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* 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} <edoardo.mancini@roche.com> * 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 <dickinson.jeffrey@gene.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Closes #1695 Establish codeowners (#1973) feat: #1695 add gordon and jeff as codeowners Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: cicdguy <26552821+cicdguy@users.noreply.github.com> * 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 <47867131+kaz462@users.noreply.github.com> * chore: #264 move assertion to different line --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Kangjie Zhang <47867131+kaz462@users.noreply.github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Propagate renv.lock from pharmaverse/admiralci (#1986) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> * 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 <ben.x.straub@gsk.com> Co-authored-by: GitHub Actions <action@github.com> Co-authored-by: Zelos Zhu <zdz2101@github.com> * 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 <ben.x.straub@gsk.com> * 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 <ben.x.straub@gsk.com> * 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 <ben.x.straub@gsk.com> * Update R/compute_age_years.R with correct backquoting Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * #2001 version change in deprecation * #2001 insert parenthesis in NEWS.md Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * #2001 chore: roxygen --------- Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <zdz2101@github.com> * 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 <ben.x.straub@gsk.com> * 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 <danield.sjoberg@gmail.com> * 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 <zdz2101@github.com> * 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 <zdz2101@github.com> * 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 <adam.forys@roche.com> --------- Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Adam Foryś <adam.forys@roche.com> * 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 <galachad@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@roche.com> * 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 <zelos.zhu@atorusresearch.com> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * remove space for lintr --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <galachad@users.noreply.github.com> * 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 <ben.x.straub@gsk.com> * 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 <zelos.zhu@atorusresearch.com> * Closes #2038 Attach See also to compute functions (#2062) Doc: #2038 Attach See also to compute functions Co-authored-by: Jeffrey Dickinson <dickinson.jeffrey@gene.com> * 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 <zdz2101@github.com> * 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 <zelos.zhu@atorusresearch.com> * #1968 compute_multiple_vars: use @Keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <zdz2101@github.com> * 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 <dickinson.jeffrey@gene.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Propagate renv.lock from pharmaverse/admiralci (#2064) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <galachad@users.noreply.github.com> * #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 <zelos.zhu@atorusresearch.com> * 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 <ben.x.straub@gsk.com> * Closes #2078 swap out admiral_eg with eg (#2080) feat: #2078 swap out admiral_eg with eg Co-authored-by: Zelos Zhu <zdz2101@github.com> * 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 <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zdz2101@github.com> * 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 <zelos.zhu@atorusresearch.com> * Fix unit test for Cal (Ionized) Low for missing ANRLO. Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Add units to description of Glucose Nonfasting, High Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Add unit to description of Glucose fasting, High Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Fix typo in description of Triglycerides, Fasting, High for Grade 3 Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <ben.x.straub@gsk.com> * Update NEWS.md following QC comment Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * 1859 address QC comments * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * 1859 Fix STYLER issue * 1859 Fix example in function header * 1859 fix LINTR issue --------- Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <zelos.zhu@atorusresearch.com> * Update NEWS.md Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * Update R/derive_extreme_records.R Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * #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 <zelos.zhu@atorusresearch.com> * #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 <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <zelos.zhu@atorusresearch.com> * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * docs: #2028 lite explanation of h.i. rule --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> * 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 <zdz2101@github.com> Co-authored-by: StefanThoma <40463122+StefanThoma@users.noreply.github.com> * Fix for Get Started on Webpage (#2093) Update _pkgdown.yml * update readme with admiral release schedule (#2095) Co-authored-by: Zelos Zhu <zdz2101@github.com> --------- Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com> Co-authored-by: sadchla-codes <sadchla.mathieu@gmail.com> Co-authored-by: Sadchla Mascary <112789549+sadchla-codes@users.noreply.github.com> Co-authored-by: lomaxj1 <jennifer.lomax@roche.com> Co-authored-by: Jennifer Lomax <125990075+J-Lox@users.noreply.github.com> Co-authored-by: Edoardo Mancini <53403957+manciniedoardo@users.noreply.github.com> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <edoardo.mancini@roche.com> Co-authored-by: Jeff Dickinson <jeffreyd@gene.com> Co-authored-by: Jeffrey Dickinson <dickinson.jeffrey@gene.com> Co-authored-by: Zelos Zhu <zdz2101@github.com> Co-authored-by: cicdguy <26552821+cicdguy@users.noreply.github.com> Co-authored-by: Kangjie Zhang <47867131+kaz462@users.noreply.github.com> Co-authored-by: pharmaverse-bot <113703390+pharmaverse-bot@users.noreply.github.com> Co-authored-by: dgrassellyb <dgrassellyb@users.noreply.github.com> Co-authored-by: GitHub Actions <action@github.com> Co-authored-by: SyedMubasheer <106958950+SyedMubasheer@users.noreply.github.com> Co-authored-by: Daniel Sjoberg <danield.sjoberg@gmail.com> Co-authored-by: asha-gsk <134052893+ashachakma@users.noreply.github.com> Co-authored-by: Sophie Shapcott <90790226+sophie-gem@users.noreply.github.com> Co-authored-by: ynsec37 <98389771+ynsec37@users.noreply.github.com> Co-authored-by: Adam Foryś <adam.forys@roche.com> Co-authored-by: galachad <galachad@users.noreply.github.com> Co-authored-by: Daphne Grasselly <daphne.grasselly@roche.com> Co-authored-by: StefanThoma <40463122+StefanThoma@users.noreply.github.com> Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> Co-authored-by: Ross Farrugia <82581364+rossfarrugia@users.noreply.github.com> Co-authored-by: Gordon Miller <80953007+millerg23@users.noreply.github.com> Co-authored-by: G Gayatri <103511237+gg106046@users.noreply.github.com>
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