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* 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: pharmaverse/admiralci#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 4a60be0.

* 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]>
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2 changes: 2 additions & 0 deletions .github/workflows/common.yml
Original file line number Diff line number Diff line change
Expand Up @@ -65,6 +65,8 @@ jobs:
check:
name: Check
uses: pharmaverse/admiralci/.github/workflows/r-cmd-check.yml@main
with:
error-on: warning # TODO: find a way to ignore specific notes
if: github.event_name == 'pull_request'
docs:
name: Documentation
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2 changes: 1 addition & 1 deletion DESCRIPTION
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
Package: admiral
Type: Package
Title: ADaM in R Asset Library
Version: 0.12.0
Version: 0.12.1
Authors@R: c(
person("Ben", "Straub", email = "[email protected]", role = c("aut", "cre")),
person("Stefan", "Bundfuss", role = "aut"),
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8 changes: 8 additions & 0 deletions NEWS.md
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@@ -1,3 +1,11 @@
# admiral 0.12.1

- `derive_extreme_records()` no longer fails if `dataset_add` is specified and a
variable specified for `order` is not in `dataset`. (#2113)

- The `type` argument in `compute_duration()` changed the underlying default behavior in `derive_vars_duration()` without allowing the user to toggle between `"duration"` and `"interval"` as originally intended. This was fixed by adding the `type` argument for `derive_vars_duration()` and a wrapper function `derive_vars_aage()` such that it gets passed through `compute_duration()` appropriately (#2112)

- Template `ad_adpp.R` updated to replace `left_join()` with `derive_vars_merged()` (#2109).

# admiral 0.12.0

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20 changes: 17 additions & 3 deletions R/derive_extreme_records.R
Original file line number Diff line number Diff line change
Expand Up @@ -284,11 +284,25 @@ derive_extreme_records <- function(dataset = NULL,
assert_expr_list(order, optional = TRUE)
assert_expr_list(keep_source_vars, optional = TRUE)

if (is.null(dataset_add)) {
expected_vars <- expr_c(by_vars, extract_vars(order))
} else {
expected_vars <- by_vars
}

assert_data_frame(
dataset,
required_vars = expr_c(
by_vars, extract_vars(order)
),
required_vars = expected_vars,
optional = TRUE
)
assert_data_frame(
dataset_add,
required_vars = expr_c(by_vars, extract_vars(order)),
optional = TRUE
)
assert_data_frame(
dataset_ref,
required_vars = by_vars,
optional = TRUE
)
mode <- assert_character_scalar(
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34 changes: 27 additions & 7 deletions R/derive_vars_aage.R
Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,8 @@
#'
#' **Note:** This is a wrapper function for the more generic `derive_vars_duration()`.
#'
#' @inheritParams derive_vars_duration
#'
#' @param dataset Input dataset
#'
#' The columns specified by the `start_date` and the `end_date` parameter are
Expand Down Expand Up @@ -37,12 +39,28 @@
#'
#' @param unit *Deprecated*, please use `age_unit` instead.
#'
#' @details The age is derived as the integer part of the duration from start to
#' end date in the specified unit. When 'years' or 'months' are specified in the `out_unit`
#' parameter, because of the underlying `lubridate::time_length()` function that is used
#' here, results are calculated based on the actual calendar length of months or years
#' rather than assuming equal days every month (30.4375 days) or every year (365.25 days).
#' @details The duration is derived as time from start to end date in the
#' specified output unit. If the end date is before the start date, the duration
#' is negative. The start and end date variable must be present in the specified
#' input dataset.
#'
#' The [lubridate](https://lubridate.tidyverse.org/) package calculates two
#' types of spans between two dates: duration and interval.
#' While these calculations are largely the same, when the unit of the time period
#' is month or year the result can be slightly different.
#'
#' The difference arises from the ambiguity in the length of `"1 month"` or
#' `"1 year"`.
#' Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years.
#' Durations and intervals help solve the ambiguity in these measures.
#'
#' The **interval** between `2000-02-01` and `2000-03-01` is `1` (i.e. one month).
#' The **duration** between these two dates is `0.95`, which accounts for the fact
#' that the year 2000 is a leap year, February has 29 days, and the average month
#' length is `30.4375`, i.e. `29 / 30.4375 = 0.95`.
#'
#' For additional details, review the
#' [lubridate time span reference page](https://lubridate.tidyverse.org/reference/timespan.html).
#'
#' @return The input dataset with ``AAGE`` and ``AAGEU`` added
#'
Expand All @@ -67,7 +85,8 @@ derive_vars_aage <- function(dataset,
start_date = BRTHDT,
end_date = RANDDT,
unit = "years",
age_unit = "years") {
age_unit = "years",
type = "interval") {
if (!missing(unit)) {
deprecate_warn("0.12.0", "derive_vars_aage(unit = )", "derive_vars_aage(age_unit = )")
age_unit <- unit
Expand All @@ -89,7 +108,8 @@ derive_vars_aage <- function(dataset,
end_date = !!end_date,
out_unit = age_unit,
add_one = FALSE,
trunc_out = TRUE
trunc_out = TRUE,
type = type
)
}

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30 changes: 28 additions & 2 deletions R/derive_vars_duration.R
Original file line number Diff line number Diff line change
Expand Up @@ -72,11 +72,35 @@
#'
#' Permitted Values: `TRUE`, `FALSE`
#'
#' @param type lubridate duration type.
#'
#' See below for details.
#'
#' Permitted Values: `"duration"`, `"interval"`
#'
#' @details The duration is derived as time from start to end date in the
#' specified output unit. If the end date is before the start date, the duration
#' is negative. The start and end date variable must be present in the specified
#' input dataset.
#'
#' The [lubridate](https://lubridate.tidyverse.org/) package calculates two
#' types of spans between two dates: duration and interval.
#' While these calculations are largely the same, when the unit of the time period
#' is month or year the result can be slightly different.
#'
#' The difference arises from the ambiguity in the length of `"1 month"` or
#' `"1 year"`.
#' Months may have 31, 30, 28, or 29 days, and years are 365 days and 366 during leap years.
#' Durations and intervals help solve the ambiguity in these measures.
#'
#' The **interval** between `2000-02-01` and `2000-03-01` is `1` (i.e. one month).
#' The **duration** between these two dates is `0.95`, which accounts for the fact
#' that the year 2000 is a leap year, February has 29 days, and the average month
#' length is `30.4375`, i.e. `29 / 30.4375 = 0.95`.
#'
#' For additional details, review the
#' [lubridate time span reference page](https://lubridate.tidyverse.org/reference/timespan.html).
#'
#'
#' @return The input dataset with the duration and unit variable added
#'
Expand Down Expand Up @@ -174,7 +198,8 @@ derive_vars_duration <- function(dataset,
out_unit = "days",
floor_in = TRUE,
add_one = TRUE,
trunc_out = FALSE) {
trunc_out = FALSE,
type = "duration") {
new_var <- assert_symbol(enexpr(new_var))
new_var_unit <- assert_symbol(enexpr(new_var_unit), optional = TRUE)
start_date <- assert_symbol(enexpr(start_date))
Expand Down Expand Up @@ -206,7 +231,8 @@ derive_vars_duration <- function(dataset,
out_unit = out_unit,
floor_in = floor_in,
add_one = add_one,
trunc_out = trunc_out
trunc_out = trunc_out,
type = type
)
)

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22 changes: 10 additions & 12 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -33,21 +33,19 @@ remotes::install_github("pharmaverse/admiral")

## Release Schedule

[{admiral}](https://pharmaverse.github.io/admiral/cran-release/)` releases are targeted for the first Monday of the last month of each quarter. Pull Requests will be frozen the week before a release.
[{admiral}](https://pharmaverse.github.io/admiral/cran-release/) releases are targeted for the first Monday of the last month of each quarter. Pull Requests will be frozen the week before a release.
The {admiral} family has several downstream and upstream dependencies and so this release shall be done in three
Phases:

* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/), [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/main/), and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core
* Phase 1 release is for [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/), [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/main/), and [{admiral}](https://pharmaverse.github.io/admiral/cran-release/) core
* Phase 2 release is extension packages, e.g. [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/), [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/), [{admiralvaccine}](https://pharmaverse.github.io/admiralvaccine/main/)


|Release Schedule | Phase 1- Date and Packages | Phase 2- Date and Packages |
|---------------- | -------------------------- | -------------------------- |
| Q4-2023 | December 4th | December 11th |
| | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/main/) | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/) |
| | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/) | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/) |
| | [{admiral}](https://pharmaverse.github.io/admiral/main/) | |

| Release Schedule | Phase 1- Date and Packages | Phase 2- Date and Packages |
| ---------------- | ------------------------------------------------------------------------ | -------------------------------------------------------------------- |
| Q4-2023 | December 4th | December 11th |
| | [{pharmaversesdtm}](https://pharmaverse.github.io/pharmaversesdtm/main/) | [{admiralonco}](https://pharmaverse.github.io/admiralonco/main/) |
| | [{admiraldev}](https://pharmaverse.github.io/admiraldev/main/) | [{admiralophtha}](https://pharmaverse.github.io/admiralophtha/main/) |
| | [{admiral}](https://pharmaverse.github.io/admiral/main/) | |
The `{admiral}` Q4-2023 release will officially be `{admiral}`'s version 1.0.0 release, where we commit to increased package maturity and pivot towards focusing on maintenance rather than new content. This does not mean that there will never be any new content in `{admiral}`, rather it means we will be more mindful about introducing new functionality and/or breaking changes. The release schedule in 2024 and onward will also shift to twice-yearly, rather than quarterly, so that our users have ample time to react to any new content and changes that do make it onto `{admiral}`.

## Main Goal
Expand Down Expand Up @@ -151,11 +149,11 @@ that all our developers and contributors must follow, so that all our code has a
* Please see [FAQ: R and Package Versions](https://pharmaverse.github.io/admiral/cran-release/articles/faq.html#why-do-we-use-a-certain-r-version-and-package-versions-for-development) for why we develop with certain R and package versions.

## Pharmaverse Blog

If you are interested in R and Clinical Reporting, then visit the [pharmaverse blog](https://pharmaverse.github.io/blog/). This contains regular, bite-sized posts showcasing how `{admiral}` and other packages in the pharmaverse can be used to realize the vision of full end-to-end Clinical Reporting in R.

We are also always looking for keen `{admiral}` users to publish their own blog posts about how they use the package. If this could be you, feel free make an issue in the [GitHub repo](https://github.com/pharmaverse/blog) and get started!


## Conference Presentations

* [Cross Industry Package Development](https://www.youtube.com/watch?v=M4L1PPMu0pU) (recording from R in Pharma 2022)
Expand All @@ -176,5 +174,5 @@ We use the following for support and communications between user and developer c

## Acknowledgments

Along with the authors and contributors, thanks to the following people for their work on the package:
Along with the authors and contributors, thanks to the following people for their work on the package:
Jaxon Abercrombie, Mahdi About, Teckla Akinyi, James Black, Claudia Carlucci, Bill Denney, Kamila Duniec, Alice Ehmann, Ania Golab, Alana Harris, Declan Hodges, Anthony Howard, Shimeng Huang, Samia Kabi, James Kim, John Kirkpatrick, Leena Khatri, Robin Koeger, Konstantina Koukourikou, Pavan Kumar, Pooja Kumari, Shan Lee, Wenyi Liu, Jack McGavigan, Jordanna Morrish, Syed Mubasheer, Yohann Omnes, Barbara O'Reilly, Hamza Rahal, Nick Ramirez, Tom Ratford, Tamara Senior, Sophie Shapcott, Ondrej Slama, Andrew Smith, Daniil Stefonishin, Vignesh Thanikachalam, Michael Thorpe, Annie Yang, Ojesh Upadhyay and Franciszek Walkowiak.
20 changes: 11 additions & 9 deletions inst/templates/ad_adpp.R
Original file line number Diff line number Diff line change
Expand Up @@ -80,11 +80,12 @@ format_avalcat1n <- function(param, aval) {
# Get list of ADSL vars required for derivations
adsl_vars <- exprs(TRTSDT, TRTEDT, DTHDT, EOSDT, TRT01P, TRT01A)

adpp <- pp %>%
adpp_pp <- pp %>%
# Join ADSL with PP (need TRTSDT for ADY derivation)
left_join(
select(admiral_adsl, STUDYID, USUBJID, !!!adsl_vars),
by = c("STUDYID", "USUBJID")
derive_vars_merged(
dataset_add = admiral_adsl,
new_vars = adsl_vars,
by_vars = exprs(STUDYID, USUBJID)
) %>%
## Calculate ADT, ADY ----
derive_vars_dt(
Expand All @@ -93,7 +94,7 @@ adpp <- pp %>%
) %>%
derive_vars_dy(reference_date = TRTSDT, source_vars = exprs(ADT))

adpp <- adpp %>%
adpp_aval <- adpp_pp %>%
## Add PARAMCD only - add PARAM etc later ----
left_join(
select(param_lookup, PPTESTCD, PARAMCD),
Expand All @@ -117,7 +118,7 @@ adpp <- adpp %>%
## Get visit info ----
# See also the "Visit and Period Variables" vignette
# (https://pharmaverse.github.io/admiral/cran-release/articles/visits_periods.html#visit_bds)
adpp <- adpp %>%
adpp_avisit <- adpp_aval %>%
# Derive Timing
mutate(
VISIT = "", # /!\ To remove
Expand All @@ -141,9 +142,10 @@ adpp <- adpp %>%
derive_vars_merged(dataset_add = avalcat_lookup, by_vars = exprs(PARAMCD, AVALCA1N))

# Add all ADSL variables
adpp <- adpp %>%
left_join(admiral_adsl,
by = c("STUDYID", "USUBJID")
adpp <- adpp_avisit %>%
derive_vars_merged(
dataset_add = select(admiral_adsl, !!!negate_vars(adsl_vars)),
by_vars = exprs(STUDYID, USUBJID)
)

# Final Steps, Select final variables and Add labels
Expand Down
36 changes: 30 additions & 6 deletions man/derive_vars_aage.Rd

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27 changes: 26 additions & 1 deletion man/derive_vars_duration.Rd

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