admiral 1.0.0

admiral 1.0.0

New Features

• The new function derive_vars_extreme_event(), which works as derive_extreme_event()
  but adds variables instead of a parameter. (#2138)

• The new function derive_var_merged_ef_msrc() is provided to add a flag
  indicating if one of the conditions in one of multiple source datasets is
  fulfilled. (#1728)

• New global option created signif_digits and added to set_admiral_options() to
  handle floating point issue, the value is set to 15, and is used with the base R
  function signif() when comparing 2 numeric values. This is implemented in admiral
  functions derive_var_atoxgr_dir() and derive_var_anrind(). (#2134)

  For more information, please see blog: How admiral handles floating points

• The new function derive_vars_computed() is provided which has the same
  functionality as derive_param_computed() but instead of adding the computed
  values as a new parameter, adds it as a new variable. (#2178)

Updates of Existing Functions

• Fixed a bug in compute_tmf() where the time imputation flag was being incorrectly
  populated when any of the existing time components (hour, minute and/or second) of the date
  character vector ('--DTC'), was imputed. (#2146)

• derive_extreme_records(), derive_var_extreme_flag(),derive_vars_joined() and derive_vars_merged() were enhanced with the arguments true_value and false_value to align with preexisting functions that had similar functionality. (#2125)

• restrict_derivation() now allows {dplyr} functions like mutate() in the
  derivation argument. (#2143)

• derive_summary_records(), derive_var_merged_summary(), and get_summary_records()
  were enhanced such that more than one summary variable can be derived, e.g.,
  AVAL as the sum and ADT as the maximum of the contributing records. (#1792)

• derive_summary_records() was enhanced with the following arguments: dataset_add (required), dataset_ref (optional), missing_values (optional). These arguments respectively, generate summary variables from additional datasets, retain/add specific records from a reference dataset, and impute user-defined missing values. Note that dataset_add can be set to the same value as dataset if a different additional dataset is not required. derive_param_exposure() was enhanced with dataset_add as well. (#2142)

• The missing_values argument was added to derive_var_merged_summary(). It
  allows to define values for by groups, e.g., subjects which are not in the
  additional dataset. (#2230)

• The argument dataset is now optional for derive_summary_records() and derive_param_exposure(). (#2142)

• The "joined" functions (derive_vars_joined(), derive_var_joined_exist_flag(),
  filter_joined(), and event_joined()) were unified: (#2126)

  • The dataset_add and filter_add arguments were added to
    derive_var_joined_exist_flag() and filter_joined().
  • The filter argument was renamed to filter_join in
    derive_var_joined_exist_flag() and filter_joined().
  • The tmp_obs_nr_var, the join_type, the first_cond_lower, and the
    first_cond_upper arguments were added to derive_vars_joined().
  • In derive_var_joined_exist_flag(), filter_joined(), and event_joined()
    the first_cond argument was renamed to first_cond_upper and the
    first_cond_lower argument was added.
  • In all "joined" functions the filter_add argument is applied to the
    additional dataset grouped by by_vars and the filter_join argument is
    applied to the joined dataset grouped by the observations from the input
    dataset. I.e., summary functions like all() or any() can be used.

• The tmp_event_nr_var argument was added to derive_extreme_records() to
  allow more control of the selection of records. It creates a temporary variable
  for the event number, which can be used in order. (#2140)

• signif_dig argument added to both derive_var_atoxgr_dir() and derive_var_anrind()
  functions with default value set to general option signif_digits. The new argument to
  these functions handles any floating point issues. (#2134)

• Fixed a bug in derive_vars_period() where the function was throwing an error whenever dataset_ref contained variables that were neither key variables, nor APERIOD, ASPER, APHASEN, nor mentioned in the new_vars argument. (#2231)

• compute_duration(), derive_vars_duration(), derive_vars_aage() now accepts more terms for the in_unit, out_unit, and age_unit arguments (#2255)

• Updated the unit test for derive_var_obs_number(). The new test checked the derivation of the default and customized new_var,
  sorting with the the missing value and expected conditions. (#2260)

• The check for existence of TERMNUM/TERMCHAR in queries dataset is now less strict depending on values of SRCVAR for derive_vars_query() (#2264)

• DAIDS grading criteria fixed for Grade = 0 for TERM = "Absolute Lymphocyte Count, Low", criteria was AVAL <= 0.65, now corrected to AVAL >= 0.65 (#2284).

• A bug in derive_extreme_event() was fixed. The condition field is no
  longer ignored if mode is specified for event() (#2291).

• A bug in derive_vars_joined() was fixed. The function no longer fails if
  renaming is used in by_vars and new_vars is not specified (#2289).

Breaking Changes

• {admiral} now only supports R >= 4.0.0

• In derive_extreme_records() the dataset_add argument is now mandatory. (#2139)

• In derive_summary_records() and get_summary_records() the arguments
  analysis_var and summary_fun were deprecated in favor of set_values_to.
  (#1792)

• In derive_summary_records() and derive_param_exposure() the argument filter was renamed to filter_add (#2142)

• In derive_var_merged_summary() the arguments new_var, analysis_var, and
  summary_fun were deprecated in favor of new_vars. (#1792)

• In derive_vars_merged(), the argument match_flag was renamed to exist_flag (#2125)

• The default value for the false_value argument in derive_extreme_records() was changed to NA_character_ (#2125)

• In consolidate_metadata(), the argument check_keys was renamed to check_type to align with other functions (#2184)

• In filter_joined() and derive_var_joined_exist_flag() (#2126)

  • the first_cond argument was deprecated in favor of first_cond_upper and
  • the filter argument was deprecated in favor of filter_join.

• In event_joined() the first_cond argument was deprecated in favor of
  first_cond_upper. (#2126)

• In derive_extreme_event(), the ignore_event_order argument was deprecated
  and the selection of the records was changed to allow more control. Before, the
  records were selected first by event and then by order. Now they are selected
  by order only, but the event number can be added to it.

  To achieve the old behavior update

order = exprs(my_order_var),
ignore_event_order = FALSE,

to

tmp_event_nr_var = event_nr,
order = exprs(event_nr, my_order_var),

and

order = exprs(my_order_var),
ignore_event_order = TRUE,

to

order = exprs(my_order_var),

• create_query_data() and derive_vars_query() were updated to rename variables in
  query data set as follows: (#2186)

  • TERMNAME to TERMCHAR
  • TERMID to TERMNUM

  Users need to adjust their get_terms() function accordingly.

• The following functions, which were deprecated in previous {admiral} versions, have been removed: (#2098)

  • 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()
  • derive_var_confirmation_flag()

• The following function arguments are entering the next phase of the deprecation process: (#2098)

  • compute_egfr(wt)
  • derive_extreme_records(filter)
  • derive_param_computed(analysis_value, analysis_var)
  • derive_var_shift(na_val)
  • derive_expected_records(dataset_expected_obs)
  • derive_var_ontrtfl(span_period)

• The derive_param_extreme_record() function has been superseded in favor of derive_extreme_event(). (#2141)

• The functions derive_var_dthcaus(), derive_var_extreme_dt(), and derive_var_extreme_dtm() have been superseded in favor of derive_vars_extreme_event(). (#2138)

Documentation

• The documentation of the by_vars and constant_by_vars argument was improved and unified across all functions where it is used. (#2137)

• The functions assert_db_requirements(), assert_terms(), assert_valid_queries(),
  extend_source_datasets(), filter_date_sources(), validate_basket_select(),
  validate_query() are no longer exported and have had documentation removed. (#2220)

• The function extract_duplicate_records() has been re-classified as an internal
  function, which means that the function still appears in our help pages but not
  on our website. (#2220)

• The "Generic Functions" vignette (now "Generic Derivations") was rewritten.
  Now it provides a more complete overview of the generic derivations, describe
  the common concepts, and makes it easier to find the appropriate function.
  (#2230)

• A way to standardize roxygen labels and descriptions for function arguments was implemented and tested. (#2034)

• A link to published CDISC Population PK (ADPPK) implementation guide was added. (#2161)

• Removed Deprecation section in Reference tab. Added new Superseded section in
  Reference tab. (#2174)

• Added a link to the previous versions of the website to the navigation bar. (#2205)

• The meaning of date_imputation = "mid" was clarified in the documentation of
  the imputation functions, e.g. derive_vars_dtm(). (#2222)

• Added an example derivation of DTHCGR1 to the ADSL vignette. (#2218)

• Moved Development Process from {admiraldev} to Contribution Model in the
  admiral website, updated GitHub strategy. (#2196)

• Added new drop downs in Get Started navigation bar- Getting Started, Admiral Discovery, Cheatsheet. Community removed from top. (#2217)

• All "Example Script(s)" sections in the User Guide vignettes were updated to point the user towards using use_ad_template("ADaM") rather
  than linking to the template in the code repository. (#2239)

• Handling of NA values was added to the documentation of the order argument
  for all functions. (#2230, #2257)