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admiral 1.2.0

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@bms63 bms63 released this 03 Jun 18:23
· 374 commits to main since this release
v1.2.0-fix
eb14ab4

admiral 1.2.0

New Features

  • New function derive_vars_cat() for deriving pairs of variables or more, e.g.
    AVALCATy & AVALCAyN. (#2480)
  • New function derive_vars_crit_flag() for deriving criterion flag variables
    (CRITy, CRITyFL, CRITyFN). (#2468)
  • New function transform_range() to transform values from a source range to a
    target range. (#2571)

Updates of Existing Functions

  • Added "message" as option for check_type argument in derive_var_obs_number() function. (#2481)

  • Added "message" as option for check_type argument in filter_extreme() function. (#2481)

  • Users can now specify how duplicate records are handled in derive_param_tte() using the check_type argument, with options including "error", "warning", "message", or "none", allowing for greater flexibility in managing duplicate data scenarios. (#2481)

  • The order argument has been added to event_source() and censor_source() and
    defaulted to NULL to allow specifying variables in addition to the date variable. This can be used to ensure the uniqueness of the select records if there is more than one record per date. (#2481)

  • NCICTCAEv5 grading criteria (atoxgr_criteria_ctcv5):

    • fix for TERM = "INR increased", criteria was wrongly using x ULN, for first part of criteria for grades 1 to 3. For example, ">2.5 x ULN" changed to ">2.5" for grade 3. (#2534).
    • when looking at abnormal baseline we now use BNRIND instead of comparing BASE with ANRHI, as ANRHI may differ within a subject and lab test due to data from different lab vendors. This effects 5 terms, namely, Alanine aminotransferase increased, Alkaline phosphatase increased, Aspartate aminotransferase increased, Blood bilirubin increased and GGT Increased. (#249)
    • derive_var_atoxgr_dir(): new argument abnormal_indicator to pass in value of BNRIND to indicate lab test is abnormal. This is only used for the 5 lab tests described above. (#249)

  • The keep_nas argument of derive_param_computed() was enhanced such that it
    is now possible to specify a list of variables for which NAs are acceptable.
    I.e., records are added even if some of the specified variables are NA.
    (#2510)

  • derive_param_tte() now provides a useful error message if in
    event_conditions or censor_conditions a dataset is referenced which is not
    specified in source_datasets. (#2519)

  • The derive_param_qtc() function accepts now both "ms" and "msec" as unit
    of the input parameters. (#2513)

  • In derive_vars_query() the error message was improved for the cases that
    some of the requested query variables are already present in the input dataset
    or that the queries dataset contains duplicates. (#2543)

  • derive_vars_atc() and create_single_dose_dataset() by_vars argument updated to use get_admiral_option("subject_keys") instead of USUBJID or STUDYID in bds_exposure.Rmd. (#2501)

  • The test scripts, R, and markdown files for create_single_dose_dataset() and occds.Rmd updated to include a STUDYID column because of get_admiral_option("subject_keys") update above. (#2501)

  • Update derive_vars_period() to make it work when there is only one new variable. (#2582)

  • A check was added to derive_vars_transposed() and derive_vars_atc() which
    stops execution if the records in dataset_merge or dataset_facm respectively
    are not unique. (#2563)

  • The functions derive_vars_joined(), derive_var_joined_exist_flag(),
    derive_extreme_event(), and filter_joined() were updated to reduce their
    memory consumption. As the new code increases the run-time, it is not used by
    default. To enable it the new admiral option save_memory has to be set to
    TRUE. (#2590)

  • The function compute_egfr() updated to allow missing values for sex which result in missing values for output. (#2612)

Breaking Changes

  • The following function arguments are entering the next phase of the deprecation process: (#2487) (#2595)

    Phase 1 (message)

    • derive_param_extreme_record() is deprecated and replaced by derive_extreme_event()
    • derive_var_dthcaus() is deprecated and replaced by derive_vars_extreme_event()
    • date_source() is deprecated and replaced by event()
    • dthcaus_source() is deprecated and replaced by event()
    • derive_var_extreme_dt() and derive_var_extreme_dtm() are deprecated and replaced by derive_vars_extreme_event()
    • get_summary_records() is deprecated. Please use derive_summary_records() with the dataset_add argument and without the dataset argument.

    Phase 2 (warning)

    No functions or arguments in this Phase

    Phase 3 (error)

    No functions or arguments in this Phase

    Phase 4 (removed)

    • consolidate_metadata(check_keys)
    • Removed at v1.1.1 compute_egfr(wt)
    • Removed at v1.1.1 derive_expected_records(dataset_expected_obs)
    • Removed at v1.1.1 derive_locf_records(dataset_expected_obs)
    • derive_extreme_event(ignore_event_order)
    • derive_vars_merged(match_flag)
    • derive_var_merged_summary(new_var, analysis_var, summary_fun)
    • Removed at v1.1.1 derive_param_computed(analysis_value, analysis_var)
    • derive_param_exposure(filter, analysis_var, summary_fun)
    • derive_summary_records(filter)
    • Removed at v1.1.1 derive_extreme_records(filter)
    • derive_var_joined_exist_flag(first_cond, filter)
    • event_joined(first_cond)
    • filter_joined(first_cond, filter)
    • In get_summary_records(), previously deprecated formal arguments analysis_var and
      summary_fun now removed from function, documentation, tests etc. (#2521)

Documentation

  • derive_locf_records() documentation example was fixed to display LOCF records. (#2461)

  • The "Find my function" and "Presentation Archive"" links were made more prominent in the website navigation bar. (#2536)

  • derive_var_joined_exist_flag() documentation updated with extra examples. (#2523)

  • In the derive_param_tte() documentation is was clarified which
    event/censoring is selected if there is more than one at the same date (for
    events the first one specified in event_conditions and for censoring the last
    one in censor_conditions). (#2639)

Various

  • Replace use of data("sdtm") with sdtm <- pharmaverse::sdtm in templates and vignettes. (#2498)
  • Remove dthcaus_source() calls in ADSL template because they are deprecated. (#2517)
  • Update ADEG template to flag ABLFL and ANL01FL based on DTYPE == "AVERAGE" records. (#2561)
Developer Notes
  • Created unit tests for developer internal function restricted_imputed_dtc_dt() (#2495)
  • Adopted data-raw/data R Package Convention (#2427, #2584)
  • compute_bsa() now uses the more common (but equivalent) version of the DuBois-DuBois formula for BSA. The results have not changed. (#2532)
  • Removed .devcontainer file (codespace) (#2524)
  • Restructured derive_adeg_parms.R and derive_advs_parms.R and related test files for easier reference (#2551)
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