* 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]>

preserve arg doc update

* superseded fun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

)

#2107 Updated the documentation for 'end window' argument

* website links

* Update website-versions.Rmd

* Update website-versions.Rmd

* progress

Add secret for `gert` date fetcher

…_event() (#2177)

* #2140 tmp_event_nr_var: add tmp_event_nr_var to derive_extreme_event()

* #2140 tmp_event_nr_var: update vignettes

* #2140 tmp_event_nr_var: update NEWS

* #2140 tmp_event_nr_var: style files

* #2140 tmp_event_nr_var: fix lintr check

* #2140 tmp_event_nr_var: fix typos

* 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

…raldev links (#2242)

* added deprecation badges

* updated admiraldev website links

* url updates

* #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

* #2126 unify_joined: remove too extensive documentation

---------

Co-authored-by: Jerry Johnson <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* #2196: move dev process from admiraldev

* #2196: update wordlist/remove testing phase

* Update vignettes/contribution_model.Rmd

Co-authored-by: Ben Straub <[email protected]>

* Update vignettes/contribution_model.Rmd

Co-authored-by: Ben Straub <[email protected]>

* Update vignettes/contribution_model.Rmd

Co-authored-by: Ben Straub <[email protected]>

* update NEWS/WORDLIST/contribution_model

* update contribution_model/wordlist

* Empty commit

* Empty commit

---------

Co-authored-by: Ben Straub <[email protected]>

* #2186 TERMID -> TERMNUM, TERMNAME -> TERMCHAR

* #2186 chroe: styling and tests

* #2186 chore: roxygen

* Test commit to retrigger workflow

* Undo test commit

* #2186 term_renaming: align sdg

---------

Co-authored-by: Bundfuss, Stefan {MDBB~Basel} <[email protected]>

…olumns (#2245)

* #2231 added check in `derive_vars_period()` to remove unused columns

* #2231 Chore: styler

* Update tests/testthat/test-period_dataset.R

Co-authored-by: Ben Straub <[email protected]>

* #2231 updates to `assert_data_frame` calls following review

---------

Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Stefan Bundfuss <[email protected]>

…2232)

* #1728 merged_exist_msrc: start it

* #1728 merged_exist_msrc: implement function and tests

* #1728 merged_exist_msrc: add documentation

* #1728 merged_exist_msrc: style files

* #1728 merged_exist_msrc: fix spelling

* #1728 merged_exist_msrc: fix lintr

* #1728 merged_exist_msrc: fix lintr (rename function)

* #1728 merged_exist_msrc: improve documentation and rename function again

* #1728 merged_exist_msrc: update roxygen2 test

---------

Co-authored-by: Ben Straub <[email protected]>

* #2130 added cheatsheet to repo

* #2130 updated admiral cheatsheet

* #2130 added cheatsheet image

* 2130 added hyperlinked cheatsheet

* #2130 added NEWS.md text

* #2130 Cheatsheet -> Cheat Sheet

* #2130 renamed files to fix CMD check issues

* #2130 added Cheat Sheet item to PR template

* #2130: fixed broken links, added PHUSE link to .lycheeignore

* chore: #2130 fix links

* #2130 added PowerPoint cheatsheet to repo instead

* #2130 updated cheatsheet with new functions and deprecations for 1.0

* #2130 removed quotations from dataset_add call in derive_vars_joined

* #2130 lycheeignore text moved to RBuildIgnore, updated screenshot

---------

Co-authored-by: Ben Straub <[email protected]>

…2253)

#2239 changed links in Example Scripts to `use_ad_template()`

* #2178 Created `derive_vars_computed()` and it's corresponding unit test and updated the NEWS.md file.

* #2178 Corrected the `devtools::check()` fails

* #2178 Added 'BMIBL' to the WORDLIST

* #2178 Updated `derive_vars_computed()` to use `derive_param_computed()`

* #2178 Updated the requested changes

* #2178 Updated the document for the need of `exprs()` in the `by_vars` argument

---------

Co-authored-by: Jerry Johnson <[email protected]>
Co-authored-by: Stefan Bundfuss <[email protected]>

)

* #2230 update_generic: create outline

* #2230 update_generic: add introduction

* #2230 update_generic: add selection method

* #2230 update_generic: add summary and compute method, enhance derive_var_merged_summary(), updated NEWS.md

* #2230 update_generic: add reactable and style files

* #2230 update_generic: fix spelling

* #2230 update_generic: fix lintr

* #2230 update_generic: update man

* #2230 update_generic: update DESCRIPTION

* #2230 update_generic: readd note on difference between joined and merged

* #2230 update_generic: improve wording

* #2230 update_generic: change order of columns

* Chore #2138 Implement derive_vars_extreme_event()

* #2138 run styler

* #2138 update documentation after styler and edit for derive_extreme().

* #2138 add lb data to derive_vars_extreme_event() example

* #2138 Update test coverage for event$order

* #2138 Run styler on test file

* #2138 minor updates to documentation

* #2138 remove derive_extreme() function.  Call derive_extreme_event() in derive_vars_extreme_event()

* #2138 run styler

* #2138 Add DTHCAUS example

* #2138 updates from feedback

* #2138 update example code

* #2138 Update to set_values_to

* #2138 update LSTALVDT in ADSL template and vignette

* #2138 Update DTHCAUS in ADSL vignette

* #2138 simplify new_vars call in ADSL

* #2138 Simplify new_vars in example

* #2138 Simplify new_vars in example

* #2138 doc updates

* #2138 Split files

* #2138 run styler on new test files

* #2138 set_values_to default NULL

* #2138 set_values_to default NULL

* #2138 doc: filter to filter_join argument

* #2138 remove set_values_to call from derive_vars_extreme_event()

---------

Co-authored-by: Jeffrey Dickinson <[email protected]>

…moved C… (#2251)

* #2217 Update in navbar - added drop down in Get started and removed Community from top

* #2217 Updated the changelog in Documentation section

* chore: #2217 spelling

---------

Co-authored-by: Jerry Johnson <[email protected]>
Co-authored-by: Edoardo Mancini <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

… sorting variables (#2262)

* #2230 update_generic: create outline

* #2230 update_generic: add introduction

* #2230 update_generic: add selection method

* #2230 update_generic: add summary and compute method, enhance derive_var_merged_summary(), updated NEWS.md

* #2230 update_generic: add reactable and style files

* #2230 update_generic: fix spelling

* #2230 update_generic: fix lintr

* #2230 update_generic: update man

* #2230 update_generic: update DESCRIPTION

* #2230 update_generic: readd note on difference between joined and merged

* #2230 update_generic: improve wording

* #2230 update_generic: change order of columns

* #2230 update_generic: add derive_vars_computed()

* #2230 update_generic: add handling of NAs for sorting variables

* #2230 update_generic: add handling of NAs for sorting variables for new functions

* #2230 update_generic: add derive_vars_extreme_event() to function overview

* #2230 update_generic: fix lintr

* #2230 update_generic: add additional example and links

…#2243)

* Added `DTHCAUS`, `DTHCGR1` to ADSL template and vignette

* #2218 chore: styler

* #2218 remove "Templates" section and move news item to "Various"

* #2218 changed death cause and traceability variables derivation

* #2218 improved Death Date dataset vignette

---------

Co-authored-by: Ben Straub <[email protected]>

* Update _pkgdown.yml

* Update _pkgdown.yml

* #2254 added missing punctuation in the README

* #2254 Added Sukalpo Saha and Romain Francois as contributors, Daniel Sjoberg as author, upgraded G Gayatri to author.

* #2254 added some available presentations and corrected typo

* #2254 - added 2024 release schedule, added references to recent conferences, fixed missing full stops in README, regenerated cheatsheet due to misaligned background

* #2254 chore: spelling

* #2254: removed erroneous full stop, archived older presentation in a new presentation archive article

* #2254 fix broken link

* #2218 moved presentation archive vignette to admiraldiscovery

* Update test for derive_var_obs_number

* Styler the file

* removed the `L`
* format code to solve the lintr error

* Add related changelog for (#2226)

* Add related changelog for (#2226)

* add vbump job

* change cran status assignes

* change paths

* Update ad_adpc.R

* add comment

---------

Co-authored-by: Ben Straub <[email protected]>

* #2220 - 8 functions no longer exported, 3 functions exported - but internally. (Full list available in issue definition.

* chore: #2220 removing functions from docs, others to internal

* chore: #2220 putting back some keywords/family

* docs: news entry, removing see also references

* fix: re-exporting chr2vars.  removing reference in derive_vars_query

* chore: #2220 spelling

* chore: #2220 styling - don't i look good!!

* fix: #2220 Note in R-CMD check

* docs: #2220 a dangling roxygen comment

---------

Co-authored-by: Sophie Shapcott <[email protected]>

* first few functions

* first few functions

* adapt description

* same for constant_by_vars

* same for constant_by_vars

* updated news.md

* updated news.md

* added short description of exprs()

* added tests

* fix comment

* remove dataset_add argument

* document

* Update R/derive_vars_transposed.R

* Update R/derive_vars_transposed.R

* fix unique

* Update R/roxygen2.R

Co-authored-by: Stefan Bundfuss <[email protected]>

* add backticks

* fixed roxygen2.R

* Update R/derive_merged.R

Co-authored-by: Zelos Zhu <[email protected]>

* fix: #2137 Apply suggestions from code review

Co-authored-by: Zelos Zhu <[email protected]>

* docs: #2137 re-render

---------

Co-authored-by: Stefan Bundfuss <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

…ive_vars… (#2268)

* 2238: clarify dates values in flag_imputation argument of derive_vars_dt() function

* 2238, updates as per review comments

…on `SRCVAR` types for queries (#2270)

* feat: #2264 working draft of new assertion

* bad copy/paste

* fix typo

* styler/lintr

* chore: #2264 styler/lintr and adopt feedback

* fix logic

* fix breaking test

* cleanup

* wrong branch

* chore: #2264 fix unit test break

* chore: #2264 add news blurb

* get around cyclocomp lintr

* clear up messaging

* adopt feedback for test label

* feat: #2264 adopt feedback

* chore: #2264 more feedback changes

* #2264 derive_vars_query_lighten_termnum_termchar_assertion: update workflows

* undo a removal

* move up the incorrect data type abort message

* accidental add

---------

Co-authored-by: Bundfuss, Stefan {MDBB~Basel} <[email protected]>

* 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

---------

Co-authored-by: Ben Straub <[email protected]>

#2275 updated cheatsheet

Co-authored-by: Ben Straub <[email protected]>

* #2277 release schedule correction

* #2277 vaccines TBC date added

* #2277 Fixed typos/improved consistency of changelog

* #2277 Deleted contribution model vignette

* #2277 Updated contribution MD file

* docs: #2277 polishing the news

* chore: #2277 remove old image

* fix: #2277 fixing pharmaversesdtm to >=0.2

* fix: #2277 urls

* fix: #2277 urls

* fix: #2277 urls

* chore: #2277 spelling

* chore: #2277 spelling

---------

Co-authored-by: Edoardo Mancini <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

…ies assertion (#2280)

* feat: #2264 add tests based on feedback

* accidental modification

* fix test as necessary

#2138 remove by_vars default

Co-authored-by: Jeffrey Dickinson <[email protected]>