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@bms63 bms63 released this 08 Mar 16:41
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v0.10.0
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admiral 0.10.0

New Features

  • Using {testthat} 3rd edition for unit testing. This is stricter in
    that messages must be addressed and deprecated functions throw errors. (#1754)

  • New function consolidate_metadata() for consolidating multiple meta datasets
    into a single one (#1479)

  • New function compute_scale() for computing the average of a vector and
    transforming the result from a source to a target range. (#1692)

  • New ADPC template script available ad_adpc.R which creates PK Concentration
    Analysis Dataset (#849). This script includes formatting suitable for
    Non-Compartmental Analysis (ADNCA) (#851)

  • New function derive_expected_records() for adding expected records (#1729)

  • New function derive_extreme_event() for adding the worst or best observation
    for each by group as new records (#1755)

Updates of Existing Functions

  • Arguments analysis_var, keep_vars were added to derive_locf_records(),
    analysis_var allows to specify analysis variable, keep_vars keeps variables
    that need carrying the last observation forward other than analysis_var
    (e.g., PARAMN, VISITNUM) (#1636).

  • The function create_single_dose_dataset() adds support for
    expanding relative nominal time (e.g. NFRLT) used in Pharmacokinetic
    (PK) analyses. The new parameter nominal_time defaults as NULL
    and does not change the normal operation of the function. If a
    nominal_time is specified such as NFRLT (Nominal Relative Time
    from First Dose) then the nominal time is incremented by the
    interval specified in EXDOSFRQ for example for "QD" records the
    NFRLT is incremented by 24 hours, e.g. 0, 24, 48...(#1640).

  • create_single_dose_dataset() is also updated for values of
    EXDOSFRQ with units in days but expected values less than 24
    hours, such as "BID", "TID", and "QID". Previously these values of
    EXDOSFRQ may result in duplicate records where the day values are
    incremented but the time values are not (#1643)

  • The function derive_var_confirmation_flag() and filter_confirmation()
    gained the tmp_obs_nr_var argument. It helps flagging or selecting consecutive
    observations or the first or last observation in a by group. (#1724)

  • The functions derive_vars_merged(), derive_var_merged_cat(),
    derive_var_merged_character(), derive_var_merged_exist_flag(),
    derive_var_merged_summary(), and derive_vars_merged_lookup() were updated to
    allow renaming in the argument by_vars (#1680).

  • The units "min" and "sec" are added as valid values of out_unit in compute_duration() and derive_vars_duration() (#1647).

  • The function derive_vars_query() now includes a consistency check for
    QUERY_SCOPE and QUERY_SCOPE_NUM values. (#652)

  • Argument new_var in derive_param_extreme_event() is made optional. (#1630)

  • derive_vars_last_dose() no longer fails if USUBJID is not included in the
    input dataset. (#1787)

Breaking Changes

  • All function arguments which expected a list of quosures created by vars()
    are now expecting a list of expressions created by exprs(). For example,
    instead of by_vars = vars(STUDYID, USUBJID) by_vars = exprs(STUDYID, USUBJID) must be used now.

    To enable running old scripts using vars() in the admiral function calls
    admiral redefines the vars() function such that it returns a list of
    expressions. This can be disabled by the admiral option force_admiral_vars
    (see set_admiral_options()). Please note that this is a temporary solution
    and will be removed in a future admiral release. (#1627)

  • Function derive_param_tte() has been updated such that only observations are
    added for subjects who have both an event or censoring and an observation in
    dataset_adsl (#1576).

  • Function derive_var_disposition_status() has been deprecated, please use derive_var_merged_cat() instead (#1681).

  • Function derive_var_worst_flag() has been deprecated, in favor of slice_derivation()/derive_var_extreme_flag() (#1682)

  • Function derive_vars_disposition_reason() has been deprecated, in favor of derive_vars_merged()(#1683)

  • The following functions have been deprecated from previous {admiral} versions using the next phase of the deprecation process: (#1712)

    • derive_derived_param()
    • derive_param_first_event()
    • derive_vars_merged_dt()
    • derive_vars_merged_dtm()
    • derive_var_agegr_ema()
    • derive_var_agegr_fda()

  • The following functions, which were deprecated in previous {admiral} versions, have been removed (#1712):

    • derive_var_ady()
    • derive_var_aendy()
    • derive_var_astdy()
    • derive_var_atirel()
    • derive_vars_suppqual()
    • smq_select()
    • sdg_select()

  • The following parameters, which were deprecated in previous {admiral} versions, have been removed (#1712):

    • meddra_version, whodd_version, get_smq_fun and get_sdg_fun from the create_query_data() function
    • date_imputation, time_imputation and preserve parameters from date_source() function
    • filter parameter from derive_var_extreme_flag()

  • ADLB metadata data set called atoxgr_criteria_ctcv5 updated to remove unit check for
    HYPERURICEMIA as grade criteria based on ANRHI only. This metadata holds criteria for lab grading
    based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0 (#1650)

  • Renamed derive_var_confirmation_flag() and filter_confirmation() to
    derive_var_joined_exist_flag() and filter_joined() respectively (#1738).

Documentation

  • New vignette "Creating a PK NCA ADaM (ADPC/ADNCA)" (#1639)

  • New vignette "Hy's Law Implementation" (#1637)

  • New vignette "Creating Questionnaire ADaMs" (#1715)

  • The expected value for the derivation argument of restrict_derivation(),
    slice_derivation(), and call_derivation() is described now. (#1698)

  • Removed authors from function documentation, as we will now only be tracking an overall list of
    authors for admiral. (#1673)

  • Added an imputation example for create_single_source_dataset() in function documentation (#1408)(#1760)

  • Updates to examples for derive_var_age_years() and derive_vars_duration() (#1620)(#1634)

  • Increased the level of documentation for derive_var_age_years() to describe the data type of the newly created new_var column. (#970)

Various

  • Functions derive_vars_dtm() and derive_vars_dt() had a bug pertaining to imputations associated with NA values that has now been fixed (#1646)
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