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Changelog

Source: NEWS.md

admiral 0.11.0

New Features

Updates of Existing Functions

Breaking Changes

Various

  • vars() which was used in the admiral function calls that expected a list of quosures has been removed (#1747).

  • Examples for derive_var_extreme_flag() were reworked to reduce runtime that occasionally led to failing CI check (#1780)

Documentation

admiral 0.10.1

CRAN release: 2023-03-14

admiral 0.10.0

CRAN release: 2023-03-08

New Features

  • Using testthat 3rd edition for unit testing. This is stricter in that messages must be addressed and deprecated functions throw errors. (#1754)

  • New function consolidate_metadata() for consolidating multiple meta datasets into a single one (#1479)

  • New function compute_scale() for computing the average of a vector and transforming the result from a source to a target range. (#1692)

  • New ADPC template script available ad_adpc.R which creates PK Concentration Analysis Dataset (#849). This script includes formatting suitable for Non-Compartmental Analysis (ADNCA) (#851)

  • New function derive_expected_records() for adding expected records (#1729)

  • New function derive_extreme_event() for adding the worst or best observation for each by group as new records (#1755)

Updates of Existing Functions

Breaking Changes

Documentation

Various

admiral 0.9.1

CRAN release: 2022-12-23

admiral 0.9.0

CRAN release: 2022-12-06

New Features

  • The new function derive_vars_joined() adds variables from an additional dataset. The selection of the observations can depend on variables from both datasets. This can be used for adding AVISIT, AWLO, AWHI based on time windows and ADY or deriving the lowest value (nadir) before the current observation (#1448).

  • New function derive_var_trtemfl() for deriving treatment emergent flags (#989)

  • The new function chr2vars() turns a character vector into a list of quosures (#1448).

  • New function derive_var_relative_flag() for flagging observations before or after a condition is fulfilled (#1453)

  • New functions get_admiral_option() and set_admiral_options() to allow more flexibility on common function inputs; e.g. like subject_keys to avoid several find and replace instances of vars(STUDYID, USUBJID). (#1338)

  • The new function create_period_dataset() for creating a reference dataset for subperiods, periods, or phases from the ADSL dataset was added. The reference dataset can be used to create subperiod, period, and phase variables in OCCDS and BDS datasets. (#1477)

  • The new function derive_vars_period() adds subperiod, period, or phase variables to ADSL. The values for the new variables are provided by a period reference dataset. (#1477)

  • New function derive_var_merged_summary() adds a variable of summarized values to the input dataset (#1564)

  • A print() method was added for all S3 objects defined by admiral, e.g., date_source(), dthcaus_source(), … (#858)

  • New metadata data set called atoxgr_criteria_ctcv5 which holds criteria for lab grading based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0

  • Removed the {assertthat} dependency in admiral (#1392)

  • Removed R Version 3.6 check in CI/CD workflows in favor of the three most recent versions: 4.0, 4.1 and 4.2. (#1556)

  • The new function derive_locf_records() adds LOCF records as new observations. This can be used when the input dataset does not contain observations for missed visits/time points or when AVAL is NA for particular visits/time points (#1316).

  • New function convert_na_to_blanks() to convert character NA to blanks (#1624)

Updates of Existing Functions

  • Function derive_param_first_event() has been replaced by a more generalized derive_param_extreme_event() function with new argument mode allowing for the selection of either the "first" or "last" event record according to the conditions provided. Also the date_var argument has been replaced with the order argument instead. In addition, three new arguments new_var, true_value, and false_value have been added to allow the user to choose what variable is used to indicate whether an event happened, and the values it is given (#1317) (#1242).

  • Argument ignore_time_for_ref_end_date was added to derive_var_ontrtfl(), which controls if time is considered for the condition if start_date is after ref_end_date + ref_end_window days (#989).

  • derive_var_atoxgr_dir() default value of atoxgr_criteria_ctcv4 removed for parameter meta_criteria. Can now also choose atoxgr_criteria_ctcv5 for parameter meta_criteria, to implement NCI-CTCAEv5 grading criteria .

  • Environment objects were consolidated into a single admiral_environment object under R/admiral__environment.R. (#1572)

  • The default value of the keep_source_vars argument in create_single_dose_dataset() was updated such that it takes the values of the other arguments into account and the start_datetime and end_datetime arguments are optional now (#1598).

  • Function create_query_data() has been updated such that the dictionary version is stored in the output dataset (#1337).

Breaking Changes

  • Function derive_param_first_event() has been deprecated. Please use derive_param_extreme_event() with the order argument instead of the date_var argument (#1317).

  • Functions smq_select() and sdg_select() have been deprecated and replaced with basket_select(). In the create_query_data() function, meddra_version and whodd_version argument has been replaced by version and get_smq_fun and get_sdg_fun argument by get_terms_fun. (#1597)

Documentation

  • New vignette “Generic Functions” (#734)
  • New vignette “Visit and Period Variables” (#1478)

Various

admiral 0.8.4

CRAN release: 2022-10-14

  • Fixed a bug where a recent update to {lifecylce} caused several admiral tests to break (#1500)

admiral 0.8.3

CRAN release: 2022-10-07

  • Second attempt to address issue where CRAN identified a failing test when “a strict Latin-1* locale” is used (#1469)
  • Fixed a bug in derive_vars_duration() that surfaced after changes in R-devel (#1486)

admiral 0.8.2

CRAN release: 2022-09-29

  • Fixed an issue where CRAN identified a failing test when “a strict Latin-1* locale” is used (#1469)

admiral 0.8.1

CRAN release: 2022-09-20

admiral 0.8.0

CRAN release: 2022-09-05

New Features

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:

    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:

Documentation

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

CRAN release: 2022-07-18

  • 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.

  • 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.

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

admiral 0.7.0

CRAN release: 2022-05-31

New Features

ADLB

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

Various

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

admiral 0.6.3

CRAN release: 2022-02-17

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

admiral 0.6.2

Address CRAN comments raised after submitting v0.6.1 (#925)

admiral 0.6.1

Address CRAN comments raised after submitting v0.6.0 (#918)

admiral 0.6.0

New Features

Updates of Existing Functions

Breaking Changes

  • derive_agegr_ema(), derive_agegr_fda(), derive_disposition_dt(), derive_disposition_status(),derive_extreme_flag(), derive_worst_flag(), derive_obs_number(), derive_disposition_reason() have been deprecated and renamed in favor of derive_var_agegr_ema(), derive_var_agegr_fda(), derive_var_disposition_dt(), derive_var_disposition_status(), derive_var_extreme_flag(), derive_var_worst_flag(), derive_var_last_dose(), derive_var_obs_number(), and derive_vars_disposition_reason() respectively (#738)

  • derive_var_basec() and derive_baseline() have been deprecated in favor of the extended derive_var_base() function (#695)

  • derive_params_exposure() has been deprecated and renamed as derive_param_exposure() (#722)

  • The derive_last_dose() function has been deprecated in favor of derive_var_last_dose_date() (#385)

  • The behavior of all functions providing the date_imputation parameter, e.g., derive_vars_dtm() and derive_vars_dt(), has changed for date_imputation = "mid". Before the date was imputed as June 15th if both month and day were missing. Now it is imputed as June 30th. For the old behavior please specify date_imputation = "06-15". Please note the behavior has not changed if only the day is missing. In this case the day is imputed as 15 (#592)

  • derive_var_ontrtfl() now has a new_var parameter to support the derivation of ONTRxxFL and ONTRTwFL variables (#721)

  • The following functions and parameters, which were deprecated in previous {admiral} versions, were removed (#513):

  • derive_var_agegr_fda() has been updated to use ranges <18, 18-64, >=65 (#829)

Documentation

  • README and site homepage has been updated with important new section around expectations of {admiral}, as well as other useful references such as links to conference talks (#868 & #802)

  • New vignette Development Process and improvements made to contribution vignettes (#765 & #758)

  • Updated Pull Request Review Guidance on using task-list-completed workflow (#817)

Various

  • GitHub repo moved to pharmaverse org and associated broken site links fixed (#803 & #820)

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

admiral 0.5.0

admiral 0.4.0

New Features

General

BDS

Developer

Updates of Existing Functions

  • Unit checks in derive_param_*() functions are no longer case sensitive (#631)

  • derive_agegr_ema() and derive_agegr_fda() gain a age_unit parameter used to specify the unit of the input age (#569)

Breaking Changes

Bug Fixes

Documentation

admiral 0.3.0

New Features

General

  • convert_blanks_to_na() can be used to convert SAS blanks, i.e. "", into proper R NA values (#482)

  • call_derivation() enables users to call the same function multiple times with some parameters being fixed across iterations and others varying (#403)

  • derive_vars_dtm_to_dt() enables the easy conversion of datetime to date variables (#376)

  • derive_var_ontrtfl() can now handle events with a start and end date rather than just a single assessment date (#395)

  • derive_worst_flag() enables the flagging of worst records (#300)

BDS

OCCDS

  • derive_var_atirel() enables the derivation of the “Analysis Time Relative to Reference” (#397)

  • derive_vars_atc() can be used to add ATC variables from FACM to ADCM (#396)

Updates of Existing Functions

  • derive_var_anrind() now checks whether the AVAL variable is present in the input dataset (#486)

  • All derivation functions check whether the input dataset is grouped and throw an error if it is (#408)

  • use_ad_template() has been refactored to no longer make use of the {usethis} package which is no longer a dependency of {admiral} (#433)

  • A performance issue in derive_vars_dt() has been resolved (#384)

Breaking Changes

  • The drop_values_from parameter has been removed from derive_summary_records() (#425)

  • The format of the date_imputation parameter of derive_vars_dt() and derive_vars_dtm() has been changed from “dd-mm” to “mm-dd”. Thus, “01-12” now refers to January 12th rather than December 1st (#492)

  • Several functions have been renamed. The old names are now deprecated. They can still be used but a warning will be issued (#507)

  • The date_var parameter of lstalvdt_source() has been renamed to date

  • The filter_rows parameter of derive_summary_records() has been renamed to filter. The fns parameter has been deprecated in favor of analysis_var and summary_fun (#491)

  • The date_var and traceabilty_vars parameters of dthcaus_source() have been renamed to date and traceability_vars, respectively (#493)

  • The flag_filter parameter of derive_extreme_flag() has been renamed to filter (#487)

Bug Fixes

  • derive_agegr_fda() used to return NA for ages less than or equal 18. It now returns <=18 (#441)

Documentation

  • New vignette on “Date and Time Imputation” has been created (#198)

  • A “Guidance for git Usage” has been created (#266)

  • “OCCDS” has been added as a new section on the reference page on the package website (#485)

  • The Programming Strategy has been updated (#495)

  • A search feature has been added to the package website (#438)

  • New template scripts for ADEX (#181), ADCM (#268) and ADEG (#258) have been created

  • New vignette for programming ADEX has been created (#372)

  • A section on how to create query variables (e.g. SMQs in ADAE) has been added to the Occurrence datasets vignette (#370)

  • The BDS vignette has been updated to incorporate examples of ADVS and ADEG specific functions (#371)

admiral 0.2.1

admiral 0.2.0

New Features

General

  • Function argument checks have been completely re-written to provide clearer error messages to users (#263, #288)

  • SDTM SUPP-- datasets can be merged onto their parent domain using derive_suppqual_vars() (#145)

  • In case a derivation detects duplicate records after applying a filter, the dataset of duplicate records is made available to users via get_duplicates_dataset() (#202)

  • derive_vars_dt() and derive_vars_dtm() gain a min_dates and max_dates parameter which can be used to ensure that the imputed date(time) is not before the min_dates nor after the max_dates, e.g. avoid that AENDT is after the data cut date or ASTDT is before the first treatment date (#158)

  • use_ad_template() can be used to open a template script for an ADaM dataset; all available templates can be displayed using list_all_templates() (#110)

ADSL

  • EMA and FDA defined age groupings can be derived using derive_agegr_ema() and derive_agegr_fda(), respectively

  • Disposition Status can be derived using derive_disposition_status() (#92)

  • Disposition Reason can be derived using derive_disposition_reason()

  • Disposition Dates can be derived using derive_disposition_dt() (#91)

  • Date Last Known Alive can be derived using derive_var_lstalvdt() (#94)

  • Cause of Death can be derived using derive_var_dthcaus() (#93)

BDS

OCCDS

  • Last Dose Date(time) can be derived using derive_last_dose()

Breaking Changes

  • derive_merged_vars() has been removed from {admiral} in favor of smaller special purpose functions, e.g. derive_disposition_status() (#167)

  • Function arguments no longer accept expressions created with expr() or exprs() as inputs; instead filter expressions can be passed “as is” and multiple variables have to be wrapped inside vars() (#187)

    Old:

    
derive_extreme_flag(
  vs,
  new_var = LASTFL,
  by_vars = exprs(USUBJID, VSTESTCD, VISIT),
  order = exprs(VSTPTNUM),
  mode = "last",
  flag_filter = expr(VISIT != "BASELINE")
)

    New:

    
derive_extreme_flag(
  vs,
  new_var = LASTFL,
  by_vars = vars(USUBJID, VSTESTCD, VISIT),
  order = vars(VSTPTNUM),
  mode = "last",
  flag_filter = VISIT != "BASELINE"
)

  • read_dap_m3() and initialize() have been migrated to {admiral.roche} (#272)

  • The start_date and end_date parameters of derive_var_ady(), derive_var_aendy() and derive_var_astdy() have been renamed to reference_date and date, respectively (#121)

Bug Fixes

  • derive_var_basetype() no longer drops records which do not match any condition defined in the basetype argument (#226)

  • Join warnings like “Column USUBJID has different attributes on LHS and RHS of join when using left_join()” are no longer displayed (#271)

  • For datetimes with time imputed to “00:00:00” the time part is now displayed (#206)

Documentation