Closes #1697 add keep_source_vars arg@devel #2070

gg106046 · 2023-08-22T12:14:05Z

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…ed relevent unit tests and updated NEWS.md.

…maverse/admiral into 1697_add_keep_vars_source_arg@devel

…reme_records()`

github-actions · 2023-08-22T12:34:41Z

Package	Line Rate	Health
admiral	98%	✔
Summary	98% (4406 / 4476)	✔

zdz2101

Mostly small stuff like grammar/phrasing

NEWS.md

R/derive_extreme_records.R

bms63 · 2023-08-27T21:51:03Z

tests/testthat/test-derive_extreme_records.R

Could we have a test to see what happens where a specified keep_source _vars variable is missing from the source dataset please.

bms63

Thanks @gg106046 this is looking good!! @bundfussr would you also mind reviewing - tyty

Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

bms63 · 2023-08-28T13:57:28Z

Hi @gg106046 we have a failing test now. Can you fix please. I think this is almost done !! yay!! thanks again for coming on to help us I know you are busy.

gg106046 · 2023-08-28T14:21:24Z

Hi @gg106046 we have a failing test now. Can you fix please. I think this is almost done !! yay!! thanks again for coming on to help us I know you are busy.

Hi @bms63, will fix the failing test! I'm updating the function derive_param_exist_flag() as well. Will push the update to github in a while. Is that fine or should I raise a separate pull request for that?

R/derive_extreme_records.R

R/derive_merged.R

bundfussr · 2023-08-31T14:49:50Z

R/derive_param_exist_flag.R

@@ -179,6 +187,7 @@ derive_param_exist_flag <- function(dataset = NULL,
                                    filter_add = NULL,
                                    aval_fun,
                                    by_vars = get_admiral_option("subject_keys"),
+                                    keep_source_vars = exprs(everything()),


Here we have the same problem as for derive_var_merged_exist_flag(): the result depends on the sort order. We could add the order and mode argument to the function. But this would make the function very similar to derive_extreme_records(). So I am not sure if this is a good idea.

For now I would not add keep_source_vars to derive_param_exist_flag().

I think we need to discuss in the clean-up group if we need the derive_*_exist_flag() functions and in the affirmative how they can be clearly distinguished from other functions like derive_extreme_records().

bms63 · 2023-09-05T19:17:19Z

@gg106046 has all the feedback been implemented?

gg106046 · 2023-09-06T03:28:12Z

@gg106046 has all the feedback been implemented?

Hi @bms63! All the comments related to derive_extreme_records() have been implemented. But there's a suggestion to not include keep_source_vars in derive_var_merged_exist_flag(). Should I create a different branch to keep only the changes made to derive_extreme_records()?

bms63 · 2023-09-06T15:40:56Z

@gg106046 has all the feedback been implemented?

Hi @bms63! All the comments related to derive_extreme_records() have been implemented. But there's a suggestion to not include keep_source_vars in derive_extreme_records(). Should I create a different branch to keep only the changes made to derive_extreme_records()?

I think you mean derive_var_merged_exist_flag? I believe we need to discuss this more internally as the two functions are converging and maybe deprecate derive_var_merged_exist_flag. For now I would revert the change for derive_var_merged_exist_flag and I will place the discussion in Clean-up Thread for us to look into next release.

@bundfussr is this what you are expecting?

bundfussr · 2023-09-06T16:05:20Z

@gg106046 has all the feedback been implemented?

Hi @bms63! All the comments related to derive_extreme_records() have been implemented. But there's a suggestion to not include keep_source_vars in derive_extreme_records(). Should I create a different branch to keep only the changes made to derive_extreme_records()?

I think you mean derive_var_merged_exist_flag? I believe we need to discuss this more internally as the two functions are converging and maybe deprecate derive_var_merged_exist_flag. For now I would revert the change for derive_var_merged_exist_flag and I will place the discussion in Clean-up Thread for us to look into next release.

@bundfussr is this what you are expecting?

In the PR keep_source_vars is added to derive_extreme_records(), derive_vars_merged_exist_flag(), and derive_param_exist_flag(). For derive_vars_merged_exist_flag() and derive_param_exist_flag() the result depends on the sort order of the input dataset, i.e., for the same call and input dataset you could get different results when the sort order of the input dataset is different. I think we should avoid this.
Thus for this release I would just add keep_source_vars to derive_extreme_records() and revert the changes made for derive_vars_merged_exist_flag() and derive_param_exist_flag().

…pdated `derive_extreme_records()`

gg106046 · 2023-09-07T06:02:01Z

@gg106046 has all the feedback been implemented?

Hi @bms63! All the comments related to derive_extreme_records() have been implemented. But there's a suggestion to not include keep_source_vars in derive_extreme_records(). Should I create a different branch to keep only the changes made to derive_extreme_records()?

I think you mean derive_var_merged_exist_flag? I believe we need to discuss this more internally as the two functions are converging and maybe deprecate derive_var_merged_exist_flag. For now I would revert the change for derive_var_merged_exist_flag and I will place the discussion in Clean-up Thread for us to look into next release.
@bundfussr is this what you are expecting?

In the PR keep_source_vars is added to derive_extreme_records(), derive_vars_merged_exist_flag(), and derive_param_exist_flag(). For derive_vars_merged_exist_flag() and derive_param_exist_flag() the result depends on the sort order of the input dataset, i.e., for the same call and input dataset you could get different results when the sort order of the input dataset is different. I think we should avoid this. Thus for this release I would just add keep_source_vars to derive_extreme_records() and revert the changes made for derive_vars_merged_exist_flag() and derive_param_exist_flag().

Reverted changes made for derive_vars_merged_exist_flag() and derive_param_exist_flag().

bundfussr

Could you add an item to the details section to describe at which point the variables from keep_source_vars are selected?

gg106046 · 2023-09-07T11:26:22Z

Could you add an item to the details section to describe at which point the variables from keep_source_vars are selected?

I've added a point for keep_source_vars in the details section. Let me know if that works!

bundfussr · 2023-09-07T11:29:15Z

Could you add an item to the details section to describe at which point the variables from keep_source_vars are selected?

I've added a point for keep_source_vars in the details section. Let me know if that works!

Thanks, looks good.

bms63

@gg106046 thank you again for seeing this through!!!!!

@Keywords

* 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>

@Keywords

* 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} <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> * 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 <dickinson.jeffrey@gene.com> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * 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 <zdz2101@github.com> * Update README.md typo Co-authored-by: Ben Straub <ben.x.straub@gsk.com> --------- Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> Co-authored-by: GitHub Actions <action@github.com> Co-authored-by: Jeff Dickinson <jeffreyd@gene.com> Co-authored-by: Jeffrey Dickinson <dickinson.jeffrey@gene.com> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zdz2101@github.com> --------- Co-authored-by: Ben Straub <ben.x.straub@gsk.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: 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> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com>

* 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: 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 <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 4a60be0d83e5bd9503eb74610160ece31ef86b7e. * 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> * 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 <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> * 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 <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> * 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 <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> * 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 <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> * 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 <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> * 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} <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: 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 <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 4a60be0d83e5bd9503eb74610160ece31ef86b7e. * 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> * 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 <dickinson.jeffrey@gene.com> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> * 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 <zdz2101@github.com> * Update README.md typo Co-authored-by: Ben Straub <ben.x.straub@gsk.com> --------- Co-authored-by: Stefan Bundfuss <80953585+bundfussr@users.noreply.github.com> Co-authored-by: GitHub Actions <action@github.com> Co-authored-by: Jeff Dickinson <jeffreyd@gene.com> Co-authored-by: Jeffrey Dickinson <dickinson.jeffrey@gene.com> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com> Co-authored-by: Ben Straub <ben.x.straub@gsk.com> Co-authored-by: Zelos Zhu <zdz2101@github.com> --------- Co-authored-by: Ben Straub <ben.x.straub@gsk.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: 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> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com> * 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 <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: Ben Straub <ben.x.straub@gsk.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> Co-authored-by: Daphné Grasselly <56442075+dgrassellyb@users.noreply.github.com>

gg106046 and others added 12 commits May 25, 2023 09:23

#1697 Added keep_vars_source arg in derive_extreme_records(), add…

fde1ea5

…ed relevent unit tests and updated NEWS.md.

Updated pkgdown.yml

b6cca13

Undoing renv.lock update

4fd03d8

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

2a410a6

Merge branch '1697_add_keep_vars_source_arg@devel' of github.com:phar…

7c51d96

…maverse/admiral into 1697_add_keep_vars_source_arg@devel

Merge branch 'devel' into 1697_add_keep_vars_source_arg@devel

0b61b02

#1697 Updated wordlist to include 'tidyselect'

b5561f7

Merge branch '1697_add_keep_vars_source_arg@devel' of github.com:phar…

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…maverse/admiral into 1697_add_keep_vars_source_arg@devel

Merge branch 'devel' into 1697_add_keep_vars_source_arg@devel

938d347

#1697 Moved select() after process_set_values_to()

0ac2788

Merge branch 'devel' into 1697_add_keep_vars_source_arg@devel

0a61144

#1697 Updated keep_vars_source to keep_source_vars in `derive_ext…

3b0fbde

…reme_records()`

gg106046 self-assigned this Aug 22, 2023

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Feature Request: Add keep_source_vars parameter #1697

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Merge branch 'devel' into 1697_add_keep_vars_source_arg@devel

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gg106046 and others added 3 commits August 28, 2023 16:59

Update NEWS.md

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Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

Update NEWS.md

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Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

Update R/derive_extreme_records.R

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Co-authored-by: Zelos Zhu <zelos.zhu@atorusresearch.com>

bundfussr requested changes Aug 31, 2023

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#1697 Reverted changes made to derive_var_merged_exist_flag() and u…

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…pdated `derive_extreme_records()`

gg106046 force-pushed the 1697_add_keep_vars_source_arg@devel branch from 8397dbe to 13b6f83 Compare September 7, 2023 05:51

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#1697 Updated 'Details' section to include keep_source_vars

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gg106046 force-pushed the 1697_add_keep_vars_source_arg@devel branch from 0b64f62 to 86582e2 Compare September 7, 2023 11:19

Merge branch 'devel' into 1697_add_keep_vars_source_arg@devel

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bms63 merged commit bdcfe12 into devel Sep 7, 2023
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Closes #1697 add keep_source_vars arg@devel #2070

Closes #1697 add keep_source_vars arg@devel #2070

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Closes #1697 add keep_source_vars arg@devel #2070

Closes #1697 add keep_source_vars arg@devel #2070

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