admiral 0.8.0

New Features

• get_summary_records() creates summary records e.g. derive analysis value (AVAL) from multiple records, only keeping the derived observations (#525)

• derive_param_framingham() adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score (#977)

• compute_qual_imputation() imputes values when qualifier exists in character result (#976)

• derive_vars_merged_lookup() maps lookup tables (#940)

• filter_confirmation() filters out confirmed observations
  (#1292) including supporting functions count_vals(), min_cond(), and
  max_cond().

• derive_var_confirmation_flag() derives a flag which
  depends on other observations of the input dataset (#1293)

• derive_var_atoxgr() derives lab toxicity/severity grade ATOXGR
  from ATOXGRL and ATOXGRH. ATOXGRL holds toxicity/severity grade for low lab values,
  and ATOXGRH holds toxicity/severity grade for high lab values.

• derive_var_atoxgr_dir() derives lab toxicity/severity grade for low
  lab values (ATOXGRL) or for high lab values (ATOXGRH). The grading is created from
  metadata.

• New metadata data set called atoxgr_criteria_ctcv4 which holds criteria for lab grading
  based on Common Terminology Criteria for Adverse Events (CTCAE) v4.0

Updates of Existing Functions

• list_tte_source_objects() gains a package parameter and is now exported (#1212)

• list_all_templates() and use_ad_template() gain a package parameter which
  can be used to indicate in which package to look for templates (#1205)

• Randomization Date RANDDT variable added to ADSL template and vignette (#1126)

• Renamed derive_derived_param() to derive_param_computed() and added a
  deprecation notice (#1229)

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

• value_var parameter added to derive_vars_atc() (#1120)

• format_eoxxstt_default() - Updated the default value of EOSSTT for screen failure patients (#885)

• The imputation functions (derive_vars_dtm(), derive_vars_dt(),
  convert_dtc_to_dtm(), convert_dtc_to_dt()) have been enhanced to address
  users feedback (#1300):

  • Partial dates with missing components in the middle like
    "2003-12-15T-:15:18", "2003-12-15T13:-:19", "2020-07--T00:00" are
    handled now.

  • The control of the level of imputation has been refined by adding the
    highest_imputation argument. For example, highest_imputation = "D"
    requests imputation for day and time but not for year and month.

    (For the date_imputation and the time_imputation argument NULL is no
    longer a permitted value.)

  • It is now possible to impute completely missing dates by specifying
    highest_imputation = "Y" and the min_dates or max_dates argument.

• order parameter added to dthcaus_source() which allows an additional
  character vector to be used for sorting the dataset, derive_vars_dthcaus()
  updated to process additional parameter (#1125).

• create_single_dose_dataset() Fixed bug where ASTDTM and AENDTM were not updated when start_date = ASTDT and end_date = AENDT. The function has been amended to now require start_datetime and end_datetime parameters in addition to start_date and end_date.The keep_source_vars has been added to specify the variables to be retained from the source dataset (#1224)

Breaking Changes

• Moved all developer-facing functions and vignettes to {admiraldev}. {admiraldev} is now a dependency of {admiral} (#1231)

• All ADaM datasets but admiral_adsl have been removed from the package (#1234)

• derive_var_agegr_ema() and derive_var_agegr_fda() have been deprecated (#1333)

• Imputation related arguments have been deprecated for all functions except the
  imputation functions themselves (#1299). I.e., if a derivation like last known alive
  date is based on dates, DTC variables have to be converted to numeric date or
  datetime variables in a preprocessing step. For examples see the ADSL
  vignette.

  The following arguments were deprecated:

  • date_imputation, time_imputation, and preserve in date_source()

  The following arguments no longer accept DTC variables:

  • date in date_source(), dthcaus_source(), censor_source(), and
    event_source()
  • dose_date and analysis_date in derive_vars_last_dose(),
    derive_var_last_dose_amt(), derive_var_last_dose_date(),
    derive_var_last_dose_grp()

  The following functions were deprecated:

  • derive_vars_merged_dt()
  • derive_vars_merged_dtm()

• For the date_imputation and the time_imputation argument of the imputation
  functions (derive_vars_dtm(), derive_vars_dt(), convert_dtc_to_dtm(),
  convert_dtc_to_dt()) NULL is no longer a permitted value. The level of
  imputation can be controlled by the highest_imputation argument now.

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

  • derive_var_disposition_dt()
  • derive_var_lstalvdt()
  • lstalvdt_source()
  • derive_var_trtedtm()
  • derive_var_trtsdtm()

• The following functions and parameters, which were deprecated in previous
  {admiral} versions, are now defunct and will output an ERROR if used:

  • derive_var_ady()
  • derive_var_aendy()
  • derive_var_astdy()
  • derive_var_atirel()
  • filter parameter in derive_var_extreme_flag() and derive_var_worst_flag()

Documentation

• New ADMH template script can be accessed using admiral::use_ad_template("admh") (#502)

• New vignette "Higher Order Functions" (#1047)

• New vignette "Lab Grading" (#1369)

• Fixed derive_var_disposition_status() argument to render correctly (#1268)

• Added link to pharmaverse YouTube channel to README

Various

• Restructured Reference page and updated all functions to use family tag
  in roxygen headers for finding similar functions. (#1105)

• Rename "Articles" page on website to "User Guides" and moved developer vignettes to {admiraldev} website (#1356)

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