General Issue: Changelog and Description Update for 0.8.0

[bms63]

Background Information

Starting off with fresh changelog is really helpful for keeping tracking of our changes. @pharmaverse/admiral what are you thoughts? Same structure as previous?

Also was going to increment the package description number from 0.7.0 to 0.8.0

Proposed new Changelog.

admiral 0.8.0

New Features

Updates of Existing Functions

Breaking Changes

Documentation

Various

admiral 0.7.0

New Features

• Updates to date/time imputation functions (Inconsistency of time_imputation default values #761):

  • convert_date_to_dtm() and convert_dtc_to_dtm() now have time_imputation = "00:00:00" as default

  • derive_vars_dt()now has flag_imputation = "auto" as default

• New functions for merging variables (Implement derive_merged_vars()-like functions #607):

  • derive_vars_merged() - Merge Variables from a Dataset to the Input Dataset
  • derive_vars_merged_dt() - Merge a (Imputed) Date Variable
  • derive_vars_merged_dtm() - Merge a (Imputed) Datetime Variable
  • derive_var_merged_cat() - Merge a Categorization Variable
  • derive_var_merged_exist_flag() - Merge an Existence Flag
  • derive_var_merged_character() - Merge a Character Variable

• create_query_data() is provided to create the queries
  dataset required as input for derive_vars_query() (Move read_query_data to admiral and enhance CQ query definition #606)

• create_single_dose_dataset() - Derives dataset of single dose from aggregate dose information (Create function to expand aggregate dosing in EX to single doese per row dataset #660)

• New functions for deriving first or last dates from multiple source datasets (Generalize derive_var_lstalvdt() #753):

  • derive_var_extreme_dtm() - Derive First or Last Datetime from Multiple Sources
  • derive_var_extreme_dt() - Derive First or Last Date from Multiple Sources

• New function derive_extreme_records() for adding the first or last
  observation within each by group to the dataset (Feature Request: Implement derive_extreme_records() #1042)

• New function derive_param_first_event(): Add a new parameter for the first
  event occurring in a dataset. (Feature Request: Implement derive_param_first_event() #1063)

• New function derive_param_exist_flag(): Add a new parameter indicating that
  a certain event exists in a dataset. (Feature Request: Implement derive_param_merged_exist_flag() #1064)

• New high order functions (Do we need a slice_derivation() function? #701):

  • restrict_derivation() - Execute a derivation on a subset of the input dataset
  • slice_derivation() - The input dataset is split into slices (subsets) and
    for each slice a derivation is called separately. Some or all arguments of the
    derivation may vary depending on the slice.

• filter_relative() - Selects observations before or after the observation
  where a specified condition is fulfilled. For example, all observations up to
  first disease progression. (Feature Request: Implement filter_relative() function #1023)

ADLB

• New ADLB template script available ad_adlb.R, specific ADLB functions developed and
  BDS Finding vignette has examples enhanced with ADLB functions. (Documentation: Update BDS Finding Vignette to include new functions #1122)

• derive_var_shift() - Derives a character shift variable containing concatenated shift in values based on user-defined pairing (Feature Request: derive_var_shift() #944)

• derive_var_analysis_ratio() - Derives a ratio variable based on user-supplied variables from a BDS dataset, e.g. ADLB. (Feature Request: derive_var_analysis_ratio() #943)

• derive_param_wbc_abs() - Adds a parameter for lab differentials converted to absolute values. (Feature Request: derive_param_wbc_abs #941)

ADPP

• New ADPP template script available ad_adpp.R which creates Pharmacokinetics Parameters Analysis Dataset (Create ADPP #850)

Updates of Existing Functions

• Datasets internal to the package have been renamed with prefix admiral_, e.g. adsl has been renamed to admiral_adsl. Corresponding SDTM datasets in {admiral.test} have also been renamed, e.g.dm to admiral_dm. These changes will impact examples,
  vignettes, unit tests and templates (Update all references to {admiraltest} data with prefix admiral_. #1108 and Suggestion: Rename {admiral} packaged ADaM Dataset #1088)

• When derive_vars_dtm_to_tm() was called for variables created by
  derive_vars_dtm() the function failed. This bug was fixed (derive_vars_dtm_to_tm() doesn't work after the usage of derive_vars_dtm() #1097).

• impute_dtc() - Fixed imputation bug. A user setting date_imputation = MID and
  preserve = FALSE would expect the date 2019---07 to be imputed to 2019-06-30,
  but the function was returning 2019-06-15. Now returns it correctly. This bug fix
  also addresses the issue in the downstream functions derive_vars_dt() and derive_vars_dtm(). (Bug: date imputation new preserve option not quite working as expected #1081)

• format_eoxxstt_default() - Updated to have a more meaningful parameter name i.e. the parameter that was x is now status (Update derive_var_disposition_status.R to have more meaningful argument #911)

Breaking Changes

• derive_var_lstalvdt() has been deprecated in favor of derive_var_extreme_dt() (Generalize derive_var_lstalvdt() #753).

• derive_vars_disposition_reason() now is updated such that the default is populating DCSREASP only when DSDECOD is equal to 'OTHER', which is consistent with ADaMIG_v1.3 (Update derive_disposition_reason() #886).

• derive_vars_suppqual() has been removed from {admiral} as adding supplementary qualifiers is now done in another package called {metatools} in a function called combine_supp() and is available on CRAN (Deprecate derive_vars_suppqual #950)

• The filter parameter in derive_var_extreme_flag() and
  derive_var_worst_flag() has been deprecated in favor of
  restrict_derivation() (Do we need a slice_derivation() function? #701).

• The following functions and parameters, which were deprecated in previous {admiral} versions, have been removed (Documentation: Remove previously deprecated functions #1056):

  • derive_agegr_ema()
  • derive_agegr_fda()
  • derive_disposition_dt()
  • derive_disposition_status()
  • derive_extreme_flag()
  • derive_worst_flag()
  • derive_obs_number()
  • derive_disposition_reason()
  • derive_var_basec()
  • derive_baseline()
  • derive_params_exposure()
  • derive_last_dose()
  • dataset parameter in lstalvdt_source and dthcaus_source

• The following functions were deprecated in favor of derive_vars_dy()
  (Decision on which "questioning" functions to deprecate? #1076):

  • derive_var_ady() - Derive Analysis Study Day
  • derive_var_aendy() - Derive Analysis End Relative Day
  • derive_var_astdy() - Derive Analysis Start Relative Day

• The following functions were deprecated in favor of derive_vars_merged_dtm()
  (Decision on which "questioning" functions to deprecate? #1076):

  • derive_var_trtedtm() - Derive Datetime of Last Exposure to Treatment
  • derive_var_trtsdtm() - Derive Datetime of First Exposure to Treatment

• The derive_var_disposition_dt() function was deprecated in favor of
  derive_vars_merged_dt() (Decision on which "questioning" functions to deprecate? #1076)

• The derive_var_atirel() function was deprecated, as it is deemed as too
  specific for admiral. Derivations like this can be implemented calling
  mutate() and case_when().

Documentation

• Additional explanation added to derive_param_* and derive_derived_param functions regarding which variables are populated in the additional rows (Documentation: Clarify variables populated by derive_param_*() functions #939)

• Updated derive_var_worst_flag() and derive_var_extreme_flag() vignettes to clarify their purpose (Clarify purpose of derive_worst_flag() #691)

• Added example of ASEQ derivation in ADCM to
  OCCDS vignette
  (Add derivation of ASEQ to ADCM script and OCCDS vignette #720)

• Examples have been added for format_reason_default(), format_eoxxstt_default(), extend_source_datasets() and filter_date_sources() (Ensure examples are included in all functions #745)

Various

• Naming convention of admiral.xxx packages change to admiralxxx from this point onwards (Change all references to <admiral.new> to <admiralnew> #968)

admiral 0.6.3

Address CRAN comments raised after submitting v0.6.2 (#946)

Definition of Done

Changelog updated in devel branch and description incremented.