Closes #2034 use functions to standardize roxygen text (#2065)

* Closes #1950 following deprecation process, update Description version and news.md

* updating documentation to fix the warnings

* added the new tests for minutes and seconds options

* Removing references in deprecated functions.

* updated comments and applied test_that format

* conflicts resolved

* Closes #1941 authors contributors@devel (#1967)

* Initial edit to `_pkgdown.yml` for #1941

* #1941 re-labelling authors and contributors

* #1941 update to enact decision of team regarding who are authors and contributors.

* #1941: Chore (spellcheck and man pages and NEWS.md update)

* #1941 chore: further updates to spellcheck

* #1941: chore: fix space after commas. move some acknowledgees to contributors. link README in authors page.

* #1941 chore: roxygenize

---------

Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]>

* Closes #1228 produce bmi records for more visits (#1957)

* feat: #1228 Produce BMI records for more visits: Add constant_height parameter

* feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail.

* docs: #1228 Produce BMI records for more visits: Fix typo in NEWS

* feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette.

* doc: #1228 Produce BMI records for more visits: Add backticks to variable.

---------

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

* Closes #1695 Establish codeowners (#1973)

feat: #1695 add gordon and jeff as codeowners

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

* Closes #1974 Swapping out deprecated assertions (#1975)

* feat: #1974 try swapping all deprecated assertions

* chore: #1974 fix parsing issue that caused vignettes to crash

* chore: #1974 simplify by_vars requirement

Co-authored-by: Kangjie Zhang <[email protected]>

* chore: #264 move assertion to different line

---------

Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Kangjie Zhang <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* Propagate renv.lock from pharmaverse/admiralci (#1986)

renv update from pharmaverse/admiralci

Co-authored-by: dgrassellyb <[email protected]>

* Catch devel up to Admiral v0.11.1 (#1997) (#1999)

Admiral v0.11.1 (#1997)

* [actions skip] Add/Update README.md for patch

* Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987)

* feat #1962 #1969 param_tte and get started fix

* forgot to add updated DESCRIPTION

* chore: #1962 thought crossing was dplyr

* chore: #1962 account for new assertions

* fix: #1962 was missing the reassignment piece?

* fix: #1966 crude answer

* feat: #1966 potential way of warning users of null new_vars

* fix: #1966 add appropriate assertions to get check to go through

* fix: #1966 appropriate function fix for order

* fix: #1966 vignette named order expression

* chore: #1966 try something

* chore: #1966 optionality of expressions is tricky

* feat: #1966 undo derive_joined stuff

* chore: run styler

---------



---------

Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

* Initiate a Stale bot for Issue Triaging (#1992)

* Create stale_bot.yml

* Update and rename stale_bot.yml to stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Closes #1927 derive param tte@devel (#2000)

Removed incorrect reference of start_imputation_flag

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

* Closes #1989 Link Fix in `README.md` (#1994)

* Update README.md

* Update WORDLIST

* Update README.md

* Update WORDLIST

* chore: #1989 spelling

---------

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

* Closes #1856 Removed the higher order file (#2008)

#1856 Removed the higher order file

* Update templates.yml (#2026)

* Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009)

* #2001 added processing for missing age_units in `compute_age_years`

* #2001 Chore: styler

* #2001 chore: lint

* #2001 chore: fix broken links

* #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`.

* #2001 chore: Fixed docs link

* #2001 chore: styler

* #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit`

* #2001 Update NEWS.md as per suggestiom

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

* Update R/compute_age_years.R with correct backquoting

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

* #2001 version change in deprecation

* #2001 insert parenthesis in NEWS.md

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

* #2001 chore: roxygen

---------

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

* Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024)

* feat: #1979 added the necessary flag_all function argument

* feat: #1979 modify check_type to supppress warnings for flag_all = TRUE

* chore: #1979 run lintr/styler

* chore: #1979 add news blurb

* typo

* chore: #1979 add additional tests and add roxygen details

* chore: #1979 adopt feedback from review

* chore: #1979 run styler

---------

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

* Closes #123 Add Edoardo to status check (#2031)

fix: https://github.com/pharmaverse/admiralci/issues/123 add Edoardo to status check

* Closes #2014 derive_var_shift change na_val@devel (#2032)

* #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`.

* #2014 - Update `NEWS.md`.

* #2014 - update tests and write deprecation parameter test

* #2014 - run required tasks for PR

---------

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

* Closes #2012_derive_vars_dy (#2013)

* derive dy_vars by argument .name in across (#2012)

use named vector to avoid the variabes end with `_temp` in input dataset

* test no error for variable end with `_temp`(#2012)

* styled file

* add update information for #2012

---------

Co-authored-by: Daniel Sjoberg <[email protected]>

* Closes #1966 address derive_vars_joined bugs (#2016)

* feat: #1966 make our check_type consistent

* feat: #1966 hacky solution to null new_vars .join problem

* chore: #1966 inserted line in wrong place

* feat: #1966 add news blurb for what was done

* feat: #1966 add tests

* chore: #1966 lintr

* chore: #1966 swap appropriate order selection and restore check_type arg

* chore: #1966 looks like that fixed it

* feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL

* chore: #1966 clean up for readability

* chore: #1966 restore original replace_values_by_names

* chore: #1966 add additional test to demonstrate how order vars were fixed/selected

* feat: #1966 adopt feedback for error messaging of naming conflicts

---------

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

* Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039)

feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref`

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

* Close #1940 Removing unnecessary runtime development-related dependencies (#1978)

* feat: #1940 try removing dev deps

* chore: #1940 still needs knitr

* #1940 diffdf needed for all the testing stuff

* chore: #1940 add back rmarkdown

Co-authored-by: Adam Foryś <[email protected]>

---------

Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>

* Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029)

* #1984 allowing missing trt end date

* Update derive_var_ontrtfl.R

* Update derive_var_ontrtfl.R

* Increment version number to 0.12.0.9000

* updating version numbers...oops!

* Update test-derive_var_ontrtfl.R

* Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048)

addressing missing treatment start dates

* Propagate renv.lock from pharmaverse/admiralci (#2046)

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* Update .Rbuildignore

* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>

* Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044)

* span_period arg update

* Update derive_var_ontrtfl.R

* Update NEWS.md

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

* Update R/derive_var_ontrtfl.R

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

* Update R/derive_var_ontrtfl.R

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

* remove space for lintr

---------

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

* add admiral src to test codespaces

* Revert "add admiral src to test codespaces"

This reverts commit 4a60be0d83e5bd9503eb74610160ece31ef86b7e.

* Propagate renv.lock from pharmaverse/admiralci (#2058)

renv / codespaces update from pharmaverse/admiralci

Co-authored-by: galachad <[email protected]>

* Closes #2020 chore: rename wt to weight in compute_egfr (#2045)

* code updated

* Chore #2020 go through checklist

* update .lycheeignore

* update .lycheeignore

* adjusted templates

* chore: removed links from .lycheeignore

* chore: #2020 removing file

---------

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

* Closes #2053 Typo in the example `impute_dtc_dt` (#2056)

Closes #2053 Typo in the example impute_dtc_dt

    * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R

    * update derive_date_vars.Rd

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

* Closes #2038 Attach See also to compute functions (#2062)

Doc: #2038 Attach See also to compute functions

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

* feat: #2034 show how this can standardize our sub-descriptions

* feat: #2034 this does seem to be a better usecase

* Closes #2042 fix compute_dtf bug (#2047)

* feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly

* feat: #2042 add appropriate logic for date-portions

* chore: #2042 add news

* feat: #2042 address month and day missing

* feat: #2042 allow - for "Y" flag

---------

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

* Closes #1968 compute multiple variables in `derive_param_computed()` (#2036)

* #1968 compute_multiple_vars: update arguments of derive_param_computed()

* #1968 compute_multiple_vars: update documentation

* #1968 compute_multiple_vars: update documentation

* #1968 compute_multiple_vars: style files

* #1968 compute_multiple_vars: fix R-CMD checks

* #1968 compute_multiple_vars: update error message of get_hori_data()

* #1968 compute_multiple_vars: improve documentation

* #1968 compute_multiple_vars: use deprecation badge

* #1968 compute_multiple_vars: use deprecation badge

* Update NEWS.md

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

* #1968 compute_multiple_vars: use @keywords internal

* #1968 compute_multiple_vars: fix typo in NEWS.md

---------

Co-authored-by: Daniel Sjoberg <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

* feat: #2034 looks like we can bundle the label into the code chunk too

* Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055)

* feat: #2054 remove print.duplciates()

* feat: #1466 add appropriate test for print.duplicates

* chore: #1466 cleanup duplicate code

* feat: #1466 use expect_snapshot() instead

---------

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

* Closes #2040 Update admiral.test to pharmaversesdtm (#2057)

* Chore: #2040 Update admiral.test to pharmaversesdtm

* Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler

* #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml

* Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg.

* Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R

* Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R

* Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data

---------

Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* chore: #2034 show the degree of variation

* Propagate renv.lock from pharmaverse/admiralci (#2064)

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <[email protected]>

* #2027 clarify reference_date in derive_vars_dy() (#2063)

* change description

* updated news.md

* closes #2069 bug: EOSSTT derivation fix (#2073)

#2069 bug: EOSSTT derivation fix

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

* Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076)

* utils_impute fns now internal

* Update NEWS.md

* adding meta.R entry back

* Closes #1875 duration and interval time difference types update (#2075)

* in progress

* updated default to duration instead of interval

* style

* spelling updates

* Update NEWS.md

* added pharmaversesdtm Remotes call

* Update DESCRIPTION

* Update test-compute_duration.R

---------

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

* feat: #2034 apply function to all dataset params

* chore: #2034 align assertion with description

* chore: #2034 fix derive_locf_records

* run lintr

* chore: #2034 nolint doesn't work in roxygen

* Closes #2078 swap out admiral_eg with eg (#2080)

feat: #2078 swap out admiral_eg with eg

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

* Closes #1960 enhance derive_extreme_event() (#2015)

* #1960 enhance_derive_extreme_event: start a draft

* #1960 enhance_derive_extreme_event: continue draft

* #1960 enhance_derive_extreme_event: continue draft

* #1960 enhance_derive_extreme_event: add tests and documentation

* #1960 enhance_derive_extreme_event: update NEWS

* #1960 enhance_derive_extreme_event: fix links

* #1960 enhance_derive_extreme_event: style files

* #1960 enhance_derive_extreme_event: add example

* #1960 enhance_derive_extreme_event: style files

* #1960 enhance_derive_extreme_event:add example and tests for event-specific modes

* #1960 enhance_derive_extreme_event: add ignore_event_order argument

* #1960 enhance_derive_extreme_event: fix spelling

* #1960 enhance_derive_extreme_event: use correct input dataset

* #1960 enhance_derive_extreme_event: improve printing of event objects

* #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars

* #1960 enhance_derive_extreme_event: add description field

* #1960 enhance_derive_extreme_event: address QC comments

* #1960 enhance_derive_extreme_event: update man pages

* #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml

* #1960 enhance_derive_extreme_event: style files

* chore: #1960 properly formatted testthat

* chore: #1960 fix lint

---------

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

* Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079)

* Closes #2068 Updated `traceability_vars` to `set_values_to`

* Clarify the explanation for the traceability_vars replacement

* Closes #2083 bug adpp and adpc still using admiraltest (#2086)

* fix: #2083 using pharmaversesdtm

* fix: #2083 using pharmaversesdtm

* chore: #2083 renaming datasets

* chore: #2083 removing admiral prefix

* chore: #2083 removing admiral suffix

* chore: #2083 remove admiral suffix

* chore: remove admiral prefix

* Closes #1859 metadata updated for DAIDs in xlsx file (#2060)

* 1859 metadata updated for DAIDs in xlsx file

* 1859 metadata for DAIDs finalised

* 1859 update data.r for atoxgr_criteria_daids

* 1859 update man files

* 1859 fix spelling

* 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests

* 1859 update man pages

* 1859 fix STYLER issue

* 1859 fix SPELLING

* 1859 fix LINTR

* 1859 Fix LINTR and add more unit tests

* 1859 added Acidosis and Alkalosis and more unit tests

* 1859 added more tests and partiallyy update gradin vignette

* 1859 all unit tests added

* 1859 fix STYLER

* 1859 use signif function in metadata

* 1859 use signif function in ncictcaev4 and v5 metadata

* Update unit test for Cal (Ionized) to test missing ANRHI

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

* Fix unit test for Cal (Ionized) Low for missing ANRLO.

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

* Add units to description of Glucose Nonfasting, High

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

* Add unit to description of Glucose fasting, High

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

* Fix typo in description of Triglycerides, Fasting, High for Grade 3

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

* 1859 address last QC comments on unit tests

* 1859 update NEWS file

* 1859 updated Vignette

* 1859 Fix SPELLING

* Update NEWS.md following QC comment

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

* Update NEWS.md following QC comment

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

* 1859 address QC comments

* Update vignettes/lab_grading.Rmd

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

* Update vignettes/lab_grading.Rmd

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

* Update vignettes/lab_grading.Rmd

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

* 1859 Fix STYLER issue

* 1859 Fix example in function header

* 1859 fix LINTR issue

---------

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

* Closes #2050 Remove print fns from pkgdown Reference page (#2087)

ref page updates

* Closes #1697 add keep_source_vars arg@devel (#2070)

* #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md.

* Updated pkgdown.yml

* Undoing renv.lock update

* #1697 Updated default from `NULL` to `exprs(everything())`

* #1697 Updated wordlist to include 'tidyselect'

* #1697 Moved `select()` after `process_set_values_to()`

* #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()`

* Update NEWS.md

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

* Update NEWS.md

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

* Update R/derive_extreme_records.R

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

* #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()`

* #1697 Updated 'Details' section to include `keep_source_vars`

---------

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

* missing reroute to get started page

* #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082)

* #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation.

* #1995 Chore: roxygen

* #1995 chore:spellcheck and roxygen

* #1995 updates to readme with release schedule and 1.0.

* grammar fix in readme

---------

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

* Closes #2028 removed erroneous section. updating rules section (#2088)

* docs: #2028 removed erroneous section. updating rules section

* docs: #2028 news and wordsmithing

* Update vignettes/imputation.Rmd

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

* Update vignettes/imputation.Rmd

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

* docs: #2028 lite explanation of h.i. rule

---------

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

* Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092)

* feat: #2091 did that work?

* chore: #2091 address errors

* fixed deprecation warning

* deprecation for analysis_var

---------

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

* Fix for Get Started on Webpage (#2093)

Update _pkgdown.yml

* update readme with admiral release schedule (#2095)

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

* feat: #2034 add testthat file

* chore: #2034 styler

* Update devel (#2133)

* admiral v0.12.0 (#2094)

* Closes #1950 following deprecation process, update Description version and news.md

* updating documentation to fix the warnings

* added the new tests for minutes and seconds options

* Removing references in deprecated functions.

* updated comments and applied test_that format

* conflicts resolved

* Closes #1941 authors contributors@devel (#1967)

* Initial edit to `_pkgdown.yml` for #1941

* #1941 re-labelling authors and contributors

* #1941 update to enact decision of team regarding who are authors and contributors.

* #1941: Chore (spellcheck and man pages and NEWS.md update)

* #1941 chore: further updates to spellcheck

* #1941: chore: fix space after commas. move some acknowledgees to contributors. link README in authors page.

* #1941 chore: roxygenize

---------

Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]>

* Closes #1228 produce bmi records for more visits (#1957)

* feat: #1228 Produce BMI records for more visits: Add constant_height parameter

* feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail.

* docs: #1228 Produce BMI records for more visits: Fix typo in NEWS

* feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette.

* doc: #1228 Produce BMI records for more visits: Add backticks to variable.

---------

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

* Closes #1695 Establish codeowners (#1973)

feat: #1695 add gordon and jeff as codeowners

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

* Closes #1974 Swapping out deprecated assertions (#1975)

* feat: #1974 try swapping all deprecated assertions

* chore: #1974 fix parsing issue that caused vignettes to crash

* chore: #1974 simplify by_vars requirement

Co-authored-by: Kangjie Zhang <[email protected]>

* chore: #264 move assertion to different line

---------

Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Kangjie Zhang <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* Propagate renv.lock from pharmaverse/admiralci (#1986)

renv update from pharmaverse/admiralci

Co-authored-by: dgrassellyb <[email protected]>

* Catch devel up to Admiral v0.11.1 (#1997) (#1999)

Admiral v0.11.1 (#1997)

* [actions skip] Add/Update README.md for patch

* Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987)

* feat #1962 #1969 param_tte and get started fix

* forgot to add updated DESCRIPTION

* chore: #1962 thought crossing was dplyr

* chore: #1962 account for new assertions

* fix: #1962 was missing the reassignment piece?

* fix: #1966 crude answer

* feat: #1966 potential way of warning users of null new_vars

* fix: #1966 add appropriate assertions to get check to go through

* fix: #1966 appropriate function fix for order

* fix: #1966 vignette named order expression

* chore: #1966 try something

* chore: #1966 optionality of expressions is tricky

* feat: #1966 undo derive_joined stuff

* chore: run styler

---------



---------

Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

* Initiate a Stale bot for Issue Triaging (#1992)

* Create stale_bot.yml

* Update and rename stale_bot.yml to stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Update stale-bot.yml

* Closes #1927 derive param tte@devel (#2000)

Removed incorrect reference of start_imputation_flag

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

* Closes #1989 Link Fix in `README.md` (#1994)

* Update README.md

* Update WORDLIST

* Update README.md

* Update WORDLIST

* chore: #1989 spelling

---------

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

* Closes #1856 Removed the higher order file (#2008)

#1856 Removed the higher order file

* Update templates.yml (#2026)

* Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009)

* #2001 added processing for missing age_units in `compute_age_years`

* #2001 Chore: styler

* #2001 chore: lint

* #2001 chore: fix broken links

* #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`.

* #2001 chore: Fixed docs link

* #2001 chore: styler

* #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit`

* #2001 Update NEWS.md as per suggestiom

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

* Update R/compute_age_years.R with correct backquoting

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

* #2001 version change in deprecation

* #2001 insert parenthesis in NEWS.md

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

* #2001 chore: roxygen

---------

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

* Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024)

* feat: #1979 added the necessary flag_all function argument

* feat: #1979 modify check_type to supppress warnings for flag_all = TRUE

* chore: #1979 run lintr/styler

* chore: #1979 add news blurb

* typo

* chore: #1979 add additional tests and add roxygen details

* chore: #1979 adopt feedback from review

* chore: #1979 run styler

---------

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

* Closes #123 Add Edoardo to status check (#2031)

fix: https://github.com/pharmaverse/admiralci/issues/123 add Edoardo to status check

* Closes #2014 derive_var_shift change na_val@devel (#2032)

* #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`.

* #2014 - Update `NEWS.md`.

* #2014 - update tests and write deprecation parameter test

* #2014 - run required tasks for PR

---------

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

* Closes #2012_derive_vars_dy (#2013)

* derive dy_vars by argument .name in across (#2012)

use named vector to avoid the variabes end with `_temp` in input dataset

* test no error for variable end with `_temp`(#2012)

* styled file

* add update information for #2012

---------

Co-authored-by: Daniel Sjoberg <[email protected]>

* Closes #1966 address derive_vars_joined bugs (#2016)

* feat: #1966 make our check_type consistent

* feat: #1966 hacky solution to null new_vars .join problem

* chore: #1966 inserted line in wrong place

* feat: #1966 add news blurb for what was done

* feat: #1966 add tests

* chore: #1966 lintr

* chore: #1966 swap appropriate order selection and restore check_type arg

* chore: #1966 looks like that fixed it

* feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL

* chore: #1966 clean up for readability

* chore: #1966 restore original replace_values_by_names

* chore: #1966 add additional test to demonstrate how order vars were fixed/selected

* feat: #1966 adopt feedback for error messaging of naming conflicts

---------

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

* Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039)

feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref`

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

* Close #1940 Removing unnecessary runtime development-related dependencies (#1978)

* feat: #1940 try removing dev deps

* chore: #1940 still needs knitr

* #1940 diffdf needed for all the testing stuff

* chore: #1940 add back rmarkdown

Co-authored-by: Adam Foryś <[email protected]>

---------

Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>

* Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029)

* #1984 allowing missing trt end date

* Update derive_var_ontrtfl.R

* Update derive_var_ontrtfl.R

* Increment version number to 0.12.0.9000

* updating version numbers...oops!

* Update test-derive_var_ontrtfl.R

* Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048)

addressing missing treatment start dates

* Propagate renv.lock from pharmaverse/admiralci (#2046)

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

* Update .Rbuildignore

* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>

* Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044)

* span_period arg update

* Update derive_var_ontrtfl.R

* Update NEWS.md

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

* Update R/derive_var_ontrtfl.R

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

* Update R/derive_var_ontrtfl.R

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

* remove space for lintr

---------

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

* add admiral src to test codespaces

* Revert "add admiral src to test codespaces"

This reverts commit 4a60be0d83e5bd9503eb74610160ece31ef86b7e.

* Propagate renv.lock from pharmaverse/admiralci (#2058)

renv / codespaces update from pharmaverse/admiralci

Co-authored-by: galachad <[email protected]>

* Closes #2020 chore: rename wt to weight in compute_egfr (#2045)

* code updated

* Chore #2020 go through checklist

* update .lycheeignore

* update .lycheeignore

* adjusted templates

* chore: removed links from .lycheeignore

* chore: #2020 removing file

---------

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

* Closes #2053 Typo in the example `impute_dtc_dt` (#2056)

Closes #2053 Typo in the example impute_dtc_dt

    * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R

    * update derive_date_vars.Rd

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

* Closes #2038 Attach See also to compute functions (#2062)

Doc: #2038 Attach See also to compute functions

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

* Closes #2042 fix compute_dtf bug (#2047)

* feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly

* feat: #2042 add appropriate logic for date-portions

* chore: #2042 add news

* feat: #2042 address month and day missing

* feat: #2042 allow - for "Y" flag

---------

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

* Closes #1968 compute multiple variables in `derive_param_computed()` (#2036)

* #1968 compute_multiple_vars: update arguments of derive_param_computed()

* #1968 compute_multiple_vars: update documentation

* #1968 compute_multiple_vars: update documentation

* #1968 compute_multiple_vars: style files

* #1968 compute_multiple_vars: fix R-CMD checks

* #1968 compute_multiple_vars: update error message of get_hori_data()

* #1968 compute_multiple_vars: improve documentation

* #1968 compute_multiple_vars: use deprecation badge

* #1968 compute_multiple_vars: use deprecation badge

* Update NEWS.md

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

* #1968 compute_multiple_vars: use @keywords internal

* #1968 compute_multiple_vars: fix typo in NEWS.md

---------

Co-authored-by: Daniel Sjoberg <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

* Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055)

* feat: #2054 remove print.duplciates()

* feat: #1466 add appropriate test for print.duplicates

* chore: #1466 cleanup duplicate code

* feat: #1466 use expect_snapshot() instead

---------

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

* Closes #2040 Update admiral.test to pharmaversesdtm (#2057)

* Chore: #2040 Update admiral.test to pharmaversesdtm

* Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler

* #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml

* Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg.

* Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R

* Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R

* Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data

---------

Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* Propagate renv.lock from pharmaverse/admiralci (#2064)

* renv / codespaces update from pharmaverse/admiralci

* renv / codespaces update from pharmaverse/admiralci

---------

Co-authored-by: galachad <[email protected]>

* #2027 clarify reference_date in derive_vars_dy() (#2063)

* change description

* updated news.md

* closes #2069 bug: EOSSTT derivation fix (#2073)

#2069 bug: EOSSTT derivation fix

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

* Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076)

* utils_impute fns now internal

* Update NEWS.md

* adding meta.R entry back

* Closes #1875 duration and interval time difference types update (#2075)

* in progress

* updated default to duration instead of interval

* style

* spelling updates

* Update NEWS.md

* added pharmaversesdtm Remotes call

* Update DESCRIPTION

* Update test-compute_duration.R

---------

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

* Closes #2078 swap out admiral_eg with eg (#2080)

feat: #2078 swap out admiral_eg with eg

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

* Closes #1960 enhance derive_extreme_event() (#2015)

* #1960 enhance_derive_extreme_event: start a draft

* #1960 enhance_derive_extreme_event: continue draft

* #1960 enhance_derive_extreme_event: continue draft

* #1960 enhance_derive_extreme_event: add tests and documentation

* #1960 enhance_derive_extreme_event: update NEWS

* #1960 enhance_derive_extreme_event: fix links

* #1960 enhance_derive_extreme_event: style files

* #1960 enhance_derive_extreme_event: add example

* #1960 enhance_derive_extreme_event: style files

* #1960 enhance_derive_extreme_event:add example and tests for event-specific modes

* #1960 enhance_derive_extreme_event: add ignore_event_order argument

* #1960 enhance_derive_extreme_event: fix spelling

* #1960 enhance_derive_extreme_event: use correct input dataset

* #1960 enhance_derive_extreme_event: improve printing of event objects

* #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars

* #1960 enhance_derive_extreme_event: add description field

* #1960 enhance_derive_extreme_event: address QC comments

* #1960 enhance_derive_extreme_event: update man pages

* #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml

* #1960 enhance_derive_extreme_event: style files

* chore: #1960 properly formatted testthat

* chore: #1960 fix lint

---------

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

* Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079)

* Closes #2068 Updated `traceability_vars` to `set_values_to`

* Clarify the explanation for the traceability_vars replacement

* Closes #2083 bug adpp and adpc still using admiraltest (#2086)

* fix: #2083 using pharmaversesdtm

* fix: #2083 using pharmaversesdtm

* chore: #2083 renaming datasets

* chore: #2083 removing admiral prefix

* chore: #2083 removing admiral suffix

* chore: #2083 remove admiral suffix

* chore: remove admiral prefix

* Closes #1859 metadata updated for DAIDs in xlsx file (#2060)

* 1859 metadata updated for DAIDs in xlsx file

* 1859 metadata for DAIDs finalised

* 1859 update data.r for atoxgr_criteria_daids

* 1859 update man files

* 1859 fix spelling

* 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests

* 1859 update man pages

* 1859 fix STYLER issue

* 1859 fix SPELLING

* 1859 fix LINTR

* 1859 Fix LINTR and add more unit tests

* 1859 added Acidosis and Alkalosis and more unit tests

* 1859 added more tests and partiallyy update gradin vignette

* 1859 all unit tests added

* 1859 fix STYLER

* 1859 use signif function in metadata

* 1859 use signif function in ncictcaev4 and v5 metadata

* Update unit test for Cal (Ionized) to test missing ANRHI

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

* Fix unit test for Cal (Ionized) Low for missing ANRLO.

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

* Add units to description of Glucose Nonfasting, High

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

* Add unit to description of Glucose fasting, High

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

* Fix typo in description of Triglycerides, Fasting, High for Grade 3

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

* 1859 address last QC comments on unit tests

* 1859 update NEWS file

* 1859 updated Vignette

* 1859 Fix SPELLING

* Update NEWS.md following QC comment

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

* Update NEWS.md following QC comment

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

* 1859 address QC comments

* Update vignettes/lab_grading.Rmd

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

* Update vignettes/lab_grading.Rmd

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

* Update vignettes/lab_grading.Rmd

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

* 1859 Fix STYLER issue

* 1859 Fix example in function header

* 1859 fix LINTR issue

---------

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

* Closes #2050 Remove print fns from pkgdown Reference page (#2087)

ref page updates

* Closes #1697 add keep_source_vars arg@devel (#2070)

* #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md.

* Updated pkgdown.yml

* Undoing renv.lock update

* #1697 Updated default from `NULL` to `exprs(everything())`

* #1697 Updated wordlist to include 'tidyselect'

* #1697 Moved `select()` after `process_set_values_to()`

* #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()`

* Update NEWS.md

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

* Update NEWS.md

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

* Update R/derive_extreme_records.R

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

* #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()`

* #1697 Updated 'Details' section to include `keep_source_vars`

---------

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

* #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082)

* #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation.

* #1995 Chore: roxygen

* #1995 chore:spellcheck and roxygen

* #1995 updates to readme with release schedule and 1.0.

* grammar fix in readme

---------

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

* Closes #2028 removed erroneous section. updating rules section (#2088)

* docs: #2028 removed erroneous section. updating rules section

* docs: #2028 news and wordsmithing

* Update vignettes/imputation.Rmd

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

* Update vignettes/imputation.Rmd

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

* docs: #2028 lite explanation of h.i. rule

---------

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

* Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092)

* feat: #2091 did that work?

* chore: #2091 address errors

* fixed deprecation warning

* deprecation for analysis_var

---------

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

* Fix for Get Started on Webpage (#2093)

Update _pkgdown.yml

* update readme with admiral release schedule (#2095)

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

---------

Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: sadchla-codes <[email protected]>
Co-authored-by: Sadchla Mascary <[email protected]>
Co-authored-by: lomaxj1 <[email protected]>
Co-authored-by: Jennifer Lomax <[email protected]>
Co-authored-by: Edoardo Mancini <[email protected]>
Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]>
Co-authored-by: Jeff Dickinson <[email protected]>
Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: cicdguy <[email protected]>
Co-authored-by: Kangjie Zhang <[email protected]>
Co-authored-by: pharmaverse-bot <[email protected]>
Co-authored-by: dgrassellyb <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: SyedMubasheer <[email protected]>
Co-authored-by: Daniel Sjoberg <[email protected]>
Co-authored-by: asha-gsk <[email protected]>
Co-authored-by: Sophie Shapcott <[email protected]>
Co-authored-by: ynsec37 <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>
Co-authored-by: galachad <[email protected]>
Co-authored-by: Daphne Grasselly <[email protected]>
Co-authored-by: StefanThoma <[email protected]>
Co-authored-by: Stefan Bundfuss <[email protected]>
Co-authored-by: Ross Farrugia <[email protected]>
Co-authored-by: Gordon Miller <[email protected]>
Co-authored-by: G Gayatri <[email protected]>

* ignore notes r cmd checks (#2114)

* admiral v0.12.1 (#2122)

* Closes #2113 fix derive extreme records (#2121)

* #2113 fix_derive_extreme_records: update function and tests

* #2113 fix_derive_extreme_records: style files

* [actions skip] Add/Update README.md for patch

* Closes #2109 ADPP template program has x and y variables (#2110)

* #2109 ADPP template program has x and y variables: Update to use `derive_vars_merged()`

* #2109 Doc: update NEWS for ADPP template change

* ignore notes r cmd checks (#2114)

---------

Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Daphné Grasselly <[email protected]>
Co-authored-by: Ben Straub <[email protected]>

* Closes #2112 add `type` to functions downstream of compute_duration() (#2118)

* feat: #2112 add type to fxns downstream of compute_duration

* feat: #2112 add test type argument for derive_vars_duration

* styler and lintr

* chore: #2112 adopt feedback

* chore: #2112 add upversion on DESCRIPTION

* chore: #2112 try inheritParams

* chore: #2112 remove mention of default

---------

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

* Update README.md typo

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

---------

Co-authored-by: Stefan Bundfuss <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: Jeff Dickinson <[email protected]>
Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Daphné Grasselly <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>

---------

Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: sadchla-codes <[email protected]>
Co-authored-by: Sadchla Mascary <[email protected]>
Co-authored-by: lomaxj1 <[email protected]>
Co-authored-by: Jennifer Lomax <[email protected]>
Co-authored-by: Edoardo Mancini <[email protected]>
Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]>
Co-authored-by: Jeff Dickinson <[email protected]>
Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: cicdguy <[email protected]>
Co-authored-by: Kangjie Zhang <[email protected]>
Co-authored-by: pharmaverse-bot <[email protected]>
Co-authored-by: dgrassellyb <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: SyedMubasheer <[email protected]>
Co-authored-by: Daniel Sjoberg <[email protected]>
Co-authored-by: asha-gsk <[email protected]>
Co-authored-by: Sophie Shapcott <[email protected]>
Co-authored-by: ynsec37 <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>
Co-authored-by: galachad <[email protected]>
Co-authored-by: Daphne Grasselly <[email protected]>
Co-authored-by: StefanThoma <[email protected]>
Co-authored-by: Ross Farrugia <[email protected]>
Co-authored-by: Gordon Miller <[email protected]>
Co-authored-by: G Gayatri <[email protected]>
Co-authored-by: Daphné Grasselly <[email protected]>

* remove merge conflict nonsense

* forgot test suite

* bad styling job from copy/paste

* feat: #2034 add back new blurb for what occured

---------

Co-authored-by: sadchla-codes <[email protected]>
Co-authored-by: Sadchla Mascary <[email protected]>
Co-authored-by: lomaxj1 <[email protected]>
Co-authored-by: Jennifer Lomax <[email protected]>
Co-authored-by: Ben Straub <[email protected]>
Co-authored-by: Edoardo Mancini <[email protected]>
Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]>
Co-authored-by: Jeff Dickinson <[email protected]>
Co-authored-by: Jeffrey Dickinson <[email protected]>
Co-authored-by: Zelos Zhu <[email protected]>
Co-authored-by: cicdguy <[email protected]>
Co-authored-by: Kangjie Zhang <[email protected]>
Co-authored-by: pharmaverse-bot <[email protected]>
Co-authored-by: dgrassellyb <[email protected]>
Co-authored-by: GitHub Actions <[email protected]>
Co-authored-by: SyedMubasheer <[email protected]>
Co-authored-by: Daniel Sjoberg <[email protected]>
Co-authored-by: asha-gsk <[email protected]>
Co-authored-by: Sophie Shapcott <[email protected]>
Co-authored-by: ynsec37 <[email protected]>
Co-authored-by: Adam Foryś <[email protected]>
Co-authored-by: galachad <[email protected]>
Co-authored-by: Daphne Grasselly <[email protected]>
Co-authored-by: StefanThoma <[email protected]>
Co-authored-by: Stefan Bundfuss <[email protected]>
Co-authored-by: Ross Farrugia <[email protected]>
Co-authored-by: Gordon Miller <[email protected]>
Co-authored-by: G Gayatri <[email protected]>
Co-authored-by: Daphné Grasselly <[email protected]>

NEWS.md

@@ -30,6 +30,8 @@
 
 ## Documentation
 
+- A way to standardize roxygen labels and descriptions for function arguments was implemented and tested (#2034)
+
 ## Various
 
 # admiral 0.12.2

R/call_derivation.R

@@ -3,7 +3,7 @@
 #' Call a single derivation multiple times with some parameters/arguments being fixed across
 #' iterations and others varying.
 #'
-#' @param dataset The input dataset
+#' @param dataset  `r roxygen_param_dataset()`
 #' @param derivation The derivation function to call
 #'
 #'   A function that performs a specific derivation is expected. A derivation

R/create_single_dose_dataset.R

@@ -185,10 +185,8 @@ dose_freq_lookup <- tribble(
 #' necessary when e.g. calculating last dose before an adverse event in `ADAE`
 #' or deriving a total dose parameter in `ADEX` when `EXDOSFRQ != ONCE`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by `dose_freq`, `start_date` and the `end_date`
-#'   parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dose_freq", "start_date", "end_date"))`
 #'
 #' @param dose_freq The dose frequency
 #'

R/derive_adeg_params.R

@@ -6,10 +6,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` and the `unit_var` parameter,
-#'   `PARAMCD`, and `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars", "get_unit_expr"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -257,10 +256,9 @@ compute_qtc <- function(qt, rr, method) {
 #' The analysis value of the new parameter is derived as
 #' \deqn{\frac{60000}{HR}}{60000 / HR}
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and `AVAL`
-#'   are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_advs_params.R

@@ -5,10 +5,9 @@
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -226,10 +225,9 @@ compute_map <- function(diabp, sysbp, hr = NULL) {
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -549,10 +547,9 @@ compute_bsa <- function(height = height,
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_param_computed()`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_basetype_records.R

@@ -12,9 +12,8 @@
 #' Adds the `BASETYPE` variable to a dataset and duplicates records based upon
 #' the provided conditions.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified in the expressions inside `basetypes` are required.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("basetypes"))`
 #'
 #' @param basetypes A *named* list of expressions created using the
 #' `rlang::exprs()` function

R/derive_date_vars.R

@@ -1252,9 +1252,8 @@ compute_tmf <- function(dtc,
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset.
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'
@@ -1461,9 +1460,8 @@ derive_vars_dt <- function(dataset, # nolint: cyclocomp_linter
 #' impute, we only enable to impute up to a highest level, i.e. you couldn't
 #' choose to say impute months, but not days.
 #'
-#' @param dataset Input dataset
-#'
-#'   The date character vector (`dtc`) must be present.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dtc"))`
 #'
 #' @param new_vars_prefix Prefix used for the output variable(s).
 #'

R/derive_expected_records.R

@@ -3,10 +3,8 @@
 #' Add expected records as new observations for each 'by group' when the dataset
 #' contains missing observations.
 #'
-#' @param dataset Input dataset
-#'
-#'   A data frame, the columns from `dataset_ref` and specified by the
-#'   `by_vars` parameter are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("dataset_ref", "by_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'

R/derive_extreme_records.R

@@ -7,7 +7,7 @@
 #' distinguishes `derive_extreme_records()` from `derive_summary_records()`,
 #' where only the by variables are populated for the new records.
 #'
-#' @param dataset Input dataset
+#' @param dataset `r roxygen_param_dataset()`
 #'
 #'   If `dataset_add` is not specified, the new records are selected from the
 #'   input dataset. In this case the variables specified by `by_vars` and
@@ -92,6 +92,14 @@
 #'   automatically.
 #'
 #'
+#' @param keep_source_vars Variables to be kept in the new records
+#'
+#'   A named list or tidyselect expressions created by `exprs()` defining the
+#'   variables to be kept for the new records. The variables specified for
+#'   `by_vars` and `set_values_to` need not be specified here as they are kept
+#'   automatically.
+#'
+#'
 #' @inheritParams filter_extreme
 #' @inheritParams derive_summary_records
 #'

R/derive_joined.R

@@ -6,9 +6,8 @@
 #' variables from both datasets. For example, add the lowest value (nadir)
 #' before the current observation.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by `by_vars` are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'

R/derive_locf_records.R

@@ -3,10 +3,8 @@
 #' Adds LOCF records as new observations for each 'by group' when the dataset
 #' does not contain observations for missed visits/time points.
 #'
-#' @param dataset Input dataset
-#'
-#'   The columns specified by the `by_vars`, `analysis_var`, `order`,
-#'   `keep_vars` parameters are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var", "order", "keep_vars"))`
 #'
 #' @param dataset_expected_obs *Deprecated*, please use `dataset_ref` instead.
 #'

R/derive_merged.R

@@ -6,9 +6,8 @@
 #' (`filter_add` argument) and/or selecting the first or last observation for
 #' each by group (`order` and `mode` argument).
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'
@@ -710,9 +709,8 @@ get_not_mapped <- function() {
 #'
 #' **Note:** This is a wrapper function for the more generic `derive_vars_merged`.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param dataset_add Additional dataset
 #'

R/derive_param_computed.R

@@ -7,9 +7,9 @@
 #' blood pressure (DIABP) with the formula
 #' \deqn{MAP = \frac{SYSBP + 2 DIABP}{3}}{MAP = (SYSBP + 2 DIABP) / 3}
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter are expected.
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'  `PARAMCD` is expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`
@@ -428,7 +428,8 @@ assert_parameters_argument <- function(parameters, optional = TRUE) {
 #' The function creates temporary parameters and variables of the form
 #' `<variable>.<parameter>`, e.g., `AVAL.WEIGHT`.
 #'
-#' @param dataset Input dataset
+#' @param dataset
+#' `r roxygen_param_dataset(expected_vars = c("by_vars"))`
 #'
 #' @param by_vars By variables
 #'

R/derive_param_doseint.R

@@ -8,10 +8,9 @@
 #' The analysis value of the new parameter is derived as
 #' Total Dose / Planned Dose * 100
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_param_exist_flag.R

@@ -5,10 +5,9 @@
 #' function can derive a parameter indicating if there is measurable disease at
 #' baseline.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified for `by_vars` and the `PARAMCD` variable are
-#'   expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD` is expected as well.
 #'
 #' @param dataset_ref Reference dataset, e.g., ADSL
 #'

R/derive_param_exposure.R

@@ -3,10 +3,9 @@
 #' Add a record computed from the aggregated analysis value of another parameter and compute the
 #' start (`ASTDT(M)`)and end date (`AENDT(M)`) as the minimum and maximum date by `by_vars`.
 #'
-#' @param dataset Input dataset
-#'
-#'   + The variables specified by the `by_vars`,`analysis_var` parameters and `PARAMCD` are
-#'   expected,
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var"))`
+#'   `PARAMCD` is expected as well,
 #'   + Either `ASTDTM` and `AENDTM` or `ASTDT` and `AENDT` are also expected.
 #'
 #' @param filter Filter condition

R/derive_param_extreme_record.R

@@ -4,7 +4,7 @@
 #' source datasets, based on user-defined filter, order and by group criteria.
 #' All variables of the selected observation are kept.
 #'
-#' @param dataset Input dataset
+#' @param dataset `r roxygen_param_dataset()`
 #'
 #' @param sources Sources
 #'

R/derive_param_framingham.R

@@ -4,10 +4,9 @@
 #' Adds a record for framingham score (FCVD101) for each by group
 #' (e.g., subject and visit) where the source parameters are available.
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` parameter, `PARAMCD`, and
-#'   `AVAL` are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset after restricting it by the filter condition (`filter`

R/derive_param_tte.R

@@ -2,9 +2,8 @@
 #'
 #' Add a time-to-event parameter to the input dataset.
 #'
-#' @param dataset Input dataset
-#'
-#'   The `PARAMCD` variable is expected.
+#' @param dataset `r roxygen_param_dataset()`
+#'   `PARAMCD` is expected.
 #'
 #' @param dataset_adsl ADSL input dataset
 #'

R/derive_param_wbc_abs.R

@@ -4,10 +4,9 @@
 #'
 #' Add a parameter by converting lab differentials from fraction or percentage to absolute values
 #'
-#' @param dataset Input dataset
-#'
-#'   The variables specified by the `by_vars` argument, `PARAMCD`, and `AVAL`
-#'   are expected to be present.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("by_vars"))`
+#'   `PARAMCD`, and `AVAL` are expected as well.
 #'
 #'   The variable specified by `by_vars` and `PARAMCD` must be a unique key of
 #'   the input dataset, and to the parameters specified by `wbc_code` and `diff_code`.

R/derive_summary_records.R

@@ -11,7 +11,7 @@
 #' retain those common values in the newly derived records. Otherwise new value
 #' will be set to `NA`.
 #'
-#' @param dataset A data frame.
+#' @param dataset  `r roxygen_param_dataset(expected_vars = c("by_vars", "analysis_var"))`
 #'
 #' @param by_vars Variables to consider for generation of groupwise summary
 #'   records. Providing the names of variables in [exprs()] will create a

R/derive_var_analysis_ratio.R

@@ -2,7 +2,8 @@
 #'
 #' Derives a ratio variable for a BDS dataset based on user specified variables.
 #'
-#' @param dataset Input dataset
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("numer_var", "denom_var"))`
 #'
 #' @param numer_var Variable containing numeric values to be used in the numerator of
 #'  the ratio calculation.

R/derive_var_anrind.R

@@ -1,6 +1,10 @@
 #' Derive Reference Range Indicator
 #'
-#' @param dataset The input dataset
+#' @param dataset
+#'   `r roxygen_param_dataset()`
+#'   `ANRLO`, `ANRHI`, and `AVAL` are expected and if `use_a1hia1lo` is set to `TRUE`,
+#'   `A1LO` and `A1H1` are expected as well.
+#'
 #' @param use_a1hia1lo A logical value indicating whether to use `A1H1` and `A1LO` in
 #' the derivation of `ANRIND`.
 #'

R/derive_var_atoxgr.R

@@ -3,9 +3,8 @@
 #' @description
 #' Derives a character lab grade based on severity/toxicity criteria.
 #'
-#' @param dataset Input data set
-#'
-#'   The columns specified by `tox_description_var` parameter is expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("tox_description_var"))`
 #'
 #' @param new_var Name of the character grade variable to create, for example, `ATOXGRH`
 #' or `ATOXGRL`.
@@ -246,10 +245,9 @@ derive_var_atoxgr_dir <- function(dataset,
 #'
 #' Derives character lab grade based on high and low severity/toxicity grade(s).
 #'
-#' @param dataset Input data set
-#'
-#'   The columns `ATOXGRL`, `ATOXGRH` and specified by `lotox_description_var`,
-#'   and `hitox_description_var` parameters are expected.
+#' @param dataset
+#'   `r roxygen_param_dataset(expected_vars = c("lotox_description_var", "hitox_description_var"))`
+#'   `ATOXGRL`, and `ATOXGRH` are expected as well.
 #'
 #' @param lotox_description_var Variable containing the toxicity grade description
 #' for low values, eg. "Anemia"