CRAN ready: Adding multi-comparator functionality lyt fun#271
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… in value_expr getFromNamespace + remove co authors form old getFromNamespace
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* 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 * docs: No data reported to no data to report fix #119 (#139) * docs a_freq_j consistencies in .stats (#140) * docs: fix #111 * 85: Fix `s_kaplan_meier()` (#141) * fix s_kaplan_meier such that it does not return NA range censoring indicators * corresponding change log entry * add regression test (also remove tern:: because tern is loaded on top of the test file) * add dev version digits * styler * update wordlist * adjust version number in NEWS file accordingly * have the same version number really --------- Co-authored-by: Daniel Sabanes Bove <daniel@rconis.com> * bump: verison 0.1.3 * update: CI/CD * update: ../reference/index.html * update: A complete list of analysis functions can be found in the \[`junco`\] package documentation. * update: rhub * update: rhub * bump 0.1.4 (#148) * Fix bug in s_summarize_desc_j function to handle sparse data (zero variance) cases (#78) (#79) * hotfix + test * news and upgrade to 0.1.1.1 for consistency sake * refactor name * create new snapshot test and S4 expect class * added CHANGELOG.md * [skip style] [skip vbump] Restyle files * fix: rcmdcheck notes and spellcheck * [skip style] [skip vbump] Restyle files * fix: rbuildignore * fix: linting issues --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Main hotfix nov 2025 (#82) * hotfix: fix #77 (hdrmpf typo) and fix too long (topleft bug fix) #80 * hotfix: fix #31 (h_subset_combo handles NA values in flag_var correctly) * minor update: changed pull request template -> added unit tests check * fix: test-tt_to_tblfile.R rollback to main version + new final regression test * Revert "Main hotfix nov 2025" (#83) * Revert "Main hotfix nov 2025 (#82)" This reverts commit baa4196. * [skip style] [skip vbump] Restyle files --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * Update pkgdown.yaml (#101) update to pkgdown 2.2.0 * fix: lint * add: snaps * remove: old pipeline * fix: lintr * update: README * bump: verison 0.1.3 * update: CI/CD * update: ../reference/index.html * update: A complete list of analysis functions can be found in the \[`junco`\] package documentation. * update: rhub * update: rhub * make it shorter * 0.1.bump: 4 --------- Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> * CRAN release v0.1.3 * #' @importFrom tern get_covariates (#163) * Notexported functions (#164) * #' @importFrom tern get_covariates * leftside export * postfun_eq5d export * ac_blank_line export * update CHANGELOG.md * update pkgdown.yml * 143 docx exporter improvements (#155) * started code refactoring * second iteration of code refactoring * replaced the snapshot tests of docx files with the docx_summary() output dataframes * linted file * Update docx_exporter_functions.R * updated documentation, removed unused arguments * Update CHANGELOG.md * Update docx_exporter_functions.R * Update docx_exporter_functions.R * Update CHANGELOG.md * minor bugfixes * docs: removing the junco:: prefixes --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> * update: export tt_to_tblfile.R (#169) * 138 hanging indent first col (#170) * addresses #138 , hanging indentation in first column is now accomplished by manipulating the XML, removed dependency of 'systemfonts' package, removed functions wrap_string_with_indent() and add_hanging_indent_first_column() * linted, updated snapshots * minor bugfix in the calculation of the left indentation, updated snapshots --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * debug ci/cd (#185) * debug ci/cd * debug ci/cd * Refactor pkgdown workflow configuration * Update GitHub Actions workflow for R-CMD-check * Update check-CRAN workflow configuration * Add name and permissions to pkgdown workflow * Update table_and_listing_customizations.rmd (#180) * Update table_and_listing_customizations.rmd * Update CHANGELOG.md * Update CHANGELOG.md * Update DESCRIPTION * Update NEWS.md * fixed tt_to_flextable_j() to have correct left-indentation in Header … (#172) * fixed tt_to_flextable_j() to have correct left-indentation in Header col 1, and fixed Footers to have first line with linebreak * Update CHANGELOG.md * 173 docx exporter single endpoint (#175) * first iteration of merging functions + added checkmate checks + updated documentation * merged export_as_docx_j() and export_graph_as_docx() into export_TLG_as_docx() * Update CHANGELOG.md * added export_TLG_as_docx() in _pkgdown.yml, updated vignette, minor bugfixes * minor bugfix * Update docx_exporter_functions.R --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * 142 optional csv (#165) * addresses #142 * Update tt_to_tblfile.R * added option to export csv in export_as_docx_j() * added option to export csv to export_as_docx_j() function, added unit tests * Update CHANGELOG.md * linted test-docx_exporter_functions.R * Update tt_to_tblfile.R * minor changes in typos * tests: add tests for for tt_to_tlgrtf() export behavior * fix: lintr * in export_as_docx_j() set the default value for argument export_csv = FALSE * argument export_csv set default to FALSE in tt_to_tlgrtf() * Update test-tt_to_tlgrtf_output.R * Update tt_to_tblfile.R --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * 188 docx exporter split incongruence (#189) * Update docx_exporter_functions.R * Update docx_exporter_functions.R * Update CHANGELOG.md --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * update snapshot * Export helpers for LS means tabulation (#203) * start with what needs to be exported * refresh docs * Update CHANGELOG.md for Export helpers for LS means tabulation --------- Co-authored-by: Daniel Sabanes Bove <DBove@ITS.JNJ.com> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * V0.1.4 (#204) * prepare for cran release * don't export files when on cran in vignette * 196 feature request make overall tests shorter for cran (#198) * skip flextable * passed the uneccessary sanity check to on_cran = FALSE * the actual rtf and docx output generation is the bottleneck, each function call takes about 5 secs, and we have 26 of them .. (as per @jkovach2 request) so I suggest to remove from .Rbuildignore because those feature are already checked in test-tt_to_tblfile.R * test-tt_to_tblfile.R: made wide Tables less wide to generate fewer RTFs * removed annoying messages in 'test-a_summarize_aval_chg_diff.R' and 'test-summarize_mmrm.R' * make export not run on CRAN --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> --------- Co-authored-by: Gabe Becker <gabembecker@gmail.com> Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * relative risk in combined column (#199) * update processing denominator dataset for combined facet in relative risk * add tests for relative risk difference column in a combined column * update CHANGELOG * add unit tests for the newly exported LS means wide split funs (#207) * decreased the unit tests to 40 secs, same as tt_to_tlgrtf() unit tests (#205) * decreased the unit tests to 40 secs, same as tt_to_tlgrtf() unit tests * Update CHANGELOG.md * 193 todo bump flextable after release (#209) * remove skip on cran and flextable bump * Update pull_request_template.md (#220) * 181 watermark (#211) * updated watermark argument to be a string * added roxygen examples * added watermark for Figures * minor bugfix related to colwidths * for consistency, fake watermark is applied to tables, listings and graphs * Update docx_exporter_functions.R * made watermarks on the DOCX match the ones on the RTFs * Update CHANGELOG.md * minor changes * always use the same template file, removed unused functions insert_watermark_XML() and remove_table_shading_XML(), improved function add_hanging_indent_in_title_XML() not to depend on string to look for * fixed roxygen examples in docx exporter * small label update for LS means wide tables (#214) * small label update for lsmeans_wide_first_split_fun_fct * updated snapshots accordingly * added change log entry --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * 67 re align a freq resp var j with a freq j regarding user input for format and na str (#147) * add `.formats` and `na_str` parameters for formatting control * docs and changelog * added CSV arguments to export_TLG_as_docx(), added argument 'validate' (#212) * added CSV arguments to export_TLG_as_docx(): export_csv, output_csv_directory, markup_df. updated roxygen docs * Added argument 'validate' to `export_TLG_as_docx()` and `tt_to_flextable_j()` * updated roxygen docs * Update table_and_listing_customizations.rmd * fixed lint issue * fixes #177 blank pages happening at the end of the docx (#215) * fixes #177, updated "template_file.docx" to have paragraph option "Widow/Orphan control" disabled in Normal style, this allows rows with more than 1 line to be split across pages if they happen at the end of the page fixes #177, updated "template_file.docx" to have paragraph option "Widow/Orphan control" disabled in Normal style, this allows rows with more than 1 line to be split across pages if they happen at the end of the page * Update CHANGELOG.md * updated snapshots docx exporter --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * fixes #216 docx little gaps in table/listing headers (#217) Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * 218 docx vertical pagination reduce first col indent (#219) * fixes #218 fixed calculation of reduce_first_col_indentation, fixed function insert_keepNext_vertical_pagination() * addresses #186, docx exporter added missing defaults (#226) * addresses #186, docx exporter added missing defaults * Docx followup (#223) * fixed location of the watermark for Listings * updated table border width from 0.75 inches to 0.875 inches * docx exporter: updated unit tests and snapshots * fixed the slight vertical misalignment in the rows between the docx and rtf, happening from page 2 onwards (only happens when there is vertical pagination) * Update snapshot test to `cran = TRUE` (#233) * Cran snapshot tests cran = TRUE (#229) * remove skip on cran and flextable bump * add CRAN = TRUE argument * Update docx_exporter_functions.R * update: CHANGELOG.md --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * Fix todos in tests and especially colwidths (#228) * The function returns a list of one‑element character vectors, identical to expected value. * Derive a safe width programmatically (max word length per column + a margin) * update: # Derive all intermediate values exactly * linter * fix: remove old TODOS * fix: remove old TODOS * fix: remove old TODOS * lintr * update: largest_word() * remove: lints * Hotfix: boxplots whose statistics follow SAS percentile definition (`PCTLDEF = 5`) (#231) * update: Add `geom_boxplot_j()` to be able to draw boxplots whose statistics follow SAS quantile(type =2) * update: CHANGELOG.md and bump DESCRIPTION * update: NEWS.md * update: WORDLIST * update: address comments about SAS specifics and make the function SAS agnostic with an added argument quantile_type * update: WORDLIST and lintr * minor visual improvement in geom_boxplot_j() roxygen example * removed warnings NAs * Update docx_exporter_functions.md --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * Hotfix: a freq j fails with countsource = altdf in nested row splits (#221) * update: Added new behavior for nested `countsource` in h_a_freq_dataprep `altdf_subset` (solves #200) * update: Added new behavior for nested `countsource` in h_a_freq_dataprep `altdf_subset` (solves #200) * update: lintr * Update docx_exporter_functions.R (#238) * update: remove private data source (#240) * update: remove private data source * update: Rbuildignore * Dev bump (#249) * Update DESCRIPTION * Update CHANGELOG.md * Update NEWS.md * - changed label from experimental to stable for default_stats_formats_labels, - styled junco_utils_default_stats_formats_labels.r * Added default label for median_range "Median (min, max)" in junco_default_labels_start. (#254) * Add multiplicity adjustment option to `fit_mmrm_j()` (#255) * some progress but hit vcov problem * first working version * update: document h_get_mult_adj_estimates * "release" pipeline : scda.test reverse dependency + hotfix + rhub (#248) * update: revdep * ! Unknown structure of `.revdeprefs.yaml` file. Returning. * repos source * internalize revdep pipeline to remove gchat * on PR * fix rhub on workcall * synchronize * @scda_test_reversedependency debug * hotfix pipeline * remove *rtf from .gitignore! * clean up * add dummy hotfix for now (just copy paste tt_to_tlgrtf * whole pipeline * [main, CRAN] * remove if condition * remove if * skip on cran hotfix * update: revdep timeout * update: bump version * update: wordlist * update: 0.1.1 actual fix * update: fix error in rhub * update: introducing an error in hotfix * update: fixing namespace * update: gcc13 * update: rerun * update: new hotfix * update: hotfix for R package injection * update: hotfix pipeline * update: hotfix NOT_CRAN = "true" * update: hotfix to fail on devtools fail * update: exports * update: remove mac builds * update: remove mac c64 builds * update: remove mac c64 builds * update: CI/CD fix #256 * update: remove sas_comparison * Update inspect.yaml * update: hotfix_v0-1-2 * 265 feature request to include the junco changelog news in the package documentation (#269) * Add NEWS.md * update: changelog for news.md * update: pipelines * update: NEWS.md * Update release.yaml * introduce safe_t_test with tryCatch to prevent problems with almost c… (#258) * introduce safe_t_test with tryCatch to prevent problems with almost constant data * adjust for mean of empty vector * lintr issues * resolve lintr issue * fix merge issues --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> * Docx mw feedback (#264) * Update docx_exporter_functions.R * in figures, shifted watermark to the left a bit * added unit tests * Update docx_exporter_functions.R * Update test-docx_exporter_functions.R * updated docx exporter so that footnotes are now merged into 1 table row/cell, updated snapshots, updated NEWS.md (#273) * Add `subgroup` variable option for `fit_mmrm_j()` and downstream tabulation (#277) * add tests from tern.mmrm package for lsmeans to have enough coverage * robustify mmrm snaps * address Copilot review comments * style files to satisfy linter * linebreaks... * again... * 117 ancova combined column revised (#227) * - refactor s_ancova_j for adding estimates in combined column - extend list of available stats for summarize_ancova_j - add tests for ancova in combined column * - update changelog - add tests for incorrect weights_combo specifications * - add test with initial bug for summarize_ancova * fix test * - add extra option for method of combined group * add the new arguments for combined group s_ancova_j to a_summarize_aval_chg_diff_j and s_aval_chg_col23_diff and pass along * add test for combined column in a_summarize_aval_chg_diff * - revise test script approach ancova combined (use snapshot approach) - refer to vignette in function documentation * explicit drop = FALSE in subsetting dataframe with [] Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * updated snapshots due to new tidytlg CRAN release v0.12.0 (#284) * calling exported functions from tidytlg (#288) * calling gentlg() with footer_one_row = TRUE, updated snapshot in unit… (#286) * calling gentlg() with footer_one_row = TRUE, updated snapshot in unit test * Update DESCRIPTION * Remove boxplot_j #280 (#293) * update: fix #280 * update: document() * update: changelog * add tests for ancova table with more than one combined column (#290) * Feature/hotfix v0.1.3 revert (#289) * renamed junco_hotfix.R to junco_hotfix_v0.1.1.R * Create junco_hotfix_v0.1.2.R * removed duplicated functions from junco_hotfix_v0.1.1.R * renamed junco_hotfix.R to junco_hotfix_v0.1.1.R * removed duplicated functions from junco_hotfix_v0.1.1.R * renamed hotfix files * Apply suggestion from @munoztd0 * Apply suggestions from code review Co-authored-by: David Muñoz Tord <david.munoztord@mailbox.org> * Update release.yaml * Create hotfix_docs.md * Create hotfix_changelog.md * Update junco_hotfix_v0-1-2.R * Create hotfix_docs.html * Create junco_hotfix_v0-1-3.R * Update release.yaml * Update release.yaml * Update release.yaml * Update junco_hotfix_v0-1-3.R * added argument 'round_type' to tt_to_tlgrtf() * Delete dev/hotfix_docs.html * Update junco_hotfix_v0-1-3.R * Revise SOP and update user template for hotfix process Updated the SOP to clarify the hotfix process and revised the template for the end-user script to reflect changes in R version and deployment instructions. * Update junco_hotfix_v0-1-3.R * Update release.yaml * Update hotfix_changelog.md * update: refactor hotpatch with hotpatchR * refactor * update: docs * wait for 0.1.1 * update pipelines * relaunch pipeline * relaunch * relaunch * relaunch pipeline * update: rename function to remove conflicts * update: relaunch * update: relaunch * Update hotfix_changelog.md * update: hotfix : 257 `s_summarize_desc_j()` fixed when applied to almost constant data due to behavior from `t.test.default()` * update: hotfix : 257 `s_summarize_desc_j()` fixed when applied to almost constant data due to behavior from `t.test.default()` * Apply suggestion from @munoztd0 * Update dev/hotfix_docs.md * update: revert back to old hotfix method + add hotfix : #257 * update: revert back to old hotfix method + add hotfix : #257 * renamed junco_hotfix.R to junco_hotfix_v0.1.1.R * Create junco_hotfix_v0.1.2.R * removed duplicated functions from junco_hotfix_v0.1.1.R * renamed junco_hotfix.R to junco_hotfix_v0.1.1.R * removed duplicated functions from junco_hotfix_v0.1.1.R * renamed hotfix files * Apply suggestion from @munoztd0 * Apply suggestions from code review Co-authored-by: David Muñoz Tord <david.munoztord@mailbox.org> * Update release.yaml * Create hotfix_docs.md * Create hotfix_changelog.md * Update junco_hotfix_v0-1-2.R * Create hotfix_docs.html * Create junco_hotfix_v0-1-3.R * Update release.yaml * Update release.yaml * Update release.yaml * Update junco_hotfix_v0-1-3.R * added argument 'round_type' to tt_to_tlgrtf() * Update junco_hotfix_v0-1-3.R * Delete dev/hotfix_docs.html * Revise SOP and update user template for hotfix process Updated the SOP to clarify the hotfix process and revised the template for the end-user script to reflect changes in R version and deployment instructions. * Update junco_hotfix_v0-1-3.R * Update release.yaml * Update hotfix_changelog.md * update: refactor hotpatch with hotpatchR * refactor * update: docs * wait for 0.1.1 * update pipelines * relaunch pipeline * relaunch * relaunch * relaunch pipeline * update: rename function to remove conflicts * update: relaunch * update: relaunch * update: hotfix : 257 `s_summarize_desc_j()` fixed when applied to almost constant data due to behavior from `t.test.default()` * Update hotfix_changelog.md * update: hotfix : 257 `s_summarize_desc_j()` fixed when applied to almost constant data due to behavior from `t.test.default()` * Apply suggestion from @munoztd0 * Update dev/hotfix_docs.md * update: revert back to old hotfix method + add hotfix : #257 * update: revert back to old hotfix method + add hotfix : #257 * update: junco::make_header_bordmat * update: @dev * update: hotfix * update: hotfix * Update junco_hotfix_v0-1-3.R * Update junco_hotfix_v0-1-3.R * Update junco_hotfix_v0-1-3.R * added back arguments alignments and validate to tt_to_tlgrtf() * Update junco_hotfix_v0-1-3.R --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * Update table_and_listing_customizations.Rmd (#297) * Update table_and_listing_customizations.Rmd * unified authors in vignettes * 225 tt to tlgrtf vectorize colwidths (#232) * updated tt_to_tlgrtf() to pass colwidths to gentlg() as list of vectors when 'allparts' * updated CHANGELOG.md and DESCRIPTION minimum dependency version of tidytlg * updated snapshot 'allparts' * Update DESCRIPTION * Apply suggestion from @munoztd0 Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Update tt_to_tblfile.R * Update tt_to_tblfile.R * Update tt_to_tblfile.R * updated snapshots * Update NEWS.md --------- Co-authored-by: Gabe Becker <gabembecker@gmail.com> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * update: lifecycle (#301) * Docx make production ready (#303) * removed "experimental" label to all docx exporter-related functions * Update WORDLIST * Lintr issues dev (#305) * update: lifecycle * update: lintr * update: last lintr * Feature/hotfix afuns for VS tables (#304) * new funs (no man files yet), copied safe_t_test() to separate file and moved add_blank_line_rcells() to blank_lines.R * updated man pages for many functions specific for VS tables updated man pages for many functions specific for VS tables * Delete R/temp_funs.r * Update s_diff_mean_ci.r * Remove commented code and update assertion for s_diff_mean_ci() Remove commented code and update assertion for s_diff_mean_ci() * Updated NEWS, _pkgdown, and fixed the man typos for a few functions. * update s_diff_mean_ci() assertion bog. * update importFrom for s_diff_mean_ci and replaced class(x) == ... to is(x, ...). Update NEWS. * export safe_t_test.r * update: afun error * update: wordlist * update: Fixed the Rd cross-reference NOTE * update: try catch stats t test + document() * update: dontrun{} * update: dontrun{} * update: dontrun{} --------- Co-authored-by: Wojciak <wwojciak@its.jnj.com> Co-authored-by: munoztd0 <david.munoztord@mailbox.org> * removed "experimental" label from junco_utils_default_stats_formats_labels (#311) * CRAN ready: Adding multi-comparator functionality lyt fun (#271) * multicomparator functionality * update: WORDLIST and lintr * add remote entry for now, and typo fix * intermediate commit with 2 versions of everything * reworked as discussed on tuesday re comp_vars, ref_paths etc * updated api and start of formal tests * Update DESCRIPTION * more tests. should pass now. re-roxygenize * adding back the docx exporter snapshots that got deleted * linting, spell check * Update test-multcomp-rrisk.R * update: moove old tests to dev/ and run devtools::document() * update: moove old tests to dev/ + run devtools::document() + wrap ::: in value_expr getFromNamespace + remove co authors form old getFromNamespace * update: DESCRIPTION * update: lintr * update: docs * update: fix merge conflicts * update: add cran comments * update: add cran comments * update: fix html * update: NEWS.md merge=union * vignette draft and some new tests. coverage still a bit low * linted, spell check, updated _pkgdown.yml, etc * Update _pkgdown.yml * linted vignette and more tests, coverage now good * lint fix (?) * clean up DESCRIPTION, ready for submission * remove vestigal debugging --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> Co-authored-by: Ezequiel <4982139+eanokian@users.noreply.github.com> * remove AEACN_DECODE from select * update: rerun pipelines * update: rerun pipelines with new fixed tests * force refresh of checks * Update .Rbuildignore --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> 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 <4982139+eanokian@users.noreply.github.com> Co-authored-by: iaugusty <iaugusty@its.jnj.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <daniel@rconis.com> Co-authored-by: Daniel Sabanes Bove <DBove@ITS.JNJ.com> Co-authored-by: Wojtek <wojciech.wojciak@gmail.com> Co-authored-by: Wojciak <wwojciak@its.jnj.com>
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Not intended for immediate merge, but for team to look through and review approach, with merge after discussions.
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