admiral 0.12.0

admiral 0.12.0

New Features

• event_joined() events were added. They can be specified for the events
  argument in derive_extreme_event(). This allows to define events based on more
  than one observation, e.g., events which need to be confirmed by a second
  assessment. (#1960)

• atoxgr_criteria_daids.rda added, which holds metadata for Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events. You can find additional documentation here atoxgr_criteria_daids()

Updates of Existing Functions

• The functions derive_param_bmi() and derive_param_bsa() are updated to have the option of producing more values at visits when only weight is collected (#1228).

• The functions derive_var_age_years() and compute_age_years() are updated to return an NA age in the case that the age unit is missing. (#2001) The argument unit for derive_vars_aage() is also changed to age_unit for consistency between these age-related functions. (#2025)

• The derive_var_ontrtfl() function has been updated to allow for the column passed in ref_end_date to contain NA values. Previously, if the end date was NA, the row would never be flagged. Now, an NA value is interpreted as the treatment being ongoing, for example. (#1984)

• The function derive_var_extreme_flag() has a new function argument, flag_all that additionally flags all records if the first or last record is not unique. (#1979)

• The function derive_param_computed() was enhanced: (#1968)

  • The analysis_value and analysis_var arguments were deprecated in favor of
    set_values_to. This enables users to compute more than one variable.
  • The keep_nas argument was added. If it is set to TRUE, observations are
    created even if values contributing to the computed values are NA.

• The function derive_vars_dy() is updated to avoid potential error when the input dataset with columns ending with temp. (#2012)

• Argument keep_source_vars was added to derive_extreme_records() which
  specifies which variables in the new observations should be kept. (#1697)

• Templates, vignettes, and other uses of {admiral.test} SDTM data are updated to use {pharmaversesdtm} instead. (#2040)

• The traceability_vars argument in date_source() and dthcaus_source were deprecated in favor of set_values_to. The date_source() function creates a date_source object as input for derive_var_extreme_dt() and derive_var_extreme_dtm(),users can now define the traceability variables by assigning those variables to the set_values_toargument.Similarly, the dthcaus_source creates a dthcaus_source Object. (#2068)

• derive_extreme_event() was enhanced (#1960):

  • event_joined() events can be specified for the events argument. This
    allows to define events based on more than one observation, e.g., events
    which need to be confirmed by a second assessment.

  • The source_datasets argument was added to the function and the
    dataset_name field to event(). It can be used to define events based on
    a different dataset than the input dataset.

  • The keep_source_vars argument was added to the function and the
    keep_source_vars field to event(). It allows to select which variables
    should be kept for the selected observations.

  • The mode and order field were added to event(). They allow to select
    the first or last observation per by group if there are multiple observation
    fulfilling the event condition.

  • The ignore_event_order argument was added.

  • The description field was added to event(). It can be used to provide
    a description of the event in plain language.

• derive_var_atoxgr_dir() was enhanced (#1859):

  • Can now select atoxgr_criteria_daids in argument meta_criteria to create ATOXGRL and ATOXGRH based on Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events

  • New argument signif_dig added to control the number of significant digits to use when comparing 2 numeric values.
    (#2060)

Breaking Changes

• The compute_duration(type) argument added the "duration" type calculation, and this is the new default (previously "interval" differences were returned). See function help file for details on the difference between "duration" and "interval" calculations. (#1875)

• The following functions, which were deprecated in previous {admiral} versions, have been removed: (#1950)

  • derive_var_disposition_status()
  • derive_vars_disposition_reason()
  • format_eoxxstt_default()
  • format_reason_default()
  • derive_var_worst_flag()

• The following functions have been deprecated from previous {admiral} versions using the next phase of the deprecation process: (#1950)

  • derive_param_extreme_event()
  • derive_vars_last_dose()
  • derive_var_last_dose_amt()
  • derive_var_last_dose_date()
  • derive_var_last_dose_grp()
  • derive_var_basetype()
  • derive_var_merged_cat()
  • derive_var_merged_character()

• The arguments dataset_adsl in the function derive_param_exist_flag() and
  subject_keys have been deprecated versions using the next phase of the deprecation process. (#1950)

• The argument wt in the function compute_egfr() was deprecated in favor of weight using the first phase of the deprecation process. (#2020)

• The filter argument in derive_extreme_records() was deprecated in favor of
  the filter_add using the next phase of the deprecation process. (#1950)

• The analysis_value and analysis_var arguments in derive_param_computed()
  were deprecated in favor of set_values_to (#1968).

• The na_val argument in derive_var_shift() has been deprecated in favor of
  missing_value using the first phase of the deprecation process. (#2014)

• The dataset_expected_obs argument in derive_expected_records() and derive_locf_records()
  has been deprecated in favor of dataset_ref. (#2037)

• The span_period argument in derive_var_ontrtfl() has been updated to only accept
  TRUE or FALSE, where is previously accepted "Y" and NULL. (#2033)

Documentation

• Non-exported utility and print functions were previously listed on the admiral website reference page. They have been removed. (#2049, #2050)

• The description of the argument reference_date in the function derive_vars_dy()
  has been clarified to make it agnostic to start/end selection. (#2027)

• Date and Time Imputation User Guide/Vignette has section on preserving partial
  dates updated (#2028)

Various

• The list of package authors/contributors has been reformatted so that those who are actively maintaining the code base are now marked as authors, whereas those who made a significant contribution in the past are now down as contributors. All other acknowledgements have been moved to README section (#1941).

• derive_vars_joined() had two bugs with regards to duplicates messaging and when new_vars was set to NULL that have now been addressed (#1966).

• compute_dtf() had a bug with regards to imputing days to full date-time character strings. (#2042)