admiral 0.9.0

admiral 0.9.0

New Features

• The new function derive_vars_joined() adds variables from an additional
  dataset. The selection of the observations can depend on variables from both
  datasets. This can be used for adding AVISIT, AWLO, AWHI based on time
  windows and ADY or deriving the lowest value (nadir) before the current
  observation (#1448).

• New function derive_var_trtemfl() for deriving treatment emergent flags (#989)

• The new function chr2vars() turns a character vector into a list of quosures
  (#1448).

• New function derive_var_relative_flag() for flagging observations before or
  after a condition is fulfilled (#1453)

• New functions get_admiral_option() and set_admiral_options() to allow more
  flexibility on common function inputs; e.g. like subject_keys to avoid several
  find and replace instances of vars(STUDYID, USUBJID). (#1338)

• The new function create_period_dataset() for creating a reference dataset
  for subperiods, periods, or phases from the ADSL dataset was added. The
  reference dataset can be used to create subperiod, period, and phase variables
  in OCCDS and BDS datasets. (#1477)

• The new function derive_vars_period() adds subperiod, period, or phase
  variables to ADSL. The values for the new variables are provided by a period
  reference dataset. (#1477)

• New function derive_var_merged_summary() adds a variable of summarized
  values to the input dataset (#1564)

• A print() method was added for all S3 objects defined by admiral, e.g.,
  date_source(), dthcaus_source(), ... (#858)

• New metadata data set called atoxgr_criteria_ctcv5 which holds criteria for lab grading
  based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0

• Removed the {assertthat} dependency in {admiral} (#1392)

• Removed R Version 3.6 check in CI/CD workflows in favor of the three most recent versions: 4.0, 4.1 and 4.2. (#1556)

• The new function derive_locf_records() adds LOCF records as new observations.
  This can be used when the input dataset does not contain observations for missed
  visits/time points or when AVAL is NA for particular visits/time points (#1316).

• New function convert_na_to_blanks() to convert character NA to blanks (#1624)

Updates of Existing Functions

• Function derive_param_first_event() has been replaced by a more generalized derive_param_extreme_event() function with new argument mode allowing for the selection of either the "first" or "last" event record according to the conditions provided. Also the date_var argument has been replaced with the order argument instead. In addition, three new arguments new_var, true_value, and false_value have been added to allow the user to choose what variable is used to indicate whether an event happened, and the values it is given (#1317) (#1242).

• Argument ignore_time_for_ref_end_date was added to derive_var_ontrtfl(),
  which controls if time is considered for the condition if start_date is after
  ref_end_date + ref_end_window days (#989).

• derive_var_atoxgr_dir() default value of atoxgr_criteria_ctcv4 removed for
  parameter meta_criteria. Can now also choose atoxgr_criteria_ctcv5 for parameter
  meta_criteria, to implement NCI-CTCAEv5 grading criteria .

• Environment objects were consolidated into a single admiral_environment object under R/admiral__environment.R. (#1572)

• The default value of the keep_source_vars argument in
  create_single_dose_dataset() was updated such that it takes the values of the
  other arguments into account and the start_datetime and end_datetime
  arguments are optional now (#1598).

• Function create_query_data() has been updated such that the dictionary
  version is stored in the output dataset (#1337).

Breaking Changes

• Function derive_param_first_event() has been deprecated. Please use derive_param_extreme_event() with the order argument instead of the date_var argument (#1317).

• Functions smq_select() and sdg_select() have been deprecated and replaced with basket_select(). In the create_query_data() function, meddra_version and whodd_version argument has been replaced by version and get_smq_fun and get_sdg_fun argument by get_terms_fun. (#1597)

Documentation

• New vignette "Generic Functions" (#734)
• New vignette "Visit and Period Variables" (#1478)

Various

• Function derive_param_tte() had a bug that set ADT to NA when start_date
  was missing, which has now been fixed (#1540)

• Function derive_vars_merged() had an improperly formatted error message
  which has been corrected (#1473)

• Templates now save datasets as .rds instead of .rda (#1501)

• Function create_single_dose_dataset() no longer fails if the input dataset
  contains observations with dose frequency "ONCE" (#1375).