tbldf()` function behavior with invalid structures (#116)

* fix: tests

* fix: rd docs

* [skip style] [skip vbump] Restyle files

* fix: lintr

* fix: lintr

* [skip style] [skip vbump] Restyle files

* update: added WWojciak as contributores

* update: remove temp_ilse

* update: remove duplicate

* update: remove pharmaverseadam

* update: keep pharmaverseadam because in news.md

* update: merge issues

* update: fix warnings

---------

Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com>
Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com>
gmbecker added a commit that referenced this pull request Dec 17, 2025
@munoztd0 @wwojciech
@iaugusty @github-actions @rmao6 @gmbecker @danielinteractive @eanokian
116 tt to tbldf function behavior with invalid structures (#124)
f0d2682 
* a_maxlev fun update: `denom_df` argument replaced by `.alt_df_full`. (#114)

* replace denom_df arg with .alt_df_full filled by the rtables machinery

* changelog update

---------

Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org>

* Added `a_two_tier()` analysis function (#122)

* first commit. just new add.

* new commit - two_tier_afun.

* added a_two_tier + unit tests

* new unit tests + CHANGELOG update

* _pkgdown.yml update

* spellcheck update

* update: add _pkgdown.yml a_two_tier

---------

Co-authored-by: munoztd0 <david.munoztord@mailbox.org>

* address bug #120: a_freq_j() - risk diff. Suspected results in the presence of upper row-split and no alt_counts_df (#123)

* resolve bug and add test

* [skip style] [skip vbump] Restyle files

* Trigger CI: empty commit

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Release rbmi suggests (#112)

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

* Submitted to cran 0.1.1 (#75)

* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* update: move rbmi to suggest

* update: prepare to CRAN release

* update: add missing snapshot stats formats

* update: rbmi related snapshots

* update: rbmi example conditionned

* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* update: added suppressPackageStartupMessages(library(rbmi))

* update: remove comment in example

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* [skip style] [skip vbump] Restyle files

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: fix linting

* update: fix example

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* update: do_exclude_split

* fix: merge issues with .rd links

* fix: WORDLIST

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

* update: remotes

* update: Consistent `tt_to_tbldf()` function behavior with invalid structures (#116)

* fix: tests

* fix: rd docs

* [skip style] [skip vbump] Restyle files

* fix: lintr

* fix: lintr

* [skip style] [skip vbump] Restyle files

* update: added WWojciak as contributores

* update: remove temp_ilse

* update: remove duplicate

* update: remove pharmaverseadam

* update: keep pharmaverseadam because in news.md

* update: merge issues

* update: fix warnings

---------

Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com>
Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com>
munoztd0 added a commit that referenced this pull request Jan 13, 2026
@munoztd0 @eanokian
@iaugusty @github-actions @danielinteractive @wwojciech @rmao6 @gmbecker
Cran Release as Main (#137)
c901dc2 
* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* added temporary make_row_df_2() and matrix_form_2(), bugfix in interpret_cell_content()

* added exporter for figures/graphs

* Update docx_exporter_functions.R

* Update docx_exporter_functions.R

* fix in the footers

* improved documentation of function export_graph_as_docx()

* Update docx_exporter_functions.R

* cmhrms and row mean score: addresses #97 (#98)

* add function h_restrict_val and apply in when val = NULL and label_map provided

* changelog

* wordlist

* pkgdown update

* document()

* add collapse_combo

* usethis::use_package("vcdExtra")

* move over new functions

* use standard formatting for cmhrms

* also more standard in the modified afun

* add to changelog

* disable air formatting - not sure if that would be appreciated here

* add `do_exclude_split()` with tests

* move wrapper afuns with level exclusions into respective files and document them

* remove note about sparse data problems because this has been fixed in vcdExtra repo

* remove @importFrom because we use the function directly from its namespace

* slight cleanup of cmhrms function code

* add full test suite for cmhrms

* add tests for h_restrict_val

* refresh docs

* add tests for a_freq_j funs with label_map

* refresh docs

* update: package version to 0.1.3 and fix air.toml errors

* update: added snapshot to be reviewed

* fix a small issue and add snapshots

* add new snapshot which seems to have been missing

* fix: note on na.omit

* fix: linting issue

* update: add do_exclude_split to exported

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: munoztd0 <david.munoztord@mailbox.org>
Co-authored-by: Daniel Sabanes Bove <DBove@ITS.JNJ.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

* [skip style] [skip vbump] Restyle files

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

* update tests for round_type

* document

* code update + styler

* update: added suppressPackageStartupMessages(library(rbmi))

* [skip style] [skip vbump] Restyle files

* update: remove comment in example

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

* update: add helper function so we don't need to repeat assert rbmi everywhere

* lintr

* [skip style] [skip vbump] Restyle files

* address spelling

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

* update: add helper function so we don't need to repeat assert rbmi everywhere

* remove 1 test, covered above

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* update ref to formatting functions

* [skip style] [skip vbump] Restyle files

* added unit tests, small bugfix on add_little_gap_bottom_borders_spanning_headers(), added getOption("docx.add_datetime"), minor bugfix in insert_title_hanging_indent_v3()

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* roxygen update + test update

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: fix linting

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

* update: fix example

* fix styler

* [skip style] [skip vbump] Restyle files

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* renamed functions with "_j" suffix

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* a_maxlev fun update: `denom_df` argument replaced by `.alt_df_full`. (#114)

* replace denom_df arg with .alt_df_full filled by the rtables machinery

* changelog update

---------

Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org>

* added "experimental" label, updated _pkgdown.yml

* orientation default changed to "portrait"

* linted docx_exporter_functions.R

* updated documentation of argument "pagenum" in both tt_to_tlgrtf() and export_as_docx_j()

* set valid_round_type as defaults for round_type

* [skip style] [skip vbump] Restyle files

* fix: codepencies

* fix: lint

* fix: .rtf .Rbuildignore

* argument "pagenum" only applicable to listings

* exported function theme_docx_default_j()

* Update docx_exporter_functions.R

* added "round_type" argument in tt_to_flextable_j() and export_as_docx_j()

* update: vignettea table_and_listing_customizations.rmd

* update: title confusion

* update: consisten “.”  before the file format.

* update: For the “Adjusting the Font Size of a Table or Listing” .docx section, can you please update the text accordingly?

To display the body of tables in Times New Roman 8-pt for .docx files, the junco::export_as_docx_j function can be called with the theme argument included. The theme argument will specify a juco::theme_docx_default_j function call.

* Update DESCRIPTION

* update: new line \n

* added argument "alignments" to tt_to_tlgrtf(), tt_to_flextable_j() and export_as_docx_j()

* update: superscript

* update: superscript

* update: table misisng

* update: multiple files

* update: multiple files

* update: rename chucks

* update: rename chuncks

* added "border_mat" argument

* Added `a_two_tier()` analysis function (#122)

* first commit. just new add.

* new commit - two_tier_afun.

* added a_two_tier + unit tests

* new unit tests + CHANGELOG update

* _pkgdown.yml update

* spellcheck update

* update: add _pkgdown.yml a_two_tier

---------

Co-authored-by: munoztd0 <david.munoztord@mailbox.org>

* just comments

* added unit tests for border_mat argument

* update joe's comments

* address bug #120: a_freq_j() - risk diff. Suspected results in the presence of upper row-split and no alt_counts_df (#123)

* resolve bug and add test

* [skip style] [skip vbump] Restyle files

* Trigger CI: empty commit

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* minor bugfix in little gap bottom borders in header

* update joe's comments

* update joe's comments

* update joe's comments

* Release rbmi suggests (#112)

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

* Submitted to cran 0.1.1 (#75)

* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* update: move rbmi to suggest

* update: prepare to CRAN release

* update: add missing snapshot stats formats

* update: rbmi related snapshots

* update: rbmi example conditionned

* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* update: added suppressPackageStartupMessages(library(rbmi))

* update: remove comment in example

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* [skip style] [skip vbump] Restyle files

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: fix linting

* update: fix example

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* update: do_exclude_split

* fix: merge issues with .rd links

* fix: WORDLIST

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

* update: remotes

* update: Consistent `tt_to_tbldf()` function behavior with invalid structures (#116)

* fix: tests

* fix: rd docs

* fix: remotes

* fix: NAMESPACE

* fix: tests

* fix: rtables.officer:::

* added Boolean "watermark" argument

* fix: code link issues

* fixed lints

* Merge branch '40_docx_exporter' of https://github.com/johnsonandjohnson/junco into 40_docx_exporter

* [skip style] [skip vbump] Restyle files

* fix: lintr

* fix: lintr

* [skip style] [skip vbump] Restyle files

* fix: quarto vignette rcmdcheck issues

* minor changes, updated snapshots

* Update export_as_docx_j.Rd

* Update DESCRIPTION

* fixed missing link error in roxygen2 documentation

* updated snapshots

* updated snapshots

* minor tweaks in unit tests test-count_pct.R and test-varia.R to make it pass the CICD pipeline

* update: added WWojciak as contributores

* update: remove temp_ilse

* update: remove duplicate

* update: remove pharmaverseadam

* update: keep pharmaverseadam because in news.md

* [skip style] [skip vbump] Restyle files

* update: merge issues

* update: fix warnings

* minor tweaks in unit tests test-count_pct.R and test-varia.R to make it pass the CICD pipeline

* updated lintr to check the pipe lints, linted again, updated snapshots

* [skip style] [skip vbump] Restyle files

* updated WORDLIST and CHANGELOG.md files, spell checks

* fixed lints, updated _pkgdown.yml to include topic "theme_docx_default_j"

* [skip style] [skip vbump] Restyle files

* update: remove styler

* update: fix linter

* update: skip_on_cran()

* update: comment out macos

* add Remotes to use main branch from tern etc.

* 116 tt to tbldf function behavior with invalid structures (#124)

* a_maxlev fun update: `denom_df` argument replaced by `.alt_df_full`. (#114)

* replace denom_df arg with .alt_df_full filled by the rtables machinery

* changelog update

---------

Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org>

* Added `a_two_tier()` analysis function (#122)

* first commit. just new add.

* new commit - two_tier_afun.

* added a_two_tier + unit tests

* new unit tests + CHANGELOG update

* _pkgdown.yml update

* spellcheck update

* update: add _pkgdown.yml a_two_tier

---------

Co-authored-by: munoztd0 <david.munoztord@mailbox.org>

* address bug #120: a_freq_j() - risk diff. Suspected results in the presence of upper row-split and no alt_counts_df (#123)

* resolve bug and add test

* [skip style] [skip vbump] Restyle files

* Trigger CI: empty commit

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Release rbmi suggests (#112)

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

* Submitted to cran 0.1.1 (#75)

* update version (finally x.x)

* merge main (#72)

* Update NEWS.md

* fix: spellcheck()

* ci.cd: add coverage report comment to PR

* test: add coverage ignore

* Moving out from old CI/CD to new one (#51)

* moving out from old CI/CD to new one

* Generate tern_utils_default_stats_formats_labels.md

* Main ci cd (#53)

* Update README.md withnew links

* Update inspect.yaml to check

* Update pkgdown.yaml to Docs

* Update README.md

* Add hexagon sticker (#38)

* Generate pkgdown site favicon

* add logo to inspect unit reports

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Issue and PR templates (#60)

* issue and PR templates

* Update pkgdown.yaml

stop running pkgdown for draft PRs

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>

* Revert "merge main (#72)" (#74)

This reverts commit 7e8c4af.

* Update NEWS.md

* [skip roxygen] [skip vbump] Roxygen Man Pages Auto Update

---------

Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* update: move rbmi to suggest

* update: prepare to CRAN release

* update: add missing snapshot stats formats

* update: rbmi related snapshots

* update: rbmi example conditionned

* update: remove rbmi rd refs

* update: prepare release

* update: R CMD check results

* update: added suppressPackageStartupMessages(library(rbmi))

* update: remove comment in example

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add helper function so we don't need to repeat assert rbmi everywhere

* update: add rhub check

* update: update get_formats_from_stats

* update: add rbmi related snaps

* update: remove .rtf from .Rbuilignore

* [skip style] [skip vbump] Restyle files

* update: add insight repos

* update: fix linting

* update: new R CMD Check

* update: new R CMD Check

* update: new R CMD Check

* [skip style] [skip vbump] Restyle files

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: new R CMD Check install rbmi

* update: fix linting

* update: fix example

* get full coverage of rbmi_pool() by adding tests from rbmi

* [skip style] [skip vbump] Restyle files

* test rbmi_analyse

* [skip style] [skip vbump] Restyle files

* add ignores around Air formatter

* add tidyr to suggests

* update: remove .rprofile

* fix: rbmi in rd docs

* fix: missing comma

* update: news.md

* [skip style] [skip vbump] Restyle files

* update: news.md

* update: WORDLIST

* update: do_exclude_split

* fix: merge issues with .rd links

* fix: WORDLIST

---------

Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>

* update: remotes

* update: Consistent `tt_to_tbldf()` function behavior with invalid structures (#116)

* fix: tests

* fix: rd docs

* [skip style] [skip vbump] Restyle files

* fix: lintr

* fix: lintr

* [skip style] [skip vbump] Restyle files

* update: added WWojciak as contributores

* update: remove temp_ilse

* update: remove duplicate

* update: remove pharmaverseadam

* update: keep pharmaverseadam because in news.md

* update: merge issues

* update: fix warnings

---------

Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com>
Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com>

* Add the two new proportion difference estimation methods to `estimate_proportion_diff()`

* update to jjcsformat_range_fct per suggestion Joe

* remove helper functions for testing prop. differences which are not needed any longer in junco

* the stats function for testing proportion differences is not needed anymore either

* refresh docs

* update snapshot

* update change log, word list, link in doc

* refresh docs

* [skip style] [skip vbump] Restyle files

* [skip style] [skip vbump] Restyle files

* add censor_char to function

* Trigger GitHub actions

* Update test-docx_exporter_functions.R

* add censor_char to function

* Update R-CMD-check.yaml

* update: lintr

* update: lintr

* Update test-docx_exporter_functions.R

* made watermarks darker

* remove deleted function from pkgdown

* update: remotes

* update: update to have CRAN check.yaml

* fix: update of vcdExtra

* fix: update of vcdExtra & add cran-comments.md

* fix: update of vcdExtra

* fix: update of vcdExtra

* fix: update of pipeline check_CRAN.yml

* update to tt_to_tbldf and add tests

* fix: update of pipeline check_CRAN.yml

* fix: s_cmhrms_j skip on linux

* in calc_one_visit only sas and iec rounding for now

* fix: update of cran comments

* [skip style] [skip vbump] Restyle files

* trigger checks

* fix: DESCRIPTION

* Update DESCRIPTION

* Update DESCRIPTION to vcdExtra back to normal fixing it in another PR

* remove expect silent (#130)

* remove expect silent

* fix: prop_diff_test

* Update WORDLIST

* Rework calc_one_visit, add 'support' for 'default' format to jjcsformats

* [skip style] [skip vbump] Restyle files

* Update test-cmhrms.R

* Update test-cmhrms.R

* move rgl.useNULL option to testthat.R

* check mac tests (#131)

* check mac tests

* fix: mac tests rgl instead xquartz

* fix: inheritParams in WORDLIST

* resolve conflict

* v0.1.2_cran (#136)

* Update README.md

* Update README.md

* update: rtables 0.6.15

* update: tern 0.9.10

* update: CHANGELOG.md

* update: spelling

* Update README.md

* Update DESCRIPTION tidytlg 	0.11.0

* Update docx_exporter_functions.R

* fix: update [-c(1:2,9)] to remove last NULL vector index

* fix: new update tidytlg border and landscape

* fix: lintr

* add: snaps .csv

* fix: extraneous empty line when we turn off timestamp line

* force text comparison

---------

Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org>
Co-authored-by: munoztd0 <david.munoztord@mailbox.org>
Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com>

* fix: lint

* add: snaps

* remove: old pipeline

* fix: lintr

* update: README

---------

Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com>
Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <DBove@ITS.JNJ.com>
Co-authored-by: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Co-authored-by: iaugusty <iaugusty@its.jnj.com>
Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com>
Co-authored-by: RMao6 <rmao6@its.jnj.com>
Co-authored-by: Gabe Becker <gabembecker@gmail.com>
Co-authored-by: Ezequiel <4982139+eanokian@users.noreply.github.com>
Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com>
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@munoztd0 @jkovach2