Repository navigation
Remove get_complete_cases() - #492
Merged
Merged
Conversation
munoztd0
added a commit
that referenced
this pull request
Oct 14, 2026
* 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> * Fixes #312: Add stats to `s_diff_mean_ci()`, and rename it to `s_diff_means()`. (#321) * initial commit * Update junco_utils_default_stats_formats_labels.R check <- to = when assigning a value to list's element * update default stat names for s_summary_diff() * update man page for s_summary_diff() * renamed s_diff_mean() to s_diff_means(), with all the correspondings statistics that are computed by this fun + default labels/formats/indents. * update examples in safe_t_test() * correct typo in NEWS.md. * Create extract_vectors() internal function that is used in s_diff_means(), update safe_t_test() to correctly handle errors when paired = TRUE. * update s_diff_means() assertions. * noRd for internal functions * remove links to internal functions with noRd from s_diff_means() + correct safe_t_test() args. * update: argument forwarding in `safe_t_test()` and preserve `conf.level` on failure. example: safe_t_test(x, x, "two.sided", 0, FALSE, FALSE, 0.80) * styler + update s_diff_means() conf.int parsing by tern::f_conf_level(). * s_summary_diff() man update. * remove safe_t_test() from pkgdown. --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> * fix: rerun docs() (#329) * Refactoring and writing unit test for safe_t_test() (#334) * refectored and added unit tests for internal function extract_vectors(). * Remove one old unit test for safe_t_test() from test-a_summarize_aval_chg_diff.r and styler the file. * remove expect_error test on t.test(). * Lintr update: removed comments between tests in test-utils-extract_vectors.r * Renamed one unit test + lintr update: Removed commented lines. * update man and add unit tests for s_diff_means(). * Add more assertions for s_diff_means() + more unit tests. * updated a_diff_means(), added unit tests for a_diff_means(). * bump to 0.1.6.900 + remove internals formatters (#339) * bump to 0.1.6.900 + remove internals formatters * update vignette * formatters::mf_col_widths * Fixes #332 - get_ref_info() (#333) * fixes get_ref_info() - #332 * Update NEWS.md --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Fix get ref info (#346) * Update get_ref_info.R * Update get_ref_info.Rd * Update get_ref_info.R * pkgdown update with a_diff_means(). * update NEWS.md about new a_diff_means(). * Fix get ref info examples (#350) * fix typo (missing bracket) in the examples of get_ref_info(). * rerun piepline head --------- Co-authored-by: Wojtek <wojciech.wojciak@gmail.com> * Ensure that any default stats defined in `tern` but not overridden here are included (#314) * Ensure that any default stats defined in `tern` but not overridden here are included * update: add test * update: adress comments * Update junco_utils_default_stats_formats_labels.R cosmetic variable name change * Update NEWS.md * Update junco_utils_default_stats_formats_labels.R --------- Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> * Modified and renamed a_summary_j() to a_summary_subset(), modified c_… (#348) * Modified and renamed a_summary_j() to a_summary_subset(), modified c_summary_subset_label(). * update NEWS.md * word spelling update. * WORDLIST update (summarization) * update example for a_summary_diff_mvars_label() --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Solves #338 - assertions for safe_t_test (#352) * assertions for safe_t_test() * refine assertions for safe_t_test() + update and add unit tests. * Solves #355: Removed filter_df_prior_afun(), a_summary_diff_mvars(). (#356) * Removed filter_df_prior_afun(), a_summary_diff_mvars(), a_summary_diff_mvars_label(). * Roxygen documentation update. * h ancova removal (#354) * deprecate: h_ancova * update: Description * 323 todo make windows runs under 8 min on GitHub (#345) * making rbmi test and examples shorter * perf(tests): build shared tbl_wide fixture once in test-tt_to_tblfile * update: NEWS.md * perf(tests): reuse shared table * test: Create a simple table for testing * perf(tests): - shared simple fixtures for validate tests * perf(tests): reuse tbl_simple and badtbl_simple in converts-without-error test: - tbl_simple and badtbl_simple reused from shared fixtures * update: DESCRIPTION * Fixes #332 - get_ref_info() (#333) * fixes get_ref_info() - #332 * Update NEWS.md --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Fix get ref info (#346) * Update get_ref_info.R * Update get_ref_info.Rd * Update get_ref_info.R * add shared tables * perf(tests): build tbl_iec once * perf(vignettes): display chunks with NOT_CRAN in auto_colwidths and table_and_listing_customizations * add timeout to check-r-package step * test --------- Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> * removed ellipsis argument (#360) * Update check_CRAN.yaml * 158 tern functions survival analysis cox ph hazard ratio with ci (#351) * update: remove old depreciated coxph_hr * uopdate NEWS * Ensure that any default stats defined in `tern` but not overridden here are included (#314) * Ensure that any default stats defined in `tern` but not overridden here are included * update: add test * update: adress comments * Update junco_utils_default_stats_formats_labels.R cosmetic variable name change * Update NEWS.md * Update junco_utils_default_stats_formats_labels.R --------- Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> * Modified and renamed a_summary_j() to a_summary_subset(), modified c_… (#348) * Modified and renamed a_summary_j() to a_summary_subset(), modified c_summary_subset_label(). * update NEWS.md * word spelling update. * WORDLIST update (summarization) * update example for a_summary_diff_mvars_label() --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * reimport Surv * Update WORDLIST * fix: rcmd check error * Update R/coxph_hr.R Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> * fix: add s_coxph_pairwise * fix: docs * fix: docs * lintr * fix: CRAN_check --------- Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> * Update check_CRAN.yaml * Update check_CRAN.yaml * Deprecate old rbmi functions (#372) * refactor: moove away from rbmi to utils * deprecate old rbmi stuff * remove assertthat * update: NEWS * docs * lint * Investigate package dependencies (#366) * perf: remove stringi from depencies * perf: replace assertthat by checkmate for consistency * perf: remove dplyr from code and use base R * Update check_CRAN.yaml * update: NEWS.md * lint * dplyr suggest * tibble re document * removed the messages when running unit tests --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * Update junco_hotfix_v0-1-3.R junco::: * Update hotfix.yaml * Update hotfix.yaml * Update hotfix.yaml * Solves #359: Update assertion, unit tests and logic for `get_ref_info()`. (#377) * update assertion, unit tests and logic for get_ref_info(); update a_diff_means() accordingly. * update NEWS.md --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * hotfix missing titles in tt_to_tlgrtf (#375) * Update tt_to_tblfile.R * added unit test that tests that the titles don't get lost * Update NEWS.md * Update hotfix_docs.md * Update hotfix_docs.md * Update hotfix_docs.md * Update WORDLIST * Update hotfix_docs.md * Update docx_exporter_functions.md * Update hotfix_docs.md * Update hotfix_docs.md * WORDLIST update * Revert "WORDLIST update" This reverts commit 2c100a7. * Solves #342. Refactored `prepend_label_cell()`. Added unit tests. (#381) * Refactored `prepend_label_cell`. Added unit tests. * WORDLIST update --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * 235-documentation for label_map in a_freq_j (#347) * update documentation for label_map and add examples * update NEWS for issue 235 * fix: R CMD check errors * address review Wojcjeck * Update NEWS.md * read example dataset adsl_jnj and advs_jnj * Update a_freq_j.R lintr * comments: address all of them * update * fix R cmd check * lintr * docs: adress WW comments * docs: adress WW comments * docs: adress WW comments --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> Co-authored-by: munoztd0 <david.munoztord@mailbox.org> * Deprecate tern kaplan and ancova (#383) * deprecate kaplan_meier() and coxph_hr() in favor of pairwise versions of each. * document() * align lsmean_diffci to lsmean_diffwith_ci * update to main tern * fix: rcmdcheck * docs * update news * Solves #343: Updated and added unit tests for a_summary_subset(), c_summary_subset_label(). (#382) * Updated doc for a_summary_subset(), updated c_summary_subset_label() default value for label arg. Added unit tests for both these functions. * uppercased file extentions (.r to .R) * 386 improve a freq j error message (#387) * update error message * update NEWS * lint and spelling * fix docs issues (#392) * add 3 new tern methods for diff in proportion: cmh_sato, cmh_mn, uncond_exact_diff (#391) Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Update air.toml * 281 error def colwidths quickfix (#395) * Update hotfix_docs.md * quick fix for #281 that prevents code from crashing * Update NEWS.md * Update test-colwidths.R * Add exclude afuns (#398) * added a_summary_j_with_exclude * add a_summarize_mmrm_with_exclude * add rightside() * add NEWS and pkgdown entries * Export splv_extra and value_expr accessors (insightsengineering#1098) (#400) * Export splv_extra and value_expr accessors (insightsengineering#1098) * updated WORDLIST --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * update workflow_dispatch condition * update skip_on_os("windows") exporter * Update new exported calls from rtables.officer (#402) * Add new cur_col_split_path_utils functions (#407) * Add new cur_col_split_path_utils functions * linter update * Update 1 unit test for in_ref_col(). * styler + add @author roxygen tag for the functions I created. * lintr update * update snapshot and tern --------- Co-authored-by: munoztd0 <dtord@its.jnj.com> * update to roxygen 8.0.0 * add checktor * Add multiple imputation functions for response output (#408) * add draft imputation functions * add pval category functions * add pooling functions * add imputation/analysis functions * add to NEWS, refresh docs * fix assertion * ignore .Renviron * update snapshot * Update WORDLIST Hilferty * rewrite namespace with roxygen 8.0.0 --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: munoztd0 <dtord@its.jnj.com> * in_ref_col() - support ref_path = NULL, minor variables change in uni… (#412) * in_ref_col() - support ref_path = NULL, minor variables change in unit tests (.spl_context to spl_context). * update docs to roxyfen 8.0.0 --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> * a_three_tier (#411) * three tier (extension to two_tier) * fix: lints --------- Co-authored-by: munoztd0 <dtord@its.jnj.com> * Deprecate rbmi_ancova() and rbmi_ancova_single() (#390) * update: move rbmi to deprecate * Update DESCRIPTION * deprecate `rbmi_ancova()` for `rbmi::ancova()` + move everything together in to deprecate * Update DESCRIPTION * Update deprecate.R remove old forked make_rbmi_cluster because in rbmi now * Update test-deprecate.R * Update NAMESPACE * Update _pkgdown.yml * Delete man/make_rbmi_cluster.Rd * add 3 new tern methods for diff in proportion: cmh_sato, cmh_mn, uncond_exact_diff (#391) Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Update air.toml * 281 error def colwidths quickfix (#395) * Update hotfix_docs.md * quick fix for #281 that prevents code from crashing * Update NEWS.md * Update test-colwidths.R * Add exclude afuns (#398) * added a_summary_j_with_exclude * add a_summarize_mmrm_with_exclude * add rightside() * add NEWS and pkgdown entries * Export splv_extra and value_expr accessors (insightsengineering#1098) (#400) * Export splv_extra and value_expr accessors (insightsengineering#1098) * updated WORDLIST --------- Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> * update workflow_dispatch condition * update skip_on_os("windows") exporter * Update new exported calls from rtables.officer (#402) * Add new cur_col_split_path_utils functions (#407) * Add new cur_col_split_path_utils functions * linter update * Update 1 unit test for in_ref_col(). * styler + add @author roxygen tag for the functions I created. * lintr update * update snapshot and tern --------- Co-authored-by: munoztd0 <dtord@its.jnj.com> * update to roxygen 8.0.0 * add checktor * document --------- Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com> Co-authored-by: Ezequiel <4982139+eanokian@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> * Renamed in_ref_col() to in_column(). (#422) * renamed in_ref_col() to in_column() + renamed its ref_path argument to col_path. * Update NEWS.md --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Feature eair: Extra combined statistic required to be able to present "n (EAIR per 100 SY)" (#362) * temp commit, not yet finished * temp commit, not yet finished * update roxygen/test/disable NULL for occ_var * update NEWS * lintr + spelling * removed duplicated section * lintr * retrigger CI * Update check_CRAN.yaml * Update check_CRAN.yaml * add new approaches for conf interval for diff in rate * add new approach for occ_var = NULL, count_events * assign cps * match precision of test a_eair_diff with snapshot version * lintr * importFrom stats ave * namespace stats, ave * added rateci github to suggest and added remotes * update label behaviour depending on rowsplit or not * a_eair_diff separate tests with ratesci from snapshot tests * address review comments Nik * remotes pharmaverseadamjnj for test test-summarize_ancova * lintr * Several updates - refactor a_eair100_j to avoid h_get_trtvar_refpath - add extra stats derivations - ensure afun can be used in horizontal layout as well * spell and lintr * fix : ! subscript out of bounds * pass ref_col_expr NULL when not relevant * fix: tests * lintr * update: test accroding to new ratesci updates * update: test to data pahrmaverse * - introduced new helper function for riskdiff setup - implemented in a_eair100_j - added tests * style + lint * style + lint * update snapshot after lintr * update to new CRAN release fo ratesci * h_incidence_rate tern got exported * new function a_eair_strat_j * spellcheck * allow scoring to be performed on other than first number in cellvalue (eg n_eair, need to perform on eair, not the n value) * temp commit, not yet finished * update roxygen/test/disable NULL for occ_var * update NEWS * temp commit, not yet finished * lintr + spelling * lintr * retrigger CI * Update check_CRAN.yaml * add new approaches for conf interval for diff in rate * add new approach for occ_var = NULL, count_events * assign cps * match precision of test a_eair_diff with snapshot version * lintr * importFrom stats ave * namespace stats, ave * added rateci github to suggest and added remotes * update label behaviour depending on rowsplit or not * update to new CRAN release fo ratesci * a_eair_diff separate tests with ratesci from snapshot tests * address review comments Nik * remotes pharmaverseadamjnj for test test-summarize_ancova * lintr * Several updates - refactor a_eair100_j to avoid h_get_trtvar_refpath - add extra stats derivations - ensure afun can be used in horizontal layout as well * spell and lintr * pass ref_col_expr NULL when not relevant * fix : ! subscript out of bounds * fix: tests * lintr * update: test accroding to new ratesci updates * update: test to data pahrmaverse * - introduced new helper function for riskdiff setup - implemented in a_eair100_j - added tests * style + lint * style + lint * update snapshot after lintr * h_incidence_rate tern got exported * new function a_eair_strat_j * spellcheck * allow scoring to be performed on other than first number in cellvalue (eg n_eair, need to perform on eair, not the n value) * in_ref_col() - support ref_path = NULL, minor variables change in uni… (#412) * in_ref_col() - support ref_path = NULL, minor variables change in unit tests (.spl_context to spl_context). * update docs to roxyfen 8.0.0 --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> * fix merge issues with rebase on dev * fix: lintr * Update R/utils.R Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Update utils.R * lintr --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> Co-authored-by: munoztd0 <david.munoztord@mailbox.org> Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> * fix for new rtables c.RowsVerticalSection * Solves issue 425: Add factor_by_order(), copy_attributes(), is_bijection(), and corresponding documentation and unit tests. * update tern/rtables links: insightsengineering -> pharmaverse * WORDLIST update * update is_bijection() to not use table(). * removed some garbage lines of in is_bijection(). * cosmetic change in is_bijection(). * PR review: mainly update unit tests for is_bijection(). * update of is_bijection() and doc for factor_by_order(); as a result of the 2nd review of PR 426. * Update man page for factor_by_order(). * Update unit tests for is_bijection(). * Update adamjnj advs (#435) * update pharmaverseadamjnj * rename file * Update check_CRAN.yaml * Updated `insightsengineering` urls to `pharmaverse` (#441) * new unified get_ref_info (#423) * new unified get_ref_info * new unified get_ref_info() * fix: examples and redocument * fix: merge issues * get_ref_info() update - refectored body proposal. * lintr update for cur_col_split_path_utils. * refactor: trt_var / ctrl_grp -> split_var / ref_level * test: make get_ref_info tests more specific to the exact length * refactor: rename test * rename split_var split_name instead to reflect the changes * lintr * f**** lint * lean get_ref_info * refactor `h_get_trtvar_refpath()` and `a_summarize_aval_chg_diff_j()` * lint + document * get_ref_info(): man update. * h_get_trtvar_refpath(): cosmetic code update. * refactor * refactor * updated h_get_trtvar_refpath() - PLEASE UPDATE UPSTREAM CODE RESPECTIVELLY. * update h_get_trtvar_refpath() and its upstream dependencies. What is left is: dev/hotfix* * styler only. * fix(h_get_trtvar_refpath): match trt var by name not position.. * vingette for get_ref_info * added match + is.na defensice checks * use pharmaverseadamjnj instead for examples * Added regression test * Implemented the positional trt_var suggestion * replace h_get_trtvar_refpath() with h_get_cur_trt_grp(). The UPSTREAM CODE NEEDS TO BE UPDATED (except a_freq_j())! * cosmetic a_freq_j() update. * Added strict_match(). * unexport * test: add unit test for strict_match * fix #446 . Update all the code (afuns) that uses the old h_get_trtvar_refpath(). * adde assertions 6. ) assertions should be added to all other functions where `ref_path` Fixes #449 * add dont run * lintr * fthis --------- Co-authored-by: Wojtek <wojciech.wojciak@gmail.com> * Update package dependencies in DESCRIPTION file * Update DESCRIPTION * Update DESCRIPTION * Add get_complete_cases(). * Added quiet argument to get_complete_cases(). * Update formatting functions jjcsformat_count_denom_fraction and jjcsformat_fraction_count_denom to adhere to internal (#451) * update function factory jjcsformat_cnt_den_fract_fct to adhere to count = 0 case formatting * styler and lintr --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * first stab at sfun * add description function, unit tests * further progress * clean up doc structure * complete tests * prefix * 436 fr function format sigfig j (#437) * formatting function format_sigfig_j * NEWS and pkgdown * minor update after discussion with WW * fix typo * fix: removed @PARAM round_type and moved the @return * rename internal function signif_j to modified_signif_j * update format_sigfig_j example code * adress feedback WW * address feedback WW * example code for internal function * update roxygen documentation --------- Co-authored-by: munoztd0 <dtord@its.jnj.com> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * address comments * add na.rm argument for stats fun * fix decision making about method * fix pkgdown and spelling * fix linter * rename files to match roxygen file * Revert "Deprecate rbmi_ancova() and rbmi_ancova_single()" (#464) * fix lints * fix * rerun docs * Fixed the `auto_colwidths` vignette so CRAN-mode rendering no longer evaluates inline expressions that depend on objects created only in NOT_CRAN chunks. * fix outdated snapshot * spelling * disable table formatting because linter does not like it * fix snapshot * fix: rename functions and remove duplicate output (#442) (#466) * remove duplicate and added a label arguement * update documentation * update function names from rel_risk to risk_diff * update documentation * add the changes to news * update documentation --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Add new arguments to format_stats(). * update NEWS. * Update pharmaverse/rtables reference to main branch * Update tern package version and remote reference * Update DESCRIPTION * Update README.md (#357) * Update hotfix.yaml (#376) * Update hotfix.yaml * Update hotfix.yaml * Update check_CRAN.yaml * Dev++ THIS IS A TEST (#489) * lints again * fix bug a_freq_resp * lints * snapshot update * 424 feature request assertion for id arg in a freq j (#482) * fix: 424 * sfreq_j * adrees comments * Apply suggestion from @munoztd0 * update unit test for a_freq_j() * Apply suggestion from @munoztd0 --------- Co-authored-by: Wojtek <wojciech.wojciak@gmail.com> * remove get complete cases (#492) * Fix: Added factor assertion on `.var` in `s_freq_j` (#469) * Fixes #453 * bum to rtables main * Update R/a_freq_j.R * comment * fix: use tern's native diff_est_ci in s_proportion_diff_j() (#495) * update_the function * update documentation * add `a_sum_ratio_j()` analysis function (#491) * INIT * add a test * update the function * add tests * update a_sum_ratio comments * update documentation * update documentation * removing deduplicate and add unique * added defaults in the pacakge * remove expected results from tests * removed section comment * removed all comments * update junco ratio * update author and remove deduplicated * update VR in wordlist * update docx snapshot * update snaps * revert snapshot changes (false positives from windows) * Update WORDLIST --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: David Muñoz Tord <david.munoztord@mailbox.org> * Added s_proportion_diff_mf() and a_proportion_diff_mf(). * WORDLIST update. * Address PR review for proportion_diff_mf functions + add comprehensive unit tests. * Changed default value for exact_footnote in a_proportion_diff_mf(). * Minor man update for h_set_labels_prop_diff_mf(). * Added new s_test_proportion_diff_mf() and a_test_proportion_diff_mf(). * add tests first * implement and document * make sure .N_row and .N_col are available and can be optionally used * modify NEWS entry * Remove `s_proportion_diff_j()` (#442, #468) (#504) * s_proportion_diff_j removed * replace tern function * replace old with new tern function * remove all tests * fixed documentation * update news * add a test for label * Apply suggestion from @munoztd0 * remove old param --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> * Remove explicit .alt_df_full from extra_args (#508) * Remove explicit .alt_df_full from extra_args * clean up * update def prog * fix * Set default RefFootnote() and add mf_threshold argument for adaptative prop diff s/a functions based on the MF criterion. * Draft format d (#462) * initial commit * updates to default formats * roxygen + tests * review file for default formats * default format count_fraction to jjcsformat_count_fraction * - update stat mean_diffci into mean_diff_with_ci - a_summary_subset afun to deal with fmt_d as format input * utilize formats_var in a_summary_subset * refactor column_stats and vars_in_cols_setup (former postfun_eq5d) * renamed vars_in_cols_setup into stats_in_cols_setup * spelling and styler * add fmt_spec_d and fmt_utils pages to pkgdown.yml * resolve check-r-package issues * lintr + description import * resolve check problems * add dplyr call in examples * resolve tribble issues in roxygen examples * resolve example problems * resolve check() issues * allow format setup for format_sigfig_j with varying precision * to prevent dependency problems * add extra tests * add vignette + some smaller updates * remove junco::: as fmt_spec_single_d is now exported * resolve merge conflict * resolve merge conflict * resolve merge conflict * spelling + update links * update link * small typos * diff_ stats are from proportions estimation, default to report to 1 decimal place, not 2 * draft vignette for PK formatting function * this will not EVAL in cran and allow random.cdisc.dat to be in suggest * fix cross linking * fix note * address review feedback Joe * to avoid hand calculation of number of d-style stats in junco_def_d_all * spelling correction * add 4th example for stats in columns --------- Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> * address review comments * document reason * fix example * correct test, remove assertion that would not hold if there are NAs * complete test coverage * doc update * unrelated update to make rbmi tests pass * make rubin_rules call conditional on rbmi package version to be safe for new release * use helper function to DRY code * update tests to reflect changes in denominator handling for row-wise calculations * address review comments * remove tests with N_col * move code to documentation helper * polish * use outdated example * fix example * final cleanup * fix example * fix another example * add test for a_freq_j using cmh sato where tern bug occured (#515) * add test for a_freq_j using cmh sato where tern bug occured * Trigger CI * per feedback limit test for bug to a_freq_j only * Added new a_combo_prop_diff_pval_mf() afun. * Adding new standard column structure functions (#431) * add grouped_cols_w_subgrps * example for diff col * test: added unit test for grouped_cols_w_subgrps and example * add shift table function * test: added shift_tbl_col_struct tests and examples * doc: added .pre, and .post source documentation * add pkgdown docs * lintr + news.md * update wordlist * add some_v_all_col_struct with doc an example * remove subgrp * fix: risk_diff_col_struct.R : .trtmap_to_post_funs(colspan_trt_map), which errored whenever colspan_trt_map = NULL * tests: added tests for some_v_all_col_struct * news.md * test: added test for grouped_cols_w_subgrps without spanning header * fix lints * adding quartile column structure * document * quartile column structure with precomputed data * lint * allow diabling of total column for subgrp struct, add to vign * lints * fix pkgdown * wordlist * final draft of vignette, some other fixes * No worries i;m dyslexic too --------- Co-authored-by: munoztd0 <david.munoztord@mailbox.org> Co-authored-by: David Muñoz Tord <david.munoz@mailbox.org> Co-authored-by: munoztd0 <dtord@its.jnj.com> * Added jjcsformat_percentage() and "unique_percentage"` as a new stat supported by s_freq_j() and a_freq_j(). * Added lowercase_words argument to string_to_title(). (#525) * Added lowercase_words argument to string_to_title(). * update pkgdown * Update two unit tests for string_to_title() after testthat issue 2363 has been clarified. * rcell with format_na_str * Trigger CI/CD * Addressed PR review comments for adding unique_fraction stat for a_freq_j(). * pkgdown update * Finishing touches 0.1.7 (#521) * up versino rtables to 0.6.17 * update news * Update DESCRIPTION * Update NEWS.md * replace the unclass approach with in_rows * revert rtables.officer * remove remotes * revert rtables.officer * remove triple colon * update snaps back * remove tests that will fails with new tern release in a week * fix: revert test and run document * # nolint --------- Co-authored-by: Joe Zhu <sha.joe.zhu@gmail.com> * apply na_str as recorded in snapshot * mf_col_widths not exported on 5.1.2 * clean up CICD * update coverage * add main * Delete prolems.R~ * Update tern 0.9.13 * update test to tern 0.9.13 * update NAMESPACE formatting from roxygenize --------- Co-authored-by: Daniel Sabanes Bove <danielinteractive@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <DBove@ITS.JNJ.com> Co-authored-by: Gabe Becker <gabembecker@gmail.com> Co-authored-by: Ezequiel Anokian <lainjoso@hotmail.com> Co-authored-by: Ilse <55379552+iaugusty@users.noreply.github.com> Co-authored-by: Ezequiel <4982139+eanokian@users.noreply.github.com> Co-authored-by: Wojtek <wojciech.wojciak@gmail.com> Co-authored-by: Wojtek <11532997+wwojciech@users.noreply.github.com> Co-authored-by: Wojciak <wwojciak@its.jnj.com> Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com> Co-authored-by: Daniel Sabanes Bove <daniel@rconis.com> Co-authored-by: Anantadinath <vickey.coool@gmail.com> Co-authored-by: Ilse Augustyns <iaugusty@its.jnj.com> Co-authored-by: Joe Zhu <sha.joe.zhu@gmail.com>
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Remove
get_complete_cases()as it was moved to{tern}inpharmaverse/tern#1515