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admiral 1.3.0

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@bms63 bms63 released this 26 Jun 11:47
· 262 commits to main since this release
v1.3.0
d9c23ff

admiral 1.3.0

New Features

  • The documentation was enhanced: (#2585)

    • The default value of an argument is now displayed in the argument description.
    • For some complex functions each example has now a title, which is also shown in
      the TOC, and a description. This enabled adding more examples without losing
      readability. The output of the structured examples used for complex functions is
      displayed in the help pages in RStudio. The following existing functions
      (as well as any new functions added in this release) received this enhancement:
      • derive_extreme_event() (#2735)
      • derive_extreme_records() (#2585)
      • derive_param_computed() (#2701)
      • derive_param_tte() (#2704)
      • derive_summary_records() (#2707)
      • derive_var_extreme_flag() (#2752)
      • derive_var_joined_exist_flag() (#2729)
      • derive_var_trtemfl() (#2746)
      • derive_vars_crit_flag() (#2744)
      • derive_vars_dt() (#2715)
      • derive_vars_dtm() (#2715)
      • derive_vars_joined() (#2727)
      • derive_vars_merged() (#2727)
      • filter_joined() (#2729)

  • New function derive_vars_joined_summary() to derive summary variables from
    selected records of an additional dataset where the selection depends on
    variables from both the input dataset and the additional dataset. For example,
    the cumulative dose up to each adverse event in ADAE can be derived with the
    new function. (#2652)

  • New lab grading metadata for US (Conventional) units for the three grading criteria
    admiral already produces for SI units (#2557).

    • atoxgr_criteria_ctcv4_uscv (NCI-CTCAEv4 criteria)
    • atoxgr_criteria_ctcv5_uscv (NCI-CTCAEv5 criteria)
    • atoxgr_criteria_daids_uscv (DAIDs criteria)

Updates of Existing Functions

  • In derive_vars_joined(), the filter_add argument is now correctly applied for all join types, fixing an issue where it was ignored when join_type != "all". (#2682)

  • The function extract_duplicate_records() was updated to consider all variables in the input dataset for the by group if the by_vars argument is omitted entirely. (#2644)

  • In slice_derivation(), previously the derivation is not called for empty
    subsets, however this can lead to issues when the input dataset is empty. Now
    the derivation is called for all subsets. (#2645)

  • The examples section for the function derive_var_trtemfl() was enhanced to include a showcasing of all scenarios discussed in the following PHUSE White Paper on Treatment-Emergent AEs. (#2455)

  • derive_var_atoxgr_dir() updated to handle more than one unit in grading metadata. Related to providing US (Conventional) units for grading (#2557).

  • NCICTCAEv4 and NCICTCAEv5 grading criteria (atoxgr_criteria_ctcv4, atoxgr_criteria_ctcv4_uscv, atoxgr_criteria_ctcv5, atoxgr_criteria_ctcv5_uscv),
    updated to add terms "Acidosis" and "Alkalosis" (#2768).

  • The functions derive_summary_records() and derive_param_exist_flag()
    were updated to fix an issue where if a variable was in both dataset_add and dataset_ref, it was
    added to the new records even if it was not in by_vars. (#2664)

  • derive_var_atoxgr_dir() updated to handle more than one unit in grading metadata. Related to providing US (Conventional) units for grading. (#2557)

  • The background checks in derive_summary_records() were too restrictive: by_vars were expected in dataset although the code did not require it. This requirement has therefore been dropped. (#2686)

  • The functions derive_vars_joined(), derive_var_joined_exist_flag(), and
    filter_joined() produce correct results now when they are used with join_type = "before" or join_type = "after" and dataset and dataset_add differ or
    the filter_add argument is used. (#2863)

  • The function derive_locf_records() was updated to include two new arguments: id_vars_ref and imputation.
    The id_vars_ref argument allows users to select the variables to group by in the reference dataset (dataset_ref)
    when determining which observations to add to the input dataset. The imputation argument lets users decide whether
    to update analysis_var when its value is NA ("update" and "update_add"), or to add a new observation instead ("add"). (#2694) (#2680) (#2717)

  • derive_vars_dt(), derive_vars_dtm(), impute_dtc_dt(), impute_dtc_dtm(), convert_dtc_to_dt(), & convert_dtc_to_dtm() and related functions will now throw an error instead of a warning when highest_imputation = "Y" but neither min_date (when date_imputation = "first") nor max_dates (when date_imputation = "last") are specified. (#2654)

  • create_query_data() no longer issues warnings when basket_select() objects
    with custom arguments of length greater than one are used. (#2751)

  • The order argument in derive_var_joined_exist_flag() and filter_joined()
    is now optional unless join_type = "after", join_type = "before",
    first_cond_lower, first_cond_upper, or tmp_obs_nr_var are specified.
    (#2729)

Breaking Changes

  • derive_vars_dtm() issues a message alerting users to a coming change in
    admiral 1.4.0 where the default behavior of ignore_seconds_flag will be changed from
    FALSE to TRUE. (#2661)

  • Lab grading metadata atoxgr_criteria_ctcv4(), atoxgr_criteria_ctcv5() and atoxgr_criteria_daids() variable SI_UNIT_CHECK renamed to UNIT_CHECK. (#2557)

  • The values of the variable specified for tmp_obs_nr_var in
    derive_vars_joined(), derive_var_joined_exist_flag(), filter_joined() are
    now populated differently if there are multiple records in dataset or
    dataset_add for the same values of by_vars and order. Before each of these
    records was assigned a different value, i.e., the variable (together with
    by_vars) was a unique identifier. Now the value is the same for all these
    records. (#2683)

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

    Phase 1 (message)

    • call_user_fun() is deprecated and will have no replacement. (#2678)

    • 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)

      No functions or arguments in this Phase

Documentation

  • Improved documentation, error messages, and argument assertions of derive_vars_dt(), derive_vars_dtm(), impute_dtc_dt(), impute_dtc_dtm(), convert_dtc_to_dt(), & convert_dtc_to_dtm(). (#2654)

  • Added an example to the derive_vars_transposed() reference page to showcase how duplicates-related errors can arise when records in dataset_merge are not uniquely identified. (#2609)

  • Default value of type in derive_vars_aage() is now shown as interval to match the function behavior. (#2685)

  • The "Lab Grading" vignette was updated to correct some typos and make text easier to
    read (#2623) and updated to include new metadata for grading using US (Conventional) units. (#2557)

  • The "BDS Time-to-Event" vignette was updated to include SRCSEQ consistently. (#2658)

  • The template for ADAE and the OCCDS vignette were updated to include an example of the DOSEON and DOSEU variables (#2737).

  • The template for ADPC and vignette were updated to include an example of using DTYPE for imputed records (#2657).

  • The "Higher Order Functions" vignette was updated to showcase an example of two higher order functions used in combination. The documentation for each of the higher order functions was also corrected by removing the stated requirement that the derivation takes a dataset argument (#2656).

  • The 'Details' section of the derive_var_analysis_ratio() function and the 'Derive Analysis Ratio' section of the "Creating a BDS Finding ADaM" vignette were updated to include references to R2AyHI and R2AyLO. (#2548)

  • The derive_basetype_records() documentation was updated to clarify BASETYPE derivations. (#2545)

  • The derive_extreme_records() documentation was updated to clarify which variables are populated
    from dataset_ref for the new observations. (#2664)

  • The 'Assign PARAMCD, PARAM, PARAMN, PARCAT1' section of the "Creating a BDS Finding ADaM" vignette was updated to clarify PARAM to PARCAT1 mapping. (#2547)

  • The package documentation for (1) all CRAN-released versions starting from {admiral} 1.0.0 up until the current version and (2) the latest development version (listed under "main") are all now accessible using the "Versions" selector in the toolbar. (#2766)

Various

Developer Notes
  • Removed CODEOWNERS file from repo (#2674)
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