Catch patch up to v1.0.0 #2314
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Catch patch up to v1.0.0 #2314
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* Closes #2147 addressing cran failure (#2149) * feat: #2147 one solution but proceed with caution * description uplevel and news blurb * pass links? --------- Co-authored-by: Zelos Zhu <[email protected]> * Update README.md (#2155) * Update README.md * URL update --------- Co-authored-by: Daniel Sjoberg <[email protected]> * Closes #2154 fix_dthcaus: fix derive_var_dthcaus() (#2162) * #2154 fix_dthcaus: fix derive_var_dthcaus() * #2154 fix_dthcaus: run templates check * #2154 fix_dthcaus: update version number and NEWS * docs: fixing curlys after feedback from CRAN * chore: styling death test --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]>
…hub issues. (#2182) * #2127 Update _pkgdown.yml navbar with two buttons. One for slack and one for issue reporting. * docs: #2127 NEWS blurb --------- Co-authored-by: Ben Straub <[email protected]>
* superseded fun * Update NEWS.md * added badge * doc update * feat: #2141 supersede section * chore: #2141 docs --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]>
* update templates * fix typo * fix style
* use ascii quotes * regular quoets in the associated .Rd file * 4 non ascii quotes in README.md
* No multiversion docs * Update links
Add secret for `gert` date fetcher
* Update website-versions.Rmd * Update website-versions.Rmd
* #2139 chore: Make dataset_add mandatory for derive_extreme_records() * #2139 Add mandatory dataset_add to examples * #2130 Chore: Update derive_extreme_records from review comments --------- Co-authored-by: Jeffrey Dickinson <[email protected]>
* #2146 Fix Time Imputation Flag * #2146 check templates error * #2146 replace do.call * Replace function short hand with function * Update changelog --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]>
…ined_exist_flag(), filter_joined() (#2163) * #2126 unify_joined: update arguments and tests of filter_joined() and derive_var_joined_exist_flag() * #2126 unify_joined: update examples for derive_var_joined_exist_flag() * #2126 unify_joined: documentation of filter_joined() and derive_var_joined_exist_flag() * #2126 unify_joined: update derive_vars_joined() * #2126 unify_joined: add get_joined_data(), update derive_extreme_event(), add tests * #2126 unify_joined: update templates * #2126 unify_joined: style files * #2126 unify_joined: update vignettes * #2126 unify_joined: update vignettes * #2126 unify_joined: style files * #2126 unify_joined: style files * #2126 unify_joined: remove commented out code * #2126 unify_joined: fix lintr issues * #2126 unify_joined: add example for first_cond_lower * #2126 unify_joined: update function documentation * #2126 unify_joined: style files * #2126 unify_joined: style files * #2126 unify_joined: update NEWS.md * #2126 unify_joined: improve documentation * #2126 unify_joined: add example to event_joined() * #2126 unify_joined: fix R-CMD check * #2126 unify_joined: check class of deprecation warning * #2126 unify_joined: improve documentation * #2126 unify_joined: style files * #2126 unify_joined: clean up globals.R * #2126 unify_joined: improve documentation --------- Co-authored-by: Jerry Johnson <[email protected]> Co-authored-by: Ben Straub <[email protected]>
#2199) * Test no R version * Consolidate check templates into common pipeline * change admiralci ref * remove pharmaverseadam push --------- Co-authored-by: Daphné Grasselly <[email protected]>
* feat: #2184 rename check_keys * chore: #2184 cleanup news * code typo * styler/lintr * feat: #2184 add appropriate deprecation test --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]>
…mmary_records()` (#2158) * feat: #2142 intiial superseding step * rough draft without missing_values implementation * rough draft of new enhancement * feat: #2142 get a good clean slate * feat: #2142 working enhanced function * feat: #2142 add appropriate test suite * feat: #2142 run styler, lintr, add news and roxygen documentation * chore: #2142 spelling/grammar * chore: #2142 fix test * should we inform superseded * retain deprecated arguments to pass cicd * chore: #2142 add remotes for admiraldev for proper branching strategy * min dev versioning * Update DESCRIPTION * chore: #2142 address feedback * upversion our description page to match current version up on github * docs: little note for running website versions * feat: #2142 rename filter to filter_add * Update R/derive_summary_records.R Co-authored-by: Ben Straub <[email protected]> * feat: #2142 get checks appropriately running * roxygen stuff and vignettes * chore: #2142 roxygen stuff * get past check-templates * finally get past templates * feat: #2142 clear up missing_values usage * chore: #2142 rename filter to filter_add internally in codebase too * chore: #2142 adopt and address all other feedback * missed a renaming * feat: #2142 remove extra fluff for missing values * update news blurb * chore: #2142 update documentation based on feedback --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Jerry Johnson <[email protected]> Co-authored-by: Ben Straub <[email protected]>
* add vbump job * change cran status assignes --------- Co-authored-by: cicdguy <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]>
* #2222 clarify_mid: Clarify date_imputation = "mid" * #2222 clarify_mid: Fix links --------- Co-authored-by: Ben Straub <[email protected]>
2225 tidy up SUBGROUP column Co-authored-by: Ben Straub <[email protected]>
* 2134 add general option signif_digits * 2134 fix SPELLING and STYLER * 2134 address QC comments and update NEWS file * 2134 fix LINTR and STYLER * Apply suggestions from code review Minor updates from QC. Co-authored-by: Ben Straub <[email protected]> Co-authored-by: StefanThoma <[email protected]> * Update vignettes/lab_grading.Rmd --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: StefanThoma <[email protected]>
Revert version in NEWS.md
…bility (#2288) * feat: #2255 add uppercase versions of untis * feat: #2255 add tests and documentation * feat: #2255 unit mapping fix * match mapping in derive_vars_duration * apply fixes to derive_vars_aage too * run styler * account for missing mappings * styler * try something * undo the something * #2255 use case_match to clean up code * try something * forgot to commit namespace * undo the something * undo the something * feat: #2255 revert changes from case_match in favor of case_when * styler * chore: #2255 clean up documentation * update news * get around spellcheck * chore: #2255 fix test and wordlist * feat: #2255 adopt feedback * Update common.yml * add back backwards-compatibility * original unit is kept unit_var in derive_vars_duration --------- Co-authored-by: Ben Straub <[email protected]>
* #2282 fix mistake in changelog * fix: #2282 global binding * chore: #2282 styling * Trigger Build --------- Co-authored-by: Ben Straub <[email protected]>
#2291 fix_derive_extreme_event: do not ignore condition Co-authored-by: Ben Straub <[email protected]>
* [skip vbump] 1.0 release * chore: remove remotes and upversion admiraldev * Trigger Build
* [skip vbump] 1.0 release * chore: remove remotes and upversion admiraldev * Trigger Build * chore: link adjustments * chore: fix broken links
Merge branch 'patch' of https://github.com/pharmaverse/admiral into current_release # Conflicts: # .github/workflows/templates.yml # NEWS.md
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I don't think the patch branch is up to date with the 1.0 release |
this PR is to catch patch up to speed |
zdz2101
requested review from
bms63
and removed request for
millerg23 and
jeffreyad
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This terrifies me |
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Closing in favor of creating new patch branch from 1.0.0 release |
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Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.
Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the
mainbranch until you have checked off each task.styler::style_file()to style R and Rmd filesinst/cheatsheet/admiral_cheatsheet.pptxand re-upload a PDF version of it to the same folder.devtools::document()so all.Rdfiles in themanfolder and theNAMESPACEfile in the project root are updated appropriatelyNEWS.mdunder the header# admiral (development version)if the changes pertain to a user-facing function (i.e. it has an@exporttag) or documentation aimed at users (rather than developers)pkgdown::build_site()and check that all affected examples are displayed correctly and that all new functions occur on the "Reference" page.lintr::lint_package()R CMD checklocally and address all errors and warnings -devtools::check()