NEWS.md

In epijim/admiral: ADaM in R Asset Library

admiral 0.6.1

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

admiral 0.6.0

New Features

• derive_vars_dy() derives the analysis day from one or more --DT(M) variables (#700)

Updates of Existing Functions

• The derive_last_dose() function has been split into a general function derive_vars_last_dose() and three wrapper functions derive_var_last_dose_amt(), derive_var_last_dose_date(), and derive_var_last_dose_grp() (#385)

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

• derive_vars_dtm(), derive_var_disposition and derive_var_lstalvdt now have preserve argument. A user can preserve partial dates when doing date imputation, e.g. 2019---07 would become 2019-06-07 by setting preserve to TRUE when doing date_imputation (#592)

• derive_vars_dtm() now has ignore_seconds_flag argument so users can suppress "S" flag if seconds are not recorded in the data (#589)

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_aage(), derive_duration(), derive_query_vars(), and derive_suppqual_vars() function

• fns and filter_rows parameters in derive_summary_records()
• date_var and traceabilty_vars parameters in dthcaus_source()
• flag_filter parameter in derive_extreme_flag()
• flag_filter parameter in derive_var_extreme_flag()
• date_var parameter in lstalvdt_source()

• date parameter in derive_var_ontrtfl()

• 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)

admiral 0.5.0

• The first truly open source release licensed under Apache 2.0 (#680)

• New vignette Contributing to admiral (#679)

• New vignette Unit Test Guidance (#679)

• Broken links in README have been fixed (#564)

admiral 0.4.0

New Features

General

• derive_vars_dtm_to_tm() enables the easy conversion of datetime to time variables (#551)

• derive_var_age_years() derives age in years from a variable providing the age in different units (#569)

BDS

• derive_param_tte() derives time-to-event-parameters (#546)

• For common time-to-event endpoints event and censoring source objects are provided (#612)

Developer

• assert_list_element() checks if an element of a list of lists/classes fulfills a condition

• assert_one_to_one() checks if there is a one to one mapping between two lists of variables

• negate_vars() negates a list of variables to remove them from a dataset with select()

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

• All SDTM datasets have been moved to the {admiral.test} package (#639)

• The min_dates and max_dates parameters of derive_vars_dt() and derive_vars_dtm() no longer expect a list() but vars() as input (#405)

Bug Fixes

• derive_vars_dtm() no longer shifts the time of the input --DTC variable (#436)

Documentation

• New vignette Creating a BDS Time-to-Event ADaM (#549)

• New vignette Queries Dataset Documentation (#561)

• New vignette Writing Vignettes (#334)

• New vignette Pull Request Review Guidance (#554)

• A section on handling missing values when working with {admiral} has been added to the "Get Started" vignette (#577)

• Package installation instructions have been added to the README (#558)

• The documentation of derive_vars_dtm() falsely stated that the flag_imputation parameter should be either TRUE or FALSE. It now correctly states that the possible values are "time", "date" or "auto" (#539)

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

• derive_derived_param() can be used to derive a new parameter from existing parameters in a BDS dataset (#325)

• derive_param_bmi(), derive_param_bsa() and derive_param_map() enables the derivation of the body mass index, body surface area and mean arterial pressure parameters respectively (#368)

• derive_param_qtc() enables the derivation of corrected QT intervals according to the formula of Bazett, Fridericia or Sagie (#325)

• derive_param_rr() enables the derivation of the RR interval (#325)

• derive_params_exposure() enables the derivation of summary exposure parameters (#400)

• derive_param_doseint() enables the derivation of dose intensity (#179)

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)

  • derive_aage() -> derive_vars_aage()
  • derive_duration() -> derive_vars_duration()
  • derive_query_vars() -> derive_vars_query()
  • derive_suppqual_vars() -> derive_vars_suppqual()

• 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

• Fixed a critical bug in use_ad_template() that prevented the function from being usable at all (#326)

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

• Summary records for BDS datasets, e.g. with DTYPE == "AVERAGE", can be derived using derive_summary_records() (#177)

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:

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

New:

r 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

• Frequently Asked Questions

• Creating ADSL

• Creating a BDS Finding ADaM

• Creating an OCCDS ADaM

epijim/admiral documentation built on Feb. 13, 2022, 12:15 a.m.