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@bms63 bms63 released this 07 Jun 17:02
· 104 commits to main since this release
v1.1.0
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admiral 1.1.0

New Features

  • Added helper functions to derive_vars_merged() (get_flagged_records()) and derive_vars_query() (get_vars_query()) so that those can be called independently as per user's request. derive_vars_merged() function call results are not impacted by the change (#2441).

  • Error Messaging has been made more "user-friendly". (#2372)

  • New country_code_lookup() metadata added to decode countries based on ISO 3166 codes. (#2388)

Updates of Existing Functions

  • group_var (optional) parameter is added to derive_var_trtemfl() to derive TRTEMFL for AE data if the data are collected as one episode of AE with multiple lines. (#2302)

  • Templates for ADPC, ADPPK and ADPP are updated to handle urine records. (#2392)

  • create_single_dose_dataset() has been updated to error if the lookup_table contains duplicates. (#2247)

  • derive_vars_merged() and derive_vars_transposed() have a relationship argument added (the same as found in dplyr::*_join() functions) for users to specify what type of join (one-to-one, one-to-many, etc.) should take place. (#2247)

  • basket_select() function updated to add ... argument to allow other qualifiers to be passed to user-defined function specified in get_terms_fun() argument for function create_query_data(). (#2265)

  • Messaging updated for derive_extreme_event() to improve clarity around duplicates. #2405

  • The id_vars argument was added to derive_vars_transposed() and derive_vars_atc() to allow additional variables, beyond those in by_vars, to uniquely identify records in the dataset_merge argument. (#2325)

  • Update PK Programming vignette and templates for ADPC and ADPPK for the nominal time formula NFRLT to reduce duplicate records in dose expansion with create_single_dose_dataset(). (#2426)

  • Template for ADSL updated so that EOSSTT is assigned as "ONGOING" when no study completion rows exist yet in DS. (#2436)

  • The slice_derivation() function was updated such that it works now when
    called in a function where objects from the function environment are used.
    (#2244)

Breaking Changes

  • The following function arguments are entering the next phase of the deprecation process: (#2299)

    • compute_egfr(wt)
    • consolidate_metadata(check_keys)
    • derive_expected_records(dataset_expected_obs)
    • derive_locf_records(dataset_expected_obs)
    • derive_extreme_event(ignore_event_order)
    • derive_vars_merged(match_flag, new_var, analysis_var, summary_fun)
    • derive_param_computed(analysis_value, analysis_var)
    • derive_param_exposure(filter, analysis_var, summary_fun)
    • derive_summary_records(filter)
    • derive_extreme_records(filter)
    • derive_var_joined_exist_flag(first_cond, filter)
    • event_joined(first_cond)
    • filter_joined(first_cond, filter)

  • The following function arguments have reached the end of the deprecation process and been removed: (#2299)

    • dthcaus_source(traceability_vars)
    • date_source(traceability_vars)
    • derive_var_ontrtfl(span_period)
    • derive_var_shift(na_val)
    • derive_vars_aage(unit)

Documentation

  • Documentation for derive_extreme_event() has been updated to include a description for the value of derive_extreme_event() when keep_source_vars = NULL. (#2398)

  • The "Visit and Period Variables" vignette was updated and refactored to include example code to create a period reference dataset. (#2321)

  • The documentation of derive_vars_merged() function is updated to describe that the check_type argument is ignored (an error is issued) if order is not specified. (#2326)

  • The "User Guides" section has been reorganized. A new "Programming Concepts and Conventions" vignette was also added to provide more context and information around common {admiral} behaviors and ways of working. (#2395)

  • The "Get Started" section has been revamped, placing greater focus on material that may help users familiarize themselves with {admiral}. There are now new sections showcasing the various types of {admiral}
    functions and some of the more advanced topics have been moved to the new "Programming Concepts and Conventions" vignette. (#2395)

  • The Examples section of derive_param_computed() now contains a new item showcasing how to create a derived parameter in the case that a variable contributing to the derived parameter has some/all of its values missing. (#2338)

Various

  • Templates and vignettes do not add or populate AVALC for BDS-findings datasets where the information contained in AVALC would be redundant with AVAL. (#2442)

  • The function dplyr::transmute() is superseded in favor of dplyr::mutate(.keep = "none"). Consequently, all the admiral functions that utilized the former have been updated accordingly. (#2274)

  • The templates for ADPP and ADPC are updated for missing variables (#2308) and to make ATPT and ATPTN consistent. (#2328)

  • ADLB template updated to make PARAM consistent for PARAMCD values "BASO" and "LYMPH". (#2327)

Developer Notes
  • In the previous version, renv was the default framework used to manage package dependencies. Now, we use devtools as our main package manager (some changes also occurred for admiralci workflows).
    There is a possibility to get package dependency versions used for the workflows to ensure local reproducibility. For this, you need to go under the latest action summary in your current PR. You can see a deps artifact. For each version of R used for R CMD CHECKS jobs, there is an associated renv.lock file (under the deps artifact).
  • Splitting out R and test files for date/time functions for cyclomatic complexity refactor (#2340)(#2339)
  • Created three unit tests for get_summary_records(). (#2304)
  • Created unit tests for developer internal function get_imputation_target_date() (#2378)
  • Modified date/time unit tests to use unified example (#2424)
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