admiral 0.7.1

• derive_vars_last_dose() no longer fails when a variable renamed in new_vars is supplied to the dose_date parameter (#1206)

• derive_vars_duration() updated to not display units when there is missing duration (#1207)

• derive_param_first_event() was updated (#1214) such that

  • AVAL is derived instead of AVALN and
  • all variables from the source dataset are kept

• slice_derivation() was updated such that it no longer fails if a slice is empty (#1309)

admiral 0.7.0

New Features

• Updates to date/time imputation functions (#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 (#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() (#606)

• create_single_dose_dataset() - Derives dataset of single dose from aggregate dose information (#660)

• New functions for deriving first or last dates from multiple source datasets (#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 (#1042)

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

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

• New high order functions (#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. (#1023)

ADLB

• New ADLB template script available ad_adlb.R, specific ADLB functions developed and
  BDS Finding vignette has examples enhanced with ADLB functions. (#1122)

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

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

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

ADPP

• New ADPP template script available ad_adpp.R which creates Pharmacokinetics Parameters Analysis Dataset (#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 (#1108 and #1088)

• When derive_vars_dtm_to_tm() was called for variables created by
  derive_vars_dtm() the function failed. This bug was fixed (#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(). (#1081)

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

Breaking Changes

• derive_var_lstalvdt() has been deprecated in favor of derive_var_extreme_dt() (#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 (#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 (#950)

• The filter parameter in derive_var_extreme_flag() and
  derive_var_worst_flag() has been deprecated in favor of
  restrict_derivation() (#701).

• The following functions and parameters, which were deprecated in previous {admiral} versions, have been removed (#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()
  (#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()
  (#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() (#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 (#939)

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

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

• Examples have been added for format_reason_default(), format_eoxxstt_default(), extend_source_datasets() and filter_date_sources() (#745)

Various

• Naming convention of admiral.xxx packages change to admiralxxx from this point onwards (#968)

First CRAN Release

#947 Address CRAN comments

* Split dev and user utilities

* Ignore man pages of dev utils when building pkg

* Don't generate Rd files for assertthat predicates

* Move assertthat checks to separate file

* Ensure docs have a `\value` field

* Remove example

* Remove 'Collate' field

* Add reference to description

* Add return value to documentation

* Bump version

* Update NEWS

* Add missing period

* Remove unused functions

* Remove `is_vars()`

* Fix typos

* Fix typos

* Optionally check if `dataset` is grouped

* Address lint line length issue

First CRAN Submission

Merge pull request #897 from pharmaverse/devel

Release v0.6.0

First Open Source Release

v0.5.0

Release v0.5.0

PHUSE EU Connect 2021 Workshop

v0.4.0

Release v0.4.0

External Testing

v0.3.0

Create v0.3.0 of admiral

Demo #3 (addendum)

Admiral package and admiral presentation for demo #3 on July, 8/9 2021.

Demo #3

Merge pull request #322 from Roche-GSK/devel

Version 0.2.0 addendum

Demo #2

Pre-release for beta testing after demo on May, 5th 2021.