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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)

admiral 0.6.3

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

  • 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)

  • 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

  • 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

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)

  • derive_vars_dtm() Change the min_dates with max_dates in the lapply statement when computing max_dates (#687)

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:

    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