Closes #2012_derive_vars_dy #2013

ynsec37 · 2023-07-17T03:35:56Z

Thank you for your Pull Request! We have developed this task checklist from the Development Process Guide to help with the final steps of the process. Completing the below tasks helps to ensure our reviewers can maximize their time on your code as well as making sure the admiral codebase remains robust and consistent.

Please check off each taskbox as an acknowledgment that you completed the task or check off that it is not relevant to your Pull Request. This checklist is part of the Github Action workflows and the Pull Request will not be merged into the devel branch until you have checked off each task.

The updates were done by passing the named vector of dy_vars to .names in across() and it will not create the temporary variables end with _temp.

A related test that the input dataset has a variable end with _temp was created and no error occurred.

The updates had no impact on user facing and I ticked the some of check list that may be not applicable.

For pkgdown::build_site(), I got the below errors, but I am not sure if it was related to this updates.

For 'lintr::lint_package()', the following message is from the previous commit, and I am not familiar with lintr and wonder if this is a problem.

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

ynsec37 · 2023-07-17T04:09:07Z

sorry for missing the reviews and I tried to reopen but not found how to add.

ddsjoberg · 2023-07-24T03:31:01Z

Thank you @ynsec37 for the PR! I'll review it this week 🚀

ddsjoberg · 2023-07-24T04:23:15Z

@ynsec37 thank you again for the PR.

I have a question about the syntax you used to correct the issue. In the across(.names) argument, you passed a vector of the new names (which works perfectly).

library(dplyr, warn.conflicts = FALSE)

mtcars[1:4, 1:4] %>%
  mutate(
    across(
      .cols = c(mpg, hp),
      .fns = ~. + 1000,
      .names = "{letters[1:2]}"
    )
  )
#>                 mpg cyl disp  hp      a    b
#> Mazda RX4      21.0   6  160 110 1021.0 1110
#> Mazda RX4 Wag  21.0   6  160 110 1021.0 1110
#> Datsun 710     22.8   4  108  93 1022.8 1093
#> Hornet 4 Drive 21.4   6  258 110 1021.4 1110

I haven't see this use of the .names argument documented within the dplyr package. Here's the description of the .names argument from the help file:

If this syntax isn't officially supported, I am concerned to include it in case support is removed in the future. Perhaps we should update it to something like the example below (unless, of course, this is an officially supported use of the argument and I missed it!).

  dataset %>%
    mutate(
      across(
        .cols = vars2chr(unname(source_vars)),
        .fns = ~ compute_duration(start_date = !!reference_date, end_date = .x),
        .names = "{str_replace_all(.col, '(DT|DTM)$', 'DY')}"
      )
    )

Is the vector input to the .names argument official, and if so, where is that documented? THANK YOU! 🍁

ynsec37 · 2023-07-25T16:59:58Z

Thank you very much for review.

I had created a related issue to confirm with dplyr developer whether this is a supported use case.

I had tried your proposal, this may not work for below example, the DEATHDY

derive_vars_dy(
  datain,
  reference_date = TRTSDT,
  source_vars = exprs(TRTSDT, DEATHDY = DTHDT)
)

bundfussr · 2023-07-25T17:27:45Z

Maybe we should also create an issue at glue to clarify what a "glue expression" is. Is

> glue::glue('Values: {c("a", "b")}')
Values: a
Values: b

intended usage and behavior?

The suggested code in this PR, the suggested code from @ddsjoberg , and also the implementation of dplyr::across() assume it is correct usage. (.col is a vector. So str_replace_all(.col, '(DT|DTM)$', 'DY') is a vector as well.)

ddsjoberg · 2023-07-25T23:18:18Z

@bundfussr good points, I agree. I am happy to merge as is. I only have a slight concern that the implementation has a small chance of changing in the future since we haven't seen it documented, and the dplyr maintaners may consider it an "off-label" use of their function. Regardless, if that does happen, we'll receive notice from them ahead of any breaking change.

Shall we just merge it?

ynsec37 · 2023-07-26T02:57:39Z

I think the glue::glue is vectorized like other stringr functions or paste0
For example stringr::str_glue

#' mtcars %>% str_glue_data("{rownames(.)} has {hp} hp")
str_glue <- function(..., .sep = "", .envir = parent.frame()) {
glue::glue(..., .sep = .sep, .envir = .envir)
}

glue::glue('Values: {c("a", "b")}')
#> Values: a
#> Values: b

stringr::str_glue('Values: {c("a", "b")}')
#> Values: a
#> Values: b

identical(
  unclass(glue::glue('Values: {c("a", "b")}')),
  paste0("Values: ", c("a", "b"))
)
#> [1] TRUE


name <- c("Fred", "Tom")
glue::glue("My name is {name}")
#> My name is Fred
#> My name is Tom

# as it is vectorized, so it can be used in the `mutate`
head(iris, 1) |>
  dplyr::mutate(description = glue::glue("This {Species} has a petal length of {Petal.Length}"))
#>   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
#> 1          5.1         3.5          1.4         0.2  setosa
#>                             description
#> 1 This setosa has a petal length of 1.4

^{Created on 2023-07-26 with reprex v2.0.2}

bundfussr · 2023-07-26T08:20:30Z

@bundfussr good points, I agree. I am happy to merge as is. I only have a slight concern that the implementation has a small chance of changing in the future since we haven't seen it documented, and the dplyr maintaners may consider it an "off-label" use of their function. Regardless, if that does happen, we'll receive notice from them ahead of any breaking change.

Shall we just merge it?

I agree that the documentation of dplyr::across() and glue::glue() is not clear and that there is a small chance that the behavior changes in future. However, the risk seems acceptable to me. So I would merge it.

bundfussr · 2023-07-26T08:26:59Z

I think the glue::glue is vectorized like other stringr functions or paste0

Yes, it is vectorized. But it is strange that it is not mentioned in the documentation and none of the examples demonstrates that it is vectorized. Should we ask the glue developers to update their documentation?

bms63 · 2023-07-26T12:32:41Z

@ynsec37 many thanks for this!!

I'm a bit hesitant to merge something that might mean a later update - is there not another way to accomplish the same task that introduces less risk?

bms63

Can you update the news @ynsec37. We decided this is a go!! tyty

ynsec37 · 2023-07-26T16:34:37Z

The news was updated.

As the usage in this pr code is pending to confirmed by dplyr developer.

I create a new branch #2012_derive_vars_dy_patch2@devel that use another way to set names of dy_vars.
It can pass all test too.

  names(source_vars) <- dy_vars


  dataset %>%
    # coping `source_var` to `dy_vars`
    mutate(!!!source_vars) %>%
    # compute on the `dy_vars`
    mutate(
      across(
        .cols = vars2chr(unname(dy_vars)),
        .fns  = ~ compute_duration(start_date = !!reference_date, end_date = .)
    ))

It first create new columns of dy_vars by coping the value of source_vars , then perform computation on newly created columns of dy_vars.

For instance,

derive_vars_dy(
  datain,
  reference_date = TRTSDTM,
  source_vars = exprs(TRTSDTM, ASTDTM, AENDT)
)

create targeted dy_vars first

compute on these columns

ddsjoberg

Thank you @ynsec37 for the pull request! very much appreciated!

ynsec37 · 2023-08-01T16:50:44Z

thanks a lot for review
I learn much from this great package admiral

@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} <[email protected]> * Closes #1228 produce bmi records for more visits (#1957) * feat: #1228 Produce BMI records for more visits: Add constant_height parameter * feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail. * docs: #1228 Produce BMI records for more visits: Fix typo in NEWS * feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette. * doc: #1228 Produce BMI records for more visits: Add backticks to variable. --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #1695 Establish codeowners (#1973) feat: #1695 add gordon and jeff as codeowners Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> * Closes #1974 Swapping out deprecated assertions (#1975) * feat: #1974 try swapping all deprecated assertions * chore: #1974 fix parsing issue that caused vignettes to crash * chore: #1974 simplify by_vars requirement Co-authored-by: Kangjie Zhang <[email protected]> * chore: #264 move assertion to different line --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#1986) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Catch devel up to Admiral v0.11.1 (#1997) (#1999) Admiral v0.11.1 (#1997) * [actions skip] Add/Update README.md for patch * Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987) * feat #1962 #1969 param_tte and get started fix * forgot to add updated DESCRIPTION * chore: #1962 thought crossing was dplyr * chore: #1962 account for new assertions * fix: #1962 was missing the reassignment piece? * fix: #1966 crude answer * feat: #1966 potential way of warning users of null new_vars * fix: #1966 add appropriate assertions to get check to go through * fix: #1966 appropriate function fix for order * fix: #1966 vignette named order expression * chore: #1966 try something * chore: #1966 optionality of expressions is tricky * feat: #1966 undo derive_joined stuff * chore: run styler --------- --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Initiate a Stale bot for Issue Triaging (#1992) * Create stale_bot.yml * Update and rename stale_bot.yml to stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Closes #1927 derive param tte@devel (#2000) Removed incorrect reference of start_imputation_flag Co-authored-by: Ben Straub <[email protected]> * Closes #1989 Link Fix in `README.md` (#1994) * Update README.md * Update WORDLIST * Update README.md * Update WORDLIST * chore: #1989 spelling --------- Co-authored-by: Ben Straub <[email protected]> * Closes #1856 Removed the higher order file (#2008) #1856 Removed the higher order file * Update templates.yml (#2026) * Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009) * #2001 added processing for missing age_units in `compute_age_years` * #2001 Chore: styler * #2001 chore: lint * #2001 chore: fix broken links * #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`. * #2001 chore: Fixed docs link * #2001 chore: styler * #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit` * #2001 Update NEWS.md as per suggestiom Co-authored-by: Ben Straub <[email protected]> * Update R/compute_age_years.R with correct backquoting Co-authored-by: Zelos Zhu <[email protected]> * #2001 version change in deprecation * #2001 insert parenthesis in NEWS.md Co-authored-by: Ben Straub <[email protected]> * #2001 chore: roxygen --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024) * feat: #1979 added the necessary flag_all function argument * feat: #1979 modify check_type to supppress warnings for flag_all = TRUE * chore: #1979 run lintr/styler * chore: #1979 add news blurb * typo * chore: #1979 add additional tests and add roxygen details * chore: #1979 adopt feedback from review * chore: #1979 run styler --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #123 Add Edoardo to status check (#2031) fix: pharmaverse/admiralci#123 add Edoardo to status check * Closes #2014 derive_var_shift change na_val@devel (#2032) * #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`. * #2014 - Update `NEWS.md`. * #2014 - update tests and write deprecation parameter test * #2014 - run required tasks for PR --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2012_derive_vars_dy (#2013) * derive dy_vars by argument .name in across (#2012) use named vector to avoid the variabes end with `_temp` in input dataset * test no error for variable end with `_temp`(#2012) * styled file * add update information for #2012 --------- Co-authored-by: Daniel Sjoberg <[email protected]> * Closes #1966 address derive_vars_joined bugs (#2016) * feat: #1966 make our check_type consistent * feat: #1966 hacky solution to null new_vars .join problem * chore: #1966 inserted line in wrong place * feat: #1966 add news blurb for what was done * feat: #1966 add tests * chore: #1966 lintr * chore: #1966 swap appropriate order selection and restore check_type arg * chore: #1966 looks like that fixed it * feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL * chore: #1966 clean up for readability * chore: #1966 restore original replace_values_by_names * chore: #1966 add additional test to demonstrate how order vars were fixed/selected * feat: #1966 adopt feedback for error messaging of naming conflicts --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039) feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref` Co-authored-by: Zelos Zhu <[email protected]> * Close #1940 Removing unnecessary runtime development-related dependencies (#1978) * feat: #1940 try removing dev deps * chore: #1940 still needs knitr * #1940 diffdf needed for all the testing stuff * chore: #1940 add back rmarkdown Co-authored-by: Adam Foryś <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029) * #1984 allowing missing trt end date * Update derive_var_ontrtfl.R * Update derive_var_ontrtfl.R * Increment version number to 0.12.0.9000 * updating version numbers...oops! * Update test-derive_var_ontrtfl.R * Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048) addressing missing treatment start dates * Propagate renv.lock from pharmaverse/admiralci (#2046) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * Update .Rbuildignore * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044) * span_period arg update * Update derive_var_ontrtfl.R * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * remove space for lintr --------- Co-authored-by: Zelos Zhu <[email protected]> * add admiral src to test codespaces * Revert "add admiral src to test codespaces" This reverts commit 4a60be0. * Propagate renv.lock from pharmaverse/admiralci (#2058) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Closes #2020 chore: rename wt to weight in compute_egfr (#2045) * code updated * Chore #2020 go through checklist * update .lycheeignore * update .lycheeignore * adjusted templates * chore: removed links from .lycheeignore * chore: #2020 removing file --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2053 Typo in the example `impute_dtc_dt` (#2056) Closes #2053 Typo in the example impute_dtc_dt * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R * update derive_date_vars.Rd Co-authored-by: Zelos Zhu <[email protected]> * Closes #2038 Attach See also to compute functions (#2062) Doc: #2038 Attach See also to compute functions Co-authored-by: Jeffrey Dickinson <[email protected]> * Closes #2042 fix compute_dtf bug (#2047) * feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly * feat: #2042 add appropriate logic for date-portions * chore: #2042 add news * feat: #2042 address month and day missing * feat: #2042 allow - for "Y" flag --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #1968 compute multiple variables in `derive_param_computed()` (#2036) * #1968 compute_multiple_vars: update arguments of derive_param_computed() * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: style files * #1968 compute_multiple_vars: fix R-CMD checks * #1968 compute_multiple_vars: update error message of get_hori_data() * #1968 compute_multiple_vars: improve documentation * #1968 compute_multiple_vars: use deprecation badge * #1968 compute_multiple_vars: use deprecation badge * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * #1968 compute_multiple_vars: use @Keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055) * feat: #2054 remove print.duplciates() * feat: #1466 add appropriate test for print.duplicates * chore: #1466 cleanup duplicate code * feat: #1466 use expect_snapshot() instead --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2040 Update admiral.test to pharmaversesdtm (#2057) * Chore: #2040 Update admiral.test to pharmaversesdtm * Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler * #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml * Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg. * Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R * Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R * Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#2064) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * #2027 clarify reference_date in derive_vars_dy() (#2063) * change description * updated news.md * closes #2069 bug: EOSSTT derivation fix (#2073) #2069 bug: EOSSTT derivation fix Co-authored-by: Zelos Zhu <[email protected]> * Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076) * utils_impute fns now internal * Update NEWS.md * adding meta.R entry back * Closes #1875 duration and interval time difference types update (#2075) * in progress * updated default to duration instead of interval * style * spelling updates * Update NEWS.md * added pharmaversesdtm Remotes call * Update DESCRIPTION * Update test-compute_duration.R --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2078 swap out admiral_eg with eg (#2080) feat: #2078 swap out admiral_eg with eg Co-authored-by: Zelos Zhu <[email protected]> * Closes #1960 enhance derive_extreme_event() (#2015) * #1960 enhance_derive_extreme_event: start a draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: add tests and documentation * #1960 enhance_derive_extreme_event: update NEWS * #1960 enhance_derive_extreme_event: fix links * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event: add example * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event:add example and tests for event-specific modes * #1960 enhance_derive_extreme_event: add ignore_event_order argument * #1960 enhance_derive_extreme_event: fix spelling * #1960 enhance_derive_extreme_event: use correct input dataset * #1960 enhance_derive_extreme_event: improve printing of event objects * #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars * #1960 enhance_derive_extreme_event: add description field * #1960 enhance_derive_extreme_event: address QC comments * #1960 enhance_derive_extreme_event: update man pages * #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml * #1960 enhance_derive_extreme_event: style files * chore: #1960 properly formatted testthat * chore: #1960 fix lint --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079) * Closes #2068 Updated `traceability_vars` to `set_values_to` * Clarify the explanation for the traceability_vars replacement * Closes #2083 bug adpp and adpc still using admiraltest (#2086) * fix: #2083 using pharmaversesdtm * fix: #2083 using pharmaversesdtm * chore: #2083 renaming datasets * chore: #2083 removing admiral prefix * chore: #2083 removing admiral suffix * chore: #2083 remove admiral suffix * chore: remove admiral prefix * Closes #1859 metadata updated for DAIDs in xlsx file (#2060) * 1859 metadata updated for DAIDs in xlsx file * 1859 metadata for DAIDs finalised * 1859 update data.r for atoxgr_criteria_daids * 1859 update man files * 1859 fix spelling * 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests * 1859 update man pages * 1859 fix STYLER issue * 1859 fix SPELLING * 1859 fix LINTR * 1859 Fix LINTR and add more unit tests * 1859 added Acidosis and Alkalosis and more unit tests * 1859 added more tests and partiallyy update gradin vignette * 1859 all unit tests added * 1859 fix STYLER * 1859 use signif function in metadata * 1859 use signif function in ncictcaev4 and v5 metadata * Update unit test for Cal (Ionized) to test missing ANRHI Co-authored-by: Zelos Zhu <[email protected]> * Fix unit test for Cal (Ionized) Low for missing ANRLO. Co-authored-by: Zelos Zhu <[email protected]> * Add units to description of Glucose Nonfasting, High Co-authored-by: Zelos Zhu <[email protected]> * Add unit to description of Glucose fasting, High Co-authored-by: Zelos Zhu <[email protected]> * Fix typo in description of Triglycerides, Fasting, High for Grade 3 Co-authored-by: Zelos Zhu <[email protected]> * 1859 address last QC comments on unit tests * 1859 update NEWS file * 1859 updated Vignette * 1859 Fix SPELLING * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * 1859 address QC comments * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * 1859 Fix STYLER issue * 1859 Fix example in function header * 1859 fix LINTR issue --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2050 Remove print fns from pkgdown Reference page (#2087) ref page updates * Closes #1697 add keep_source_vars arg@devel (#2070) * #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md. * Updated pkgdown.yml * Undoing renv.lock update * #1697 Updated default from `NULL` to `exprs(everything())` * #1697 Updated wordlist to include 'tidyselect' * #1697 Moved `select()` after `process_set_values_to()` * #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()` * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_extreme_records.R Co-authored-by: Zelos Zhu <[email protected]> * #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()` * #1697 Updated 'Details' section to include `keep_source_vars` --------- Co-authored-by: Zelos Zhu <[email protected]> * #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082) * #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation. * #1995 Chore: roxygen * #1995 chore:spellcheck and roxygen * #1995 updates to readme with release schedule and 1.0. * grammar fix in readme --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2028 removed erroneous section. updating rules section (#2088) * docs: #2028 removed erroneous section. updating rules section * docs: #2028 news and wordsmithing * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * docs: #2028 lite explanation of h.i. rule --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092) * feat: #2091 did that work? * chore: #2091 address errors * fixed deprecation warning * deprecation for analysis_var --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: StefanThoma <[email protected]> * Fix for Get Started on Webpage (#2093) Update _pkgdown.yml * update readme with admiral release schedule (#2095) Co-authored-by: Zelos Zhu <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]>

@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} <[email protected]> * Closes #1228 produce bmi records for more visits (#1957) * feat: #1228 Produce BMI records for more visits: Add constant_height parameter * feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail. * docs: #1228 Produce BMI records for more visits: Fix typo in NEWS * feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette. * doc: #1228 Produce BMI records for more visits: Add backticks to variable. --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #1695 Establish codeowners (#1973) feat: #1695 add gordon and jeff as codeowners Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> * Closes #1974 Swapping out deprecated assertions (#1975) * feat: #1974 try swapping all deprecated assertions * chore: #1974 fix parsing issue that caused vignettes to crash * chore: #1974 simplify by_vars requirement Co-authored-by: Kangjie Zhang <[email protected]> * chore: #264 move assertion to different line --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#1986) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Catch devel up to Admiral v0.11.1 (#1997) (#1999) Admiral v0.11.1 (#1997) * [actions skip] Add/Update README.md for patch * Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987) * feat #1962 #1969 param_tte and get started fix * forgot to add updated DESCRIPTION * chore: #1962 thought crossing was dplyr * chore: #1962 account for new assertions * fix: #1962 was missing the reassignment piece? * fix: #1966 crude answer * feat: #1966 potential way of warning users of null new_vars * fix: #1966 add appropriate assertions to get check to go through * fix: #1966 appropriate function fix for order * fix: #1966 vignette named order expression * chore: #1966 try something * chore: #1966 optionality of expressions is tricky * feat: #1966 undo derive_joined stuff * chore: run styler --------- --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Initiate a Stale bot for Issue Triaging (#1992) * Create stale_bot.yml * Update and rename stale_bot.yml to stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Closes #1927 derive param tte@devel (#2000) Removed incorrect reference of start_imputation_flag Co-authored-by: Ben Straub <[email protected]> * Closes #1989 Link Fix in `README.md` (#1994) * Update README.md * Update WORDLIST * Update README.md * Update WORDLIST * chore: #1989 spelling --------- Co-authored-by: Ben Straub <[email protected]> * Closes #1856 Removed the higher order file (#2008) #1856 Removed the higher order file * Update templates.yml (#2026) * Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009) * #2001 added processing for missing age_units in `compute_age_years` * #2001 Chore: styler * #2001 chore: lint * #2001 chore: fix broken links * #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`. * #2001 chore: Fixed docs link * #2001 chore: styler * #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit` * #2001 Update NEWS.md as per suggestiom Co-authored-by: Ben Straub <[email protected]> * Update R/compute_age_years.R with correct backquoting Co-authored-by: Zelos Zhu <[email protected]> * #2001 version change in deprecation * #2001 insert parenthesis in NEWS.md Co-authored-by: Ben Straub <[email protected]> * #2001 chore: roxygen --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024) * feat: #1979 added the necessary flag_all function argument * feat: #1979 modify check_type to supppress warnings for flag_all = TRUE * chore: #1979 run lintr/styler * chore: #1979 add news blurb * typo * chore: #1979 add additional tests and add roxygen details * chore: #1979 adopt feedback from review * chore: #1979 run styler --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #123 Add Edoardo to status check (#2031) fix: pharmaverse/admiralci#123 add Edoardo to status check * Closes #2014 derive_var_shift change na_val@devel (#2032) * #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`. * #2014 - Update `NEWS.md`. * #2014 - update tests and write deprecation parameter test * #2014 - run required tasks for PR --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2012_derive_vars_dy (#2013) * derive dy_vars by argument .name in across (#2012) use named vector to avoid the variabes end with `_temp` in input dataset * test no error for variable end with `_temp`(#2012) * styled file * add update information for #2012 --------- Co-authored-by: Daniel Sjoberg <[email protected]> * Closes #1966 address derive_vars_joined bugs (#2016) * feat: #1966 make our check_type consistent * feat: #1966 hacky solution to null new_vars .join problem * chore: #1966 inserted line in wrong place * feat: #1966 add news blurb for what was done * feat: #1966 add tests * chore: #1966 lintr * chore: #1966 swap appropriate order selection and restore check_type arg * chore: #1966 looks like that fixed it * feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL * chore: #1966 clean up for readability * chore: #1966 restore original replace_values_by_names * chore: #1966 add additional test to demonstrate how order vars were fixed/selected * feat: #1966 adopt feedback for error messaging of naming conflicts --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039) feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref` Co-authored-by: Zelos Zhu <[email protected]> * Close #1940 Removing unnecessary runtime development-related dependencies (#1978) * feat: #1940 try removing dev deps * chore: #1940 still needs knitr * #1940 diffdf needed for all the testing stuff * chore: #1940 add back rmarkdown Co-authored-by: Adam Foryś <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029) * #1984 allowing missing trt end date * Update derive_var_ontrtfl.R * Update derive_var_ontrtfl.R * Increment version number to 0.12.0.9000 * updating version numbers...oops! * Update test-derive_var_ontrtfl.R * Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048) addressing missing treatment start dates * Propagate renv.lock from pharmaverse/admiralci (#2046) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * Update .Rbuildignore * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044) * span_period arg update * Update derive_var_ontrtfl.R * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * remove space for lintr --------- Co-authored-by: Zelos Zhu <[email protected]> * add admiral src to test codespaces * Revert "add admiral src to test codespaces" This reverts commit 4a60be0. * Propagate renv.lock from pharmaverse/admiralci (#2058) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Closes #2020 chore: rename wt to weight in compute_egfr (#2045) * code updated * Chore #2020 go through checklist * update .lycheeignore * update .lycheeignore * adjusted templates * chore: removed links from .lycheeignore * chore: #2020 removing file --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2053 Typo in the example `impute_dtc_dt` (#2056) Closes #2053 Typo in the example impute_dtc_dt * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R * update derive_date_vars.Rd Co-authored-by: Zelos Zhu <[email protected]> * Closes #2038 Attach See also to compute functions (#2062) Doc: #2038 Attach See also to compute functions Co-authored-by: Jeffrey Dickinson <[email protected]> * Closes #2042 fix compute_dtf bug (#2047) * feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly * feat: #2042 add appropriate logic for date-portions * chore: #2042 add news * feat: #2042 address month and day missing * feat: #2042 allow - for "Y" flag --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #1968 compute multiple variables in `derive_param_computed()` (#2036) * #1968 compute_multiple_vars: update arguments of derive_param_computed() * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: style files * #1968 compute_multiple_vars: fix R-CMD checks * #1968 compute_multiple_vars: update error message of get_hori_data() * #1968 compute_multiple_vars: improve documentation * #1968 compute_multiple_vars: use deprecation badge * #1968 compute_multiple_vars: use deprecation badge * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * #1968 compute_multiple_vars: use @Keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055) * feat: #2054 remove print.duplciates() * feat: #1466 add appropriate test for print.duplicates * chore: #1466 cleanup duplicate code * feat: #1466 use expect_snapshot() instead --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2040 Update admiral.test to pharmaversesdtm (#2057) * Chore: #2040 Update admiral.test to pharmaversesdtm * Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler * #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml * Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg. * Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R * Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R * Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#2064) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * #2027 clarify reference_date in derive_vars_dy() (#2063) * change description * updated news.md * closes #2069 bug: EOSSTT derivation fix (#2073) #2069 bug: EOSSTT derivation fix Co-authored-by: Zelos Zhu <[email protected]> * Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076) * utils_impute fns now internal * Update NEWS.md * adding meta.R entry back * Closes #1875 duration and interval time difference types update (#2075) * in progress * updated default to duration instead of interval * style * spelling updates * Update NEWS.md * added pharmaversesdtm Remotes call * Update DESCRIPTION * Update test-compute_duration.R --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2078 swap out admiral_eg with eg (#2080) feat: #2078 swap out admiral_eg with eg Co-authored-by: Zelos Zhu <[email protected]> * Closes #1960 enhance derive_extreme_event() (#2015) * #1960 enhance_derive_extreme_event: start a draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: add tests and documentation * #1960 enhance_derive_extreme_event: update NEWS * #1960 enhance_derive_extreme_event: fix links * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event: add example * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event:add example and tests for event-specific modes * #1960 enhance_derive_extreme_event: add ignore_event_order argument * #1960 enhance_derive_extreme_event: fix spelling * #1960 enhance_derive_extreme_event: use correct input dataset * #1960 enhance_derive_extreme_event: improve printing of event objects * #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars * #1960 enhance_derive_extreme_event: add description field * #1960 enhance_derive_extreme_event: address QC comments * #1960 enhance_derive_extreme_event: update man pages * #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml * #1960 enhance_derive_extreme_event: style files * chore: #1960 properly formatted testthat * chore: #1960 fix lint --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079) * Closes #2068 Updated `traceability_vars` to `set_values_to` * Clarify the explanation for the traceability_vars replacement * Closes #2083 bug adpp and adpc still using admiraltest (#2086) * fix: #2083 using pharmaversesdtm * fix: #2083 using pharmaversesdtm * chore: #2083 renaming datasets * chore: #2083 removing admiral prefix * chore: #2083 removing admiral suffix * chore: #2083 remove admiral suffix * chore: remove admiral prefix * Closes #1859 metadata updated for DAIDs in xlsx file (#2060) * 1859 metadata updated for DAIDs in xlsx file * 1859 metadata for DAIDs finalised * 1859 update data.r for atoxgr_criteria_daids * 1859 update man files * 1859 fix spelling * 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests * 1859 update man pages * 1859 fix STYLER issue * 1859 fix SPELLING * 1859 fix LINTR * 1859 Fix LINTR and add more unit tests * 1859 added Acidosis and Alkalosis and more unit tests * 1859 added more tests and partiallyy update gradin vignette * 1859 all unit tests added * 1859 fix STYLER * 1859 use signif function in metadata * 1859 use signif function in ncictcaev4 and v5 metadata * Update unit test for Cal (Ionized) to test missing ANRHI Co-authored-by: Zelos Zhu <[email protected]> * Fix unit test for Cal (Ionized) Low for missing ANRLO. Co-authored-by: Zelos Zhu <[email protected]> * Add units to description of Glucose Nonfasting, High Co-authored-by: Zelos Zhu <[email protected]> * Add unit to description of Glucose fasting, High Co-authored-by: Zelos Zhu <[email protected]> * Fix typo in description of Triglycerides, Fasting, High for Grade 3 Co-authored-by: Zelos Zhu <[email protected]> * 1859 address last QC comments on unit tests * 1859 update NEWS file * 1859 updated Vignette * 1859 Fix SPELLING * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * 1859 address QC comments * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * 1859 Fix STYLER issue * 1859 Fix example in function header * 1859 fix LINTR issue --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2050 Remove print fns from pkgdown Reference page (#2087) ref page updates * Closes #1697 add keep_source_vars arg@devel (#2070) * #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md. * Updated pkgdown.yml * Undoing renv.lock update * #1697 Updated default from `NULL` to `exprs(everything())` * #1697 Updated wordlist to include 'tidyselect' * #1697 Moved `select()` after `process_set_values_to()` * #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()` * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_extreme_records.R Co-authored-by: Zelos Zhu <[email protected]> * #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()` * #1697 Updated 'Details' section to include `keep_source_vars` --------- Co-authored-by: Zelos Zhu <[email protected]> * #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082) * #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation. * #1995 Chore: roxygen * #1995 chore:spellcheck and roxygen * #1995 updates to readme with release schedule and 1.0. * grammar fix in readme --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2028 removed erroneous section. updating rules section (#2088) * docs: #2028 removed erroneous section. updating rules section * docs: #2028 news and wordsmithing * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * docs: #2028 lite explanation of h.i. rule --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092) * feat: #2091 did that work? * chore: #2091 address errors * fixed deprecation warning * deprecation for analysis_var --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: StefanThoma <[email protected]> * Fix for Get Started on Webpage (#2093) Update _pkgdown.yml * update readme with admiral release schedule (#2095) Co-authored-by: Zelos Zhu <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]> * ignore notes r cmd checks (#2114) * admiral v0.12.1 (#2122) * Closes #2113 fix derive extreme records (#2121) * #2113 fix_derive_extreme_records: update function and tests * #2113 fix_derive_extreme_records: style files * [actions skip] Add/Update README.md for patch * Closes #2109 ADPP template program has x and y variables (#2110) * #2109 ADPP template program has x and y variables: Update to use `derive_vars_merged()` * #2109 Doc: update NEWS for ADPP template change * ignore notes r cmd checks (#2114) --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #2112 add `type` to functions downstream of compute_duration() (#2118) * feat: #2112 add type to fxns downstream of compute_duration * feat: #2112 add test type argument for derive_vars_duration * styler and lintr * chore: #2112 adopt feedback * chore: #2112 add upversion on DESCRIPTION * chore: #2112 try inheritParams * chore: #2112 remove mention of default --------- Co-authored-by: Zelos Zhu <[email protected]> * Update README.md typo Co-authored-by: Ben Straub <[email protected]> --------- Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]>

* Closes #1950 following deprecation process, update Description version and news.md * updating documentation to fix the warnings * added the new tests for minutes and seconds options * Removing references in deprecated functions. * updated comments and applied test_that format * conflicts resolved * Closes #1941 authors contributors@devel (#1967) * Initial edit to `_pkgdown.yml` for #1941 * #1941 re-labelling authors and contributors * #1941 update to enact decision of team regarding who are authors and contributors. * #1941: Chore (spellcheck and man pages and NEWS.md update) * #1941 chore: further updates to spellcheck * #1941: chore: fix space after commas. move some acknowledgees to contributors. link README in authors page. * #1941 chore: roxygenize --------- Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> * Closes #1228 produce bmi records for more visits (#1957) * feat: #1228 Produce BMI records for more visits: Add constant_height parameter * feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail. * docs: #1228 Produce BMI records for more visits: Fix typo in NEWS * feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette. * doc: #1228 Produce BMI records for more visits: Add backticks to variable. --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #1695 Establish codeowners (#1973) feat: #1695 add gordon and jeff as codeowners Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> * Closes #1974 Swapping out deprecated assertions (#1975) * feat: #1974 try swapping all deprecated assertions * chore: #1974 fix parsing issue that caused vignettes to crash * chore: #1974 simplify by_vars requirement Co-authored-by: Kangjie Zhang <[email protected]> * chore: #264 move assertion to different line --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#1986) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Catch devel up to Admiral v0.11.1 (#1997) (#1999) Admiral v0.11.1 (#1997) * [actions skip] Add/Update README.md for patch * Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987) * feat #1962 #1969 param_tte and get started fix * forgot to add updated DESCRIPTION * chore: #1962 thought crossing was dplyr * chore: #1962 account for new assertions * fix: #1962 was missing the reassignment piece? * fix: #1966 crude answer * feat: #1966 potential way of warning users of null new_vars * fix: #1966 add appropriate assertions to get check to go through * fix: #1966 appropriate function fix for order * fix: #1966 vignette named order expression * chore: #1966 try something * chore: #1966 optionality of expressions is tricky * feat: #1966 undo derive_joined stuff * chore: run styler --------- --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Initiate a Stale bot for Issue Triaging (#1992) * Create stale_bot.yml * Update and rename stale_bot.yml to stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Closes #1927 derive param tte@devel (#2000) Removed incorrect reference of start_imputation_flag Co-authored-by: Ben Straub <[email protected]> * Closes #1989 Link Fix in `README.md` (#1994) * Update README.md * Update WORDLIST * Update README.md * Update WORDLIST * chore: #1989 spelling --------- Co-authored-by: Ben Straub <[email protected]> * Closes #1856 Removed the higher order file (#2008) #1856 Removed the higher order file * Update templates.yml (#2026) * Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009) * #2001 added processing for missing age_units in `compute_age_years` * #2001 Chore: styler * #2001 chore: lint * #2001 chore: fix broken links * #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`. * #2001 chore: Fixed docs link * #2001 chore: styler * #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit` * #2001 Update NEWS.md as per suggestiom Co-authored-by: Ben Straub <[email protected]> * Update R/compute_age_years.R with correct backquoting Co-authored-by: Zelos Zhu <[email protected]> * #2001 version change in deprecation * #2001 insert parenthesis in NEWS.md Co-authored-by: Ben Straub <[email protected]> * #2001 chore: roxygen --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024) * feat: #1979 added the necessary flag_all function argument * feat: #1979 modify check_type to supppress warnings for flag_all = TRUE * chore: #1979 run lintr/styler * chore: #1979 add news blurb * typo * chore: #1979 add additional tests and add roxygen details * chore: #1979 adopt feedback from review * chore: #1979 run styler --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #123 Add Edoardo to status check (#2031) fix: https://github.com/pharmaverse/admiralci/issues/123 add Edoardo to status check * Closes #2014 derive_var_shift change na_val@devel (#2032) * #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`. * #2014 - Update `NEWS.md`. * #2014 - update tests and write deprecation parameter test * #2014 - run required tasks for PR --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2012_derive_vars_dy (#2013) * derive dy_vars by argument .name in across (#2012) use named vector to avoid the variabes end with `_temp` in input dataset * test no error for variable end with `_temp`(#2012) * styled file * add update information for #2012 --------- Co-authored-by: Daniel Sjoberg <[email protected]> * Closes #1966 address derive_vars_joined bugs (#2016) * feat: #1966 make our check_type consistent * feat: #1966 hacky solution to null new_vars .join problem * chore: #1966 inserted line in wrong place * feat: #1966 add news blurb for what was done * feat: #1966 add tests * chore: #1966 lintr * chore: #1966 swap appropriate order selection and restore check_type arg * chore: #1966 looks like that fixed it * feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL * chore: #1966 clean up for readability * chore: #1966 restore original replace_values_by_names * chore: #1966 add additional test to demonstrate how order vars were fixed/selected * feat: #1966 adopt feedback for error messaging of naming conflicts --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039) feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref` Co-authored-by: Zelos Zhu <[email protected]> * Close #1940 Removing unnecessary runtime development-related dependencies (#1978) * feat: #1940 try removing dev deps * chore: #1940 still needs knitr * #1940 diffdf needed for all the testing stuff * chore: #1940 add back rmarkdown Co-authored-by: Adam Foryś <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029) * #1984 allowing missing trt end date * Update derive_var_ontrtfl.R * Update derive_var_ontrtfl.R * Increment version number to 0.12.0.9000 * updating version numbers...oops! * Update test-derive_var_ontrtfl.R * Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048) addressing missing treatment start dates * Propagate renv.lock from pharmaverse/admiralci (#2046) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * Update .Rbuildignore * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044) * span_period arg update * Update derive_var_ontrtfl.R * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * remove space for lintr --------- Co-authored-by: Zelos Zhu <[email protected]> * add admiral src to test codespaces * Revert "add admiral src to test codespaces" This reverts commit 4a60be0d83e5bd9503eb74610160ece31ef86b7e. * Propagate renv.lock from pharmaverse/admiralci (#2058) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Closes #2020 chore: rename wt to weight in compute_egfr (#2045) * code updated * Chore #2020 go through checklist * update .lycheeignore * update .lycheeignore * adjusted templates * chore: removed links from .lycheeignore * chore: #2020 removing file --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2053 Typo in the example `impute_dtc_dt` (#2056) Closes #2053 Typo in the example impute_dtc_dt * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R * update derive_date_vars.Rd Co-authored-by: Zelos Zhu <[email protected]> * Closes #2038 Attach See also to compute functions (#2062) Doc: #2038 Attach See also to compute functions Co-authored-by: Jeffrey Dickinson <[email protected]> * feat: #2034 show how this can standardize our sub-descriptions * feat: #2034 this does seem to be a better usecase * Closes #2042 fix compute_dtf bug (#2047) * feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly * feat: #2042 add appropriate logic for date-portions * chore: #2042 add news * feat: #2042 address month and day missing * feat: #2042 allow - for "Y" flag --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #1968 compute multiple variables in `derive_param_computed()` (#2036) * #1968 compute_multiple_vars: update arguments of derive_param_computed() * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: style files * #1968 compute_multiple_vars: fix R-CMD checks * #1968 compute_multiple_vars: update error message of get_hori_data() * #1968 compute_multiple_vars: improve documentation * #1968 compute_multiple_vars: use deprecation badge * #1968 compute_multiple_vars: use deprecation badge * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * #1968 compute_multiple_vars: use @keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * feat: #2034 looks like we can bundle the label into the code chunk too * Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055) * feat: #2054 remove print.duplciates() * feat: #1466 add appropriate test for print.duplicates * chore: #1466 cleanup duplicate code * feat: #1466 use expect_snapshot() instead --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2040 Update admiral.test to pharmaversesdtm (#2057) * Chore: #2040 Update admiral.test to pharmaversesdtm * Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler * #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml * Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg. * Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R * Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R * Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> * chore: #2034 show the degree of variation * Propagate renv.lock from pharmaverse/admiralci (#2064) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * #2027 clarify reference_date in derive_vars_dy() (#2063) * change description * updated news.md * closes #2069 bug: EOSSTT derivation fix (#2073) #2069 bug: EOSSTT derivation fix Co-authored-by: Zelos Zhu <[email protected]> * Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076) * utils_impute fns now internal * Update NEWS.md * adding meta.R entry back * Closes #1875 duration and interval time difference types update (#2075) * in progress * updated default to duration instead of interval * style * spelling updates * Update NEWS.md * added pharmaversesdtm Remotes call * Update DESCRIPTION * Update test-compute_duration.R --------- Co-authored-by: Ben Straub <[email protected]> * feat: #2034 apply function to all dataset params * chore: #2034 align assertion with description * chore: #2034 fix derive_locf_records * run lintr * chore: #2034 nolint doesn't work in roxygen * Closes #2078 swap out admiral_eg with eg (#2080) feat: #2078 swap out admiral_eg with eg Co-authored-by: Zelos Zhu <[email protected]> * Closes #1960 enhance derive_extreme_event() (#2015) * #1960 enhance_derive_extreme_event: start a draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: add tests and documentation * #1960 enhance_derive_extreme_event: update NEWS * #1960 enhance_derive_extreme_event: fix links * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event: add example * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event:add example and tests for event-specific modes * #1960 enhance_derive_extreme_event: add ignore_event_order argument * #1960 enhance_derive_extreme_event: fix spelling * #1960 enhance_derive_extreme_event: use correct input dataset * #1960 enhance_derive_extreme_event: improve printing of event objects * #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars * #1960 enhance_derive_extreme_event: add description field * #1960 enhance_derive_extreme_event: address QC comments * #1960 enhance_derive_extreme_event: update man pages * #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml * #1960 enhance_derive_extreme_event: style files * chore: #1960 properly formatted testthat * chore: #1960 fix lint --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079) * Closes #2068 Updated `traceability_vars` to `set_values_to` * Clarify the explanation for the traceability_vars replacement * Closes #2083 bug adpp and adpc still using admiraltest (#2086) * fix: #2083 using pharmaversesdtm * fix: #2083 using pharmaversesdtm * chore: #2083 renaming datasets * chore: #2083 removing admiral prefix * chore: #2083 removing admiral suffix * chore: #2083 remove admiral suffix * chore: remove admiral prefix * Closes #1859 metadata updated for DAIDs in xlsx file (#2060) * 1859 metadata updated for DAIDs in xlsx file * 1859 metadata for DAIDs finalised * 1859 update data.r for atoxgr_criteria_daids * 1859 update man files * 1859 fix spelling * 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests * 1859 update man pages * 1859 fix STYLER issue * 1859 fix SPELLING * 1859 fix LINTR * 1859 Fix LINTR and add more unit tests * 1859 added Acidosis and Alkalosis and more unit tests * 1859 added more tests and partiallyy update gradin vignette * 1859 all unit tests added * 1859 fix STYLER * 1859 use signif function in metadata * 1859 use signif function in ncictcaev4 and v5 metadata * Update unit test for Cal (Ionized) to test missing ANRHI Co-authored-by: Zelos Zhu <[email protected]> * Fix unit test for Cal (Ionized) Low for missing ANRLO. Co-authored-by: Zelos Zhu <[email protected]> * Add units to description of Glucose Nonfasting, High Co-authored-by: Zelos Zhu <[email protected]> * Add unit to description of Glucose fasting, High Co-authored-by: Zelos Zhu <[email protected]> * Fix typo in description of Triglycerides, Fasting, High for Grade 3 Co-authored-by: Zelos Zhu <[email protected]> * 1859 address last QC comments on unit tests * 1859 update NEWS file * 1859 updated Vignette * 1859 Fix SPELLING * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * 1859 address QC comments * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * 1859 Fix STYLER issue * 1859 Fix example in function header * 1859 fix LINTR issue --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2050 Remove print fns from pkgdown Reference page (#2087) ref page updates * Closes #1697 add keep_source_vars arg@devel (#2070) * #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md. * Updated pkgdown.yml * Undoing renv.lock update * #1697 Updated default from `NULL` to `exprs(everything())` * #1697 Updated wordlist to include 'tidyselect' * #1697 Moved `select()` after `process_set_values_to()` * #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()` * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_extreme_records.R Co-authored-by: Zelos Zhu <[email protected]> * #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()` * #1697 Updated 'Details' section to include `keep_source_vars` --------- Co-authored-by: Zelos Zhu <[email protected]> * missing reroute to get started page * #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082) * #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation. * #1995 Chore: roxygen * #1995 chore:spellcheck and roxygen * #1995 updates to readme with release schedule and 1.0. * grammar fix in readme --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2028 removed erroneous section. updating rules section (#2088) * docs: #2028 removed erroneous section. updating rules section * docs: #2028 news and wordsmithing * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * docs: #2028 lite explanation of h.i. rule --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092) * feat: #2091 did that work? * chore: #2091 address errors * fixed deprecation warning * deprecation for analysis_var --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: StefanThoma <[email protected]> * Fix for Get Started on Webpage (#2093) Update _pkgdown.yml * update readme with admiral release schedule (#2095) Co-authored-by: Zelos Zhu <[email protected]> * feat: #2034 add testthat file * chore: #2034 styler * Update devel (#2133) * admiral v0.12.0 (#2094) * Closes #1950 following deprecation process, update Description version and news.md * updating documentation to fix the warnings * added the new tests for minutes and seconds options * Removing references in deprecated functions. * updated comments and applied test_that format * conflicts resolved * Closes #1941 authors contributors@devel (#1967) * Initial edit to `_pkgdown.yml` for #1941 * #1941 re-labelling authors and contributors * #1941 update to enact decision of team regarding who are authors and contributors. * #1941: Chore (spellcheck and man pages and NEWS.md update) * #1941 chore: further updates to spellcheck * #1941: chore: fix space after commas. move some acknowledgees to contributors. link README in authors page. * #1941 chore: roxygenize --------- Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> * Closes #1228 produce bmi records for more visits (#1957) * feat: #1228 Produce BMI records for more visits: Add constant_height parameter * feat: #1228 Produce BMI records for more visits: Update to use constant_by_vars as switch and update examples with more detail. * docs: #1228 Produce BMI records for more visits: Fix typo in NEWS * feat: #1228 Produce BMI records for more visits: Update ADVS template and vignette. * doc: #1228 Produce BMI records for more visits: Add backticks to variable. --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #1695 Establish codeowners (#1973) feat: #1695 add gordon and jeff as codeowners Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> * Closes #1974 Swapping out deprecated assertions (#1975) * feat: #1974 try swapping all deprecated assertions * chore: #1974 fix parsing issue that caused vignettes to crash * chore: #1974 simplify by_vars requirement Co-authored-by: Kangjie Zhang <[email protected]> * chore: #264 move assertion to different line --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#1986) renv update from pharmaverse/admiralci Co-authored-by: dgrassellyb <[email protected]> * Catch devel up to Admiral v0.11.1 (#1997) (#1999) Admiral v0.11.1 (#1997) * [actions skip] Add/Update README.md for patch * Closes #1962 #1969 admiral 0.11.1 hotfix for get started link, derive_param_tte, derive_vars_joined (#1987) * feat #1962 #1969 param_tte and get started fix * forgot to add updated DESCRIPTION * chore: #1962 thought crossing was dplyr * chore: #1962 account for new assertions * fix: #1962 was missing the reassignment piece? * fix: #1966 crude answer * feat: #1966 potential way of warning users of null new_vars * fix: #1966 add appropriate assertions to get check to go through * fix: #1966 appropriate function fix for order * fix: #1966 vignette named order expression * chore: #1966 try something * chore: #1966 optionality of expressions is tricky * feat: #1966 undo derive_joined stuff * chore: run styler --------- --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Initiate a Stale bot for Issue Triaging (#1992) * Create stale_bot.yml * Update and rename stale_bot.yml to stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Update stale-bot.yml * Closes #1927 derive param tte@devel (#2000) Removed incorrect reference of start_imputation_flag Co-authored-by: Ben Straub <[email protected]> * Closes #1989 Link Fix in `README.md` (#1994) * Update README.md * Update WORDLIST * Update README.md * Update WORDLIST * chore: #1989 spelling --------- Co-authored-by: Ben Straub <[email protected]> * Closes #1856 Removed the higher order file (#2008) #1856 Removed the higher order file * Update templates.yml (#2026) * Closes #2001 Added processing for missing age_units in `compute_age_years` (#2009) * #2001 added processing for missing age_units in `compute_age_years` * #2001 Chore: styler * #2001 chore: lint * #2001 chore: fix broken links * #2001 - removed for loop, changed unit in `derive_vars_aage`, restored `docs/pkgdown.yml`. * #2001 chore: Fixed docs link * #2001 chore: styler * #2001 implemented prop[er deprecation strategy for `age_unit` in `derive_vars_aage` and added extra test for `age_unit` * #2001 Update NEWS.md as per suggestiom Co-authored-by: Ben Straub <[email protected]> * Update R/compute_age_years.R with correct backquoting Co-authored-by: Zelos Zhu <[email protected]> * #2001 version change in deprecation * #2001 insert parenthesis in NEWS.md Co-authored-by: Ben Straub <[email protected]> * #2001 chore: roxygen --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1979 Add a flag_all function argument to enhance `derive_var_extreme_flag()` (#2024) * feat: #1979 added the necessary flag_all function argument * feat: #1979 modify check_type to supppress warnings for flag_all = TRUE * chore: #1979 run lintr/styler * chore: #1979 add news blurb * typo * chore: #1979 add additional tests and add roxygen details * chore: #1979 adopt feedback from review * chore: #1979 run styler --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #123 Add Edoardo to status check (#2031) fix: https://github.com/pharmaverse/admiralci/issues/123 add Edoardo to status check * Closes #2014 derive_var_shift change na_val@devel (#2032) * #2014 `na_val` deprecated and `missing_value` inserted into `derive_var_shift`. * #2014 - Update `NEWS.md`. * #2014 - update tests and write deprecation parameter test * #2014 - run required tasks for PR --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2012_derive_vars_dy (#2013) * derive dy_vars by argument .name in across (#2012) use named vector to avoid the variabes end with `_temp` in input dataset * test no error for variable end with `_temp`(#2012) * styled file * add update information for #2012 --------- Co-authored-by: Daniel Sjoberg <[email protected]> * Closes #1966 address derive_vars_joined bugs (#2016) * feat: #1966 make our check_type consistent * feat: #1966 hacky solution to null new_vars .join problem * chore: #1966 inserted line in wrong place * feat: #1966 add news blurb for what was done * feat: #1966 add tests * chore: #1966 lintr * chore: #1966 swap appropriate order selection and restore check_type arg * chore: #1966 looks like that fixed it * feat: #1966 issue warning for dataset_add naming conflicts when `new_vars` is NULL * chore: #1966 clean up for readability * chore: #1966 restore original replace_values_by_names * chore: #1966 add additional test to demonstrate how order vars were fixed/selected * feat: #1966 adopt feedback for error messaging of naming conflicts --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2037 deprecate `dataset_expected_obs` for `dataset_ref` in respective functions (#2039) feat: #2037 deprecate `dataset_expected_obs` for `dataset_ref` Co-authored-by: Zelos Zhu <[email protected]> * Close #1940 Removing unnecessary runtime development-related dependencies (#1978) * feat: #1940 try removing dev deps * chore: #1940 still needs knitr * #1940 diffdf needed for all the testing stuff * chore: #1940 add back rmarkdown Co-authored-by: Adam Foryś <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #1984 Allowing missing trt end date in `derive_var_ontrtfl()` (#2029) * #1984 allowing missing trt end date * Update derive_var_ontrtfl.R * Update derive_var_ontrtfl.R * Increment version number to 0.12.0.9000 * updating version numbers...oops! * Update test-derive_var_ontrtfl.R * Closes #1984 Addressing missing treatment start dates in `derive_var_ontrtfl()` (#2048) addressing missing treatment start dates * Propagate renv.lock from pharmaverse/admiralci (#2046) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci * Update .Rbuildignore * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> Co-authored-by: Adam Foryś <[email protected]> * Closes #2033 `derive_var_ontrtfl(span_period)` arg updated to accept T/F (#2044) * span_period arg update * Update derive_var_ontrtfl.R * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_var_ontrtfl.R Co-authored-by: Zelos Zhu <[email protected]> * remove space for lintr --------- Co-authored-by: Zelos Zhu <[email protected]> * add admiral src to test codespaces * Revert "add admiral src to test codespaces" This reverts commit 4a60be0d83e5bd9503eb74610160ece31ef86b7e. * Propagate renv.lock from pharmaverse/admiralci (#2058) renv / codespaces update from pharmaverse/admiralci Co-authored-by: galachad <[email protected]> * Closes #2020 chore: rename wt to weight in compute_egfr (#2045) * code updated * Chore #2020 go through checklist * update .lycheeignore * update .lycheeignore * adjusted templates * chore: removed links from .lycheeignore * chore: #2020 removing file --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2053 Typo in the example `impute_dtc_dt` (#2056) Closes #2053 Typo in the example impute_dtc_dt * update `impute_dtc_dtm` to `impute_dtc_dt` in derive_date_vars.R * update derive_date_vars.Rd Co-authored-by: Zelos Zhu <[email protected]> * Closes #2038 Attach See also to compute functions (#2062) Doc: #2038 Attach See also to compute functions Co-authored-by: Jeffrey Dickinson <[email protected]> * Closes #2042 fix compute_dtf bug (#2047) * feat: #2042 needs to incorporate date portion and location of the double hyphen to parse out correctly * feat: #2042 add appropriate logic for date-portions * chore: #2042 add news * feat: #2042 address month and day missing * feat: #2042 allow - for "Y" flag --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #1968 compute multiple variables in `derive_param_computed()` (#2036) * #1968 compute_multiple_vars: update arguments of derive_param_computed() * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: update documentation * #1968 compute_multiple_vars: style files * #1968 compute_multiple_vars: fix R-CMD checks * #1968 compute_multiple_vars: update error message of get_hori_data() * #1968 compute_multiple_vars: improve documentation * #1968 compute_multiple_vars: use deprecation badge * #1968 compute_multiple_vars: use deprecation badge * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * #1968 compute_multiple_vars: use @keywords internal * #1968 compute_multiple_vars: fix typo in NEWS.md --------- Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #1466 Unit test for `print.duplicates()` which closes test coverage gap (#2055) * feat: #2054 remove print.duplciates() * feat: #1466 add appropriate test for print.duplicates * chore: #1466 cleanup duplicate code * feat: #1466 use expect_snapshot() instead --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2040 Update admiral.test to pharmaversesdtm (#2057) * Chore: #2040 Update admiral.test to pharmaversesdtm * Chore: #2040 Update admiraltest to pharmaversesdtm: Update WORDLIST and run styler * #2040 Update admiral.test to pharmaversesdtm: udpate staged_dependencies.yaml * Chore: #2040 Update admiral.test to pharmaversesdtm: rename suppae and admiral_eg. * Chore #2040 Update admiral.test to pharmaversesdtm: Update test-call_derivation.R * Chore: #2040 Update admiral.test to pharmaversesdtm: Update create_query_data.R * Chore: #2040 Update admiral.test to pharmaversesdtm run documentation for create_query_data --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Propagate renv.lock from pharmaverse/admiralci (#2064) * renv / codespaces update from pharmaverse/admiralci * renv / codespaces update from pharmaverse/admiralci --------- Co-authored-by: galachad <[email protected]> * #2027 clarify reference_date in derive_vars_dy() (#2063) * change description * updated news.md * closes #2069 bug: EOSSTT derivation fix (#2073) #2069 bug: EOSSTT derivation fix Co-authored-by: Zelos Zhu <[email protected]> * Closes #2049 Date/Time Imputation Utilities are no Longer listed on pkgdown site (#2076) * utils_impute fns now internal * Update NEWS.md * adding meta.R entry back * Closes #1875 duration and interval time difference types update (#2075) * in progress * updated default to duration instead of interval * style * spelling updates * Update NEWS.md * added pharmaversesdtm Remotes call * Update DESCRIPTION * Update test-compute_duration.R --------- Co-authored-by: Ben Straub <[email protected]> * Closes #2078 swap out admiral_eg with eg (#2080) feat: #2078 swap out admiral_eg with eg Co-authored-by: Zelos Zhu <[email protected]> * Closes #1960 enhance derive_extreme_event() (#2015) * #1960 enhance_derive_extreme_event: start a draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: continue draft * #1960 enhance_derive_extreme_event: add tests and documentation * #1960 enhance_derive_extreme_event: update NEWS * #1960 enhance_derive_extreme_event: fix links * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event: add example * #1960 enhance_derive_extreme_event: style files * #1960 enhance_derive_extreme_event:add example and tests for event-specific modes * #1960 enhance_derive_extreme_event: add ignore_event_order argument * #1960 enhance_derive_extreme_event: fix spelling * #1960 enhance_derive_extreme_event: use correct input dataset * #1960 enhance_derive_extreme_event: improve printing of event objects * #1960 enhance_derive_extreme_event: rename keep_vars_source to keep_source_vars * #1960 enhance_derive_extreme_event: add description field * #1960 enhance_derive_extreme_event: address QC comments * #1960 enhance_derive_extreme_event: update man pages * #1960 enhance_derive_extreme_event: remove docs/pkgdown.yml * #1960 enhance_derive_extreme_event: style files * chore: #1960 properly formatted testthat * chore: #1960 fix lint --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2068 Updated `traceability_vars` to `set_values_to` (#2079) * Closes #2068 Updated `traceability_vars` to `set_values_to` * Clarify the explanation for the traceability_vars replacement * Closes #2083 bug adpp and adpc still using admiraltest (#2086) * fix: #2083 using pharmaversesdtm * fix: #2083 using pharmaversesdtm * chore: #2083 renaming datasets * chore: #2083 removing admiral prefix * chore: #2083 removing admiral suffix * chore: #2083 remove admiral suffix * chore: remove admiral prefix * Closes #1859 metadata updated for DAIDs in xlsx file (#2060) * 1859 metadata updated for DAIDs in xlsx file * 1859 metadata for DAIDs finalised * 1859 update data.r for atoxgr_criteria_daids * 1859 update man files * 1859 fix spelling * 1859 updated derive_var_atoxgr to read in DAIDS and create unit tests * 1859 update man pages * 1859 fix STYLER issue * 1859 fix SPELLING * 1859 fix LINTR * 1859 Fix LINTR and add more unit tests * 1859 added Acidosis and Alkalosis and more unit tests * 1859 added more tests and partiallyy update gradin vignette * 1859 all unit tests added * 1859 fix STYLER * 1859 use signif function in metadata * 1859 use signif function in ncictcaev4 and v5 metadata * Update unit test for Cal (Ionized) to test missing ANRHI Co-authored-by: Zelos Zhu <[email protected]> * Fix unit test for Cal (Ionized) Low for missing ANRLO. Co-authored-by: Zelos Zhu <[email protected]> * Add units to description of Glucose Nonfasting, High Co-authored-by: Zelos Zhu <[email protected]> * Add unit to description of Glucose fasting, High Co-authored-by: Zelos Zhu <[email protected]> * Fix typo in description of Triglycerides, Fasting, High for Grade 3 Co-authored-by: Zelos Zhu <[email protected]> * 1859 address last QC comments on unit tests * 1859 update NEWS file * 1859 updated Vignette * 1859 Fix SPELLING * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * Update NEWS.md following QC comment Co-authored-by: Ben Straub <[email protected]> * 1859 address QC comments * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * Update vignettes/lab_grading.Rmd Co-authored-by: Ben Straub <[email protected]> * 1859 Fix STYLER issue * 1859 Fix example in function header * 1859 fix LINTR issue --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2050 Remove print fns from pkgdown Reference page (#2087) ref page updates * Closes #1697 add keep_source_vars arg@devel (#2070) * #1697 Added `keep_vars_source` arg in `derive_extreme_records()`, added relevent unit tests and updated NEWS.md. * Updated pkgdown.yml * Undoing renv.lock update * #1697 Updated default from `NULL` to `exprs(everything())` * #1697 Updated wordlist to include 'tidyselect' * #1697 Moved `select()` after `process_set_values_to()` * #1697 Updated `keep_vars_source` to `keep_source_vars` in `derive_extreme_records()` * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update NEWS.md Co-authored-by: Zelos Zhu <[email protected]> * Update R/derive_extreme_records.R Co-authored-by: Zelos Zhu <[email protected]> * #1697 Reverted changes made to `derive_var_merged_exist_flag()` and updated `derive_extreme_records()` * #1697 Updated 'Details' section to include `keep_source_vars` --------- Co-authored-by: Zelos Zhu <[email protected]> * #1995 Update to add Sophie as Author and Stefan's R in Pharma presentation. (#2082) * #1995 Update to add Sophie as Autor and Stefan's R in Pharma presentation. * #1995 Chore: roxygen * #1995 chore:spellcheck and roxygen * #1995 updates to readme with release schedule and 1.0. * grammar fix in readme --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> * Closes #2028 removed erroneous section. updating rules section (#2088) * docs: #2028 removed erroneous section. updating rules section * docs: #2028 news and wordsmithing * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * Update vignettes/imputation.Rmd Co-authored-by: Zelos Zhu <[email protected]> * docs: #2028 lite explanation of h.i. rule --------- Co-authored-by: Zelos Zhu <[email protected]> * Closes #2091 fixing deprecation messaging in `derive_param_doseint()` (#2092) * feat: #2091 did that work? * chore: #2091 address errors * fixed deprecation warning * deprecation for analysis_var --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: StefanThoma <[email protected]> * Fix for Get Started on Webpage (#2093) Update _pkgdown.yml * update readme with admiral release schedule (#2095) Co-authored-by: Zelos Zhu <[email protected]> --------- Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]> * ignore notes r cmd checks (#2114) * admiral v0.12.1 (#2122) * Closes #2113 fix derive extreme records (#2121) * #2113 fix_derive_extreme_records: update function and tests * #2113 fix_derive_extreme_records: style files * [actions skip] Add/Update README.md for patch * Closes #2109 ADPP template program has x and y variables (#2110) * #2109 ADPP template program has x and y variables: Update to use `derive_vars_merged()` * #2109 Doc: update NEWS for ADPP template change * ignore notes r cmd checks (#2114) --------- Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]> Co-authored-by: Ben Straub <[email protected]> * Closes #2112 add `type` to functions downstream of compute_duration() (#2118) * feat: #2112 add type to fxns downstream of compute_duration * feat: #2112 add test type argument for derive_vars_duration * styler and lintr * chore: #2112 adopt feedback * chore: #2112 add upversion on DESCRIPTION * chore: #2112 try inheritParams * chore: #2112 remove mention of default --------- Co-authored-by: Zelos Zhu <[email protected]> * Update README.md typo Co-authored-by: Ben Straub <[email protected]> --------- Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> --------- Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]> * remove merge conflict nonsense * forgot test suite * bad styling job from copy/paste * feat: #2034 add back new blurb for what occured --------- Co-authored-by: sadchla-codes <[email protected]> Co-authored-by: Sadchla Mascary <[email protected]> Co-authored-by: lomaxj1 <[email protected]> Co-authored-by: Jennifer Lomax <[email protected]> Co-authored-by: Ben Straub <[email protected]> Co-authored-by: Edoardo Mancini <[email protected]> Co-authored-by: Mancini, Edoardo {MDBB~Welwyn} <[email protected]> Co-authored-by: Jeff Dickinson <[email protected]> Co-authored-by: Jeffrey Dickinson <[email protected]> Co-authored-by: Zelos Zhu <[email protected]> Co-authored-by: cicdguy <[email protected]> Co-authored-by: Kangjie Zhang <[email protected]> Co-authored-by: pharmaverse-bot <[email protected]> Co-authored-by: dgrassellyb <[email protected]> Co-authored-by: GitHub Actions <[email protected]> Co-authored-by: SyedMubasheer <[email protected]> Co-authored-by: Daniel Sjoberg <[email protected]> Co-authored-by: asha-gsk <[email protected]> Co-authored-by: Sophie Shapcott <[email protected]> Co-authored-by: ynsec37 <[email protected]> Co-authored-by: Adam Foryś <[email protected]> Co-authored-by: galachad <[email protected]> Co-authored-by: Daphne Grasselly <[email protected]> Co-authored-by: StefanThoma <[email protected]> Co-authored-by: Stefan Bundfuss <[email protected]> Co-authored-by: Ross Farrugia <[email protected]> Co-authored-by: Gordon Miller <[email protected]> Co-authored-by: G Gayatri <[email protected]> Co-authored-by: Daphné Grasselly <[email protected]>

ynsec37 added 2 commits July 17, 2023 09:50

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

4c6d37d

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

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

28382b1

ynsec37 force-pushed the #2012_derive_vars_dy@devel branch from 2ade808 to 28382b1 Compare July 17, 2023 03:48

ynsec37 marked this pull request as ready for review July 17, 2023 03:52

ynsec37 marked this pull request as draft July 17, 2023 03:57

ynsec37 closed this Jul 17, 2023

ynsec37 reopened this Jul 17, 2023

ynsec37 closed this Jul 17, 2023

ynsec37 reopened this Jul 17, 2023

ynsec37 marked this pull request as ready for review July 17, 2023 04:06

ynsec37 marked this pull request as draft July 17, 2023 04:06

ynsec37 changed the title ~~Closes #2012~~ Closes wrong pull requests Jul 17, 2023

ynsec37 closed this Jul 17, 2023

ynsec37 reopened this Jul 17, 2023

ynsec37 changed the title ~~Closes wrong pull requests~~ Closes #2012_derive_vars_dy Jul 17, 2023

ynsec37 marked this pull request as ready for review July 17, 2023 04:18

ynsec37 mentioned this pull request Jul 17, 2023

Bug: derive_vars_dy() return error when input dataset with columns end with "temp" #2012

Closed

manciniedoardo requested a review from ddsjoberg July 19, 2023 13:22

ddsjoberg added 2 commits July 23, 2023 19:57

Merge branch 'devel' into #2012_derive_vars_dy@devel

0861025

styled file

8d6ca42

Merge branch 'devel' into #2012_derive_vars_dy@devel

417d195

Merge branch 'devel' into #2012_derive_vars_dy@devel

73cb018

bms63 reviewed Jul 26, 2023

View reviewed changes

add update information for pharmaverse#2012

f6c00c4

bms63 linked an issue Jul 28, 2023 that may be closed by this pull request

Bug: derive_vars_dy() return error when input dataset with columns end with "temp" #2012

Closed

Merge branch 'devel' into #2012_derive_vars_dy@devel

4e2c866

ddsjoberg approved these changes Aug 1, 2023

View reviewed changes

ddsjoberg merged commit 01c6be7 into pharmaverse:devel Aug 1, 2023
20 checks passed

ynsec37 deleted the #2012_derive_vars_dy@devel branch December 1, 2023 04:49

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Closes #2012_derive_vars_dy #2013

Closes #2012_derive_vars_dy #2013

ynsec37 commented Jul 17, 2023 •

edited by ddsjoberg

Loading

ynsec37 commented Jul 17, 2023

ddsjoberg commented Jul 24, 2023

ddsjoberg commented Jul 24, 2023 •

edited

Loading

ynsec37 commented Jul 25, 2023

bundfussr commented Jul 25, 2023

ddsjoberg commented Jul 25, 2023

ynsec37 commented Jul 26, 2023

bundfussr commented Jul 26, 2023

bundfussr commented Jul 26, 2023

bms63 commented Jul 26, 2023

bms63 left a comment

ynsec37 commented Jul 26, 2023 •

edited

Loading

ddsjoberg left a comment

ynsec37 commented Aug 1, 2023

Closes #2012_derive_vars_dy #2013

Closes #2012_derive_vars_dy #2013

Conversation

ynsec37 commented Jul 17, 2023 • edited by ddsjoberg Loading

ynsec37 commented Jul 17, 2023

ddsjoberg commented Jul 24, 2023

ddsjoberg commented Jul 24, 2023 • edited Loading

ynsec37 commented Jul 25, 2023

bundfussr commented Jul 25, 2023

ddsjoberg commented Jul 25, 2023

ynsec37 commented Jul 26, 2023

bundfussr commented Jul 26, 2023

bundfussr commented Jul 26, 2023

bms63 commented Jul 26, 2023

bms63 left a comment

Choose a reason for hiding this comment

ynsec37 commented Jul 26, 2023 • edited Loading

ddsjoberg left a comment

Choose a reason for hiding this comment

ynsec37 commented Aug 1, 2023

ynsec37 commented Jul 17, 2023 •

edited by ddsjoberg

Loading

ddsjoberg commented Jul 24, 2023 •

edited

Loading

ynsec37 commented Jul 26, 2023 •

edited

Loading