NEWS.md

In admiral: ADaM in R Asset Library

admiral 0.12.3

• Fixed a bug in derive_var_dthcaus() where if a subject has observations in more than one of the sources, the one from the last source was selected regardless of the date. Now the function works as described in its documentation. (#2154)

admiral 0.12.2

• A unit test for derive_param_computed() was modified in anticipation of major user-facing changes to R version 4.4 (#2147)

admiral 0.12.1

• derive_extreme_records() no longer fails if dataset_add is specified and a variable specified for order is not in dataset. (#2113)

• The type argument in compute_duration() changed the underlying default behavior in derive_vars_duration() without allowing the user to toggle between "duration" and "interval" as originally intended. This was fixed by adding the type argument for derive_vars_duration() and a wrapper function derive_vars_aage() such that it gets passed through compute_duration() appropriately (#2112)

• Template ad_adpp.R updated to replace left_join() with derive_vars_merged() (#2109).

admiral 0.12.0

New Features

• event_joined() events were added. They can be specified for the events argument in derive_extreme_event(). This allows to define events based on more than one observation, e.g., events which need to be confirmed by a second assessment. (#1960)

• atoxgr_criteria_daids.rda added, which holds metadata for Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events. You can find additional documentation here atoxgr_criteria_daids()

Updates of Existing Functions

• The functions derive_param_bmi() and derive_param_bsa() are updated to have the option of producing more values at visits when only weight is collected (#1228).
• The functions derive_var_age_years() and compute_age_years() are updated to return an NA age in the case that the age unit is missing. (#2001) The argument unit for derive_vars_aage() is also changed to age_unit for consistency between these age-related functions. (#2025)

• The derive_var_ontrtfl() function has been updated to allow for the column passed in ref_end_date to contain NA values. Previously, if the end date was NA, the row would never be flagged. Now, an NA value is interpreted as the treatment being ongoing, for example. (#1984)

• The function derive_var_extreme_flag() has a new function argument, flag_all that additionally flags all records if the first or last record is not unique. (#1979)

• The function derive_param_computed() was enhanced: (#1968)

• The analysis_value and analysis_var arguments were deprecated in favor of set_values_to. This enables users to compute more than one variable.

• The keep_nas argument was added. If it is set to TRUE, observations are created even if values contributing to the computed values are NA.

• The function derive_vars_dy() is updated to avoid potential error when the input dataset with columns ending with temp. (#2012)

• Argument keep_source_vars was added to derive_extreme_records() which specifies which variables in the new observations should be kept. (#1697)

• Templates, vignettes, and other uses of {admiral.test} SDTM data are updated to use {pharmaversesdtm} instead. (#2040)

• The traceability_vars argument in date_source() and dthcaus_source were deprecated in favor of set_values_to. The date_source() function creates a date_source object as input for derive_var_extreme_dt() and derive_var_extreme_dtm(),users can now define the traceability variables by assigning those variables to the set_values_toargument.Similarly, the dthcaus_source creates a dthcaus_source Object. (#2068)

• derive_extreme_event() was enhanced (#1960):

  • event_joined() events can be specified for the events argument. This allows to define events based on more than one observation, e.g., events which need to be confirmed by a second assessment.

  • The source_datasets argument was added to the function and the dataset_name field to event(). It can be used to define events based on a different dataset than the input dataset.

  • The keep_source_vars argument was added to the function and the keep_source_vars field to event(). It allows to select which variables should be kept for the selected observations.

  • The mode and order field were added to event(). They allow to select the first or last observation per by group if there are multiple observation fulfilling the event condition.

  • The ignore_event_order argument was added.

  • The description field was added to event(). It can be used to provide a description of the event in plain language.

• derive_var_atoxgr_dir() was enhanced (#1859):

• Can now select atoxgr_criteria_daids in argument meta_criteria to create ATOXGRL and ATOXGRH based on Division of AIDS (DAIDS) Table for Grading the Severity of Adult and Pediatric Adverse Events

• New argument signif_dig added to control the number of significant digits to use when comparing 2 numeric values. (https://github.com/pharmaverse/admiral/pull/2060)

Breaking Changes

• The compute_duration(type) argument added the "duration" type calculation, and this is the new default (previously "interval" differences were returned). See function help file for details on the difference between "duration" and "interval" calculations. (#1875)

• The following functions, which were deprecated in previous {admiral} versions, have been removed: (#1950)

• derive_var_disposition_status()

• derive_vars_disposition_reason()
• format_eoxxstt_default()
• format_reason_default()

• derive_var_worst_flag()

• The following functions have been deprecated from previous {admiral} versions using the next phase of the deprecation process: (#1950)

• derive_param_extreme_event()

• derive_vars_last_dose()
• derive_var_last_dose_amt()
• derive_var_last_dose_date()
• derive_var_last_dose_grp()
• derive_var_basetype()
• derive_var_merged_cat()

• derive_var_merged_character()

• The arguments dataset_adsl in the function derive_param_exist_flag() and subject_keys have been deprecated versions using the next phase of the deprecation process. (#1950)

• The argument wt in the function compute_egfr() was deprecated in favor of weight using the first phase of the deprecation process. (#2020)

• The filter argument in derive_extreme_records() was deprecated in favor of the filter_add using the next phase of the deprecation process. (#1950)

• The analysis_value and analysis_var arguments in derive_param_computed() were deprecated in favor of set_values_to (#1968).

• The na_val argument in derive_var_shift() has been deprecated in favor of missing_value using the first phase of the deprecation process. (#2014)

• The dataset_expected_obs argument in derive_expected_records() and derive_locf_records() has been deprecated in favor of dataset_ref. (#2037)

• The span_period argument in derive_var_ontrtfl() has been updated to only accept TRUE or FALSE, where is previously accepted "Y" and NULL. (#2033)

Documentation

• Non-exported utility and print functions were previously listed on the admiral website reference page. They have been removed. (#2049, #2050)

• The description of the argument reference_date in the function derive_vars_dy() has been clarified to make it agnostic to start/end selection. (#2027)

• Date and Time Imputation User Guide/Vignette has section on preserving partial dates updated (#2028)

Various

• The list of package authors/contributors has been reformatted so that those who are actively maintaining the code base are now marked as authors, whereas those who made a significant contribution in the past are now down as contributors. All other acknowledgements have been moved to README section (#1941).

• derive_vars_joined() had two bugs with regards to duplicates messaging and when new_vars was set to NULL that have now been addressed (#1966).

• compute_dtf() had a bug with regards to imputing days to full date-time character strings. (#2042)

admiral 0.11.1

• Fix bug in derive_param_tte(). (#1962)
• Get Started page now points to correct article. (#1969)

admiral 0.11.0

New Features

• In the function derive_var_anrind(), added argument use_a1hia1lo to turn the usage of A1HI and A1LO off and on, with the default being off. (#1795)

• Added a "Report a bug" link to {admiral} website. (#1836)

• New function compute_age_years() for converting a vector of age values to years. (#1794)

• New functions filter_exist() and filter_not_exist() for selecting records from a dataset dependent on the existence of the corresponding by groups in a filtered source dataset. (#1699)

• New function derive_param_extreme_record() that adds parameter based on the first or last record from multiple sources. (#1822)

• New ADPPK template script available ad_adppk.R which creates Population PK Analysis Dataset based on forthcoming CDISC Implementation guide. (#1772)

• New function compute_egfr() for calculating Estimated Glomerular Filtration Rate (eGFR) and Creatinine Clearance for Kidney Function. (#1826)

Updates of Existing Functions

• derive_extreme_records() was enhanced such that it includes the functionality of derive_param_extreme_event(). (#1725)

• For the set_values_to argument expressions are accepted now. For example, set_values_to = exprs(PARAMCD = str_to_upper(QSTESTCD)). This affects censor_source(), derive_expected_records(), derive_extreme_event(), derive_extreme_records(), derive_param_bmi(), derive_param_bsa(), derive_param_computed(), derive_param_doseint(), derive_param_exposure(), derive_param_framingham(), derive_param_map(), derive_param_exist_flag(), derive_param_extreme_event(), derive_param_qtc(), derive_param_rr(), derive_param_wbc_abs(), derive_summary_records(), event_source(), get_summary_records(). (#1727)

• For the order argument expressions are accepted now. (#1727)

• derive_vars_merged() updates: (#1727)

  • The missing_values argument to assign values to the new variables for non-matching observations was added.
  • The new_vars argument accepts expressions now.

• derive_vars_joined() updates: (#1727)

  • The missing_values argument to assign values to the new variables for non-matching observations was added.
  • The new_vars and the join_vars argument accept expressions now.

• The date field of date_source() accepts expressions now. This affects derive_var_extreme_dt() and derive_var_extreme_dtm(). (#1727)

• The date and dthcaus field of dthcaus_source() accept expressions now. This affects derive_var_dthcaus(). (#1727)

• The date field of event_source() and censor_source() accepts expressions now. This affects derive_param_tte(). (#1727)

• The derive_param_computed() function was enhanced: (#1873)

  • The new dataset_add argument allows to consider parameters from a different dataset than the input dataset.
  • The new analysis_var argument allows to specify the variable to be populated, e.g., AVALC.
  • For parameters and constant_parameters a list of expressions can be specified now. This allows to create temporary parameter codes, e.g., if SDTM data is used as input.
  • The analysis_value argument was enhanced such that any variable of the form <variable>.<parameter> can be used, e.g., QSORRES.CHSF13.

Breaking Changes

• create_query_data() and derive_vars_query() updated to rename variables in query data set as follows: (#1907)

  • VAR_PREFIX to PREFIX
  • QUERY_NAME to GRPNAME
  • QUERY_ID to GRPID
  • QUERY_SCOPE to SCOPE
  • QUERY_SCOPE_NUM to SCOPEN
  • TERM_LEVEL to SRCVAR
  • TERM_NAME to TERMNAME
  • TERM_ID to TERMID

  Users need to adjust their get_terms() function accordingly.

• The aval_fun argument of derive_param_exist_flag() was deprecated in favor of the set_values_to argument. (#1727)

• derive_var_merged_cat() and derive_var_merged_character() have been deprecated in favor of derive_vars_merged(). (#1727)

• The following functions, which were deprecated in previous {admiral} versions, have been removed: (#1747)

• derive_vars_merged_dt()

• derive_vars_merged_dtm()
• derive_var_agegr_ema()
• derive_var_agegr_fda()
• derive_param_first_event()
• derive_derived_param()
• derive_var_confirmation_flag()

• filter_confirmation()

• The following functions have been deprecated from previous {admiral} versions using the next phase of the deprecation process: (#1747)

• derive_var_disposition_status()

• derive_vars_disposition_reason()
• format_eoxxstt_default()
• format_reason_default()

• derive_var_worst_flag()

• derive_param_extreme_event() was deprecated in favor of derive_extreme_records(). (#1725)

• The filter argument in derive_extreme_records() was deprecated in favor of the filter_add argument. (#1725)

• derive_vars_last_dose(), derive_var_last_dose_amt(), derive_var_last_dose_date(), derive_var_last_dose_grp(), were deprecated in favor of derive_vars_joined(). (#1797)

• derive_var_basetype() was deprecated in favor of derive_basetype_records(). (#1796)

• In the function derive_param_exist_flag() the arguments dataset_adsl and subject_keys have been renamed to dataset_ref and by_vars respectively. (#1793)

Documentation

• Updated example dataset to trigger deterioration flags in the vignette "Creating Questionnaire ADaMs". (#1853, #1854)

• Updated PK Programming vignette to include new Population PK Template ad_adppk.R. (#1772)

• Updated "Lab Grading" Vignette to link to grading metadata available in {admiral} and clarify how abnormal baseline values are assigned in NCI-CTCAEv5. (#1863)

• Updated "Visit and Period Variables" Vignette to add more detail about Study Specific Code that is required. (#1831)

• Increased documentation for those functions which are regarded as wrapper functions. (#1726)

• Examples in function documentation no longer rely on library(admiral.test). (#1752)

• Conferences where {admiral} was presented were updated on the README.md. (#1890)

Various

• vars() which was used in the admiral function calls that expected a list of quosures has been removed. The admiral option force_admiral_vars was removed as well. (#1694)

• derive_vars_dtm() and derive_vars_dt() had a bug pertaining to imputations associated with supplying both min_dates and max_dates that has now been resolved. (#1843)

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

• create_period_dataset() had a bug that led to an error when both DT and DTM columns existed. (#1845)

• External functions are now consistently imported via namespace. package::function() calls have been removed from admiral functions. (#1842)

• restrict_derivation() had a bug which led to failure if the derivation argument was not in the global environment. (#1765)

admiral 0.10.2

• Changing package maintainer from Thomas Neitmann to Ben Straub. (#1848)

admiral 0.10.1

• Fix checks on derive_vars_dtm() and derive_vars_dt() that were too restrictive. (#1810)

admiral 0.10.0

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

• Arguments analysis_var, keep_vars were added to derive_locf_records(), analysis_var allows to specify analysis variable, keep_vars keeps variables that need carrying the last observation forward other than analysis_var (e.g., PARAMN, VISITNUM). (#1636)

• The function create_single_dose_dataset() adds support for expanding relative nominal time (e.g. NFRLT) used in Pharmacokinetic (PK) analyses. The new parameter nominal_time defaults as NULL and does not change the normal operation of the function. If a nominal_time is specified such as NFRLT (Nominal Relative Time from First Dose) then the nominal time is incremented by the interval specified in EXDOSFRQ for example for "QD" records the NFRLT is incremented by 24 hours, e.g. 0, 24, 48... (#1640)

• create_single_dose_dataset() is also updated for values of EXDOSFRQ with units in days but expected values less than 24 hours, such as "BID", "TID", and "QID". Previously these values of EXDOSFRQ may result in duplicate records where the day values are incremented but the time values are not. (#1643)

• The function derive_var_confirmation_flag() and filter_confirmation() gained the tmp_obs_nr_var argument. It helps flagging or selecting consecutive observations or the first or last observation in a by group. (#1724)

• The functions derive_vars_merged(), derive_var_merged_cat(), derive_var_merged_character(), derive_var_merged_exist_flag(), derive_var_merged_summary(), and derive_vars_merged_lookup() were updated to allow renaming in the argument by_vars. (#1680)

• The units "min" and "sec" are added as valid values of out_unit in compute_duration() and derive_vars_duration(). (#1647)

• The function derive_vars_query() now includes a consistency check for QUERY_SCOPE and QUERY_SCOPE_NUM values. (#652)

• Argument new_var in derive_param_extreme_event() is made optional. (#1630)

• derive_vars_last_dose() no longer fails if USUBJID is not included in the input dataset. (#1787)

Breaking Changes

• All function arguments which expected a list of quosures created by vars() are now expecting a list of expressions created by exprs(). For example, instead of by_vars = vars(STUDYID, USUBJID) by_vars = exprs(STUDYID, USUBJID) must be used now.

  To enable running old scripts using vars() in the admiral function calls admiral redefines the vars() function such that it returns a list of expressions. This can be disabled by the admiral option force_admiral_vars (see set_admiral_options()). Please note that this is a temporary solution and will be removed in a future admiral release. (#1627)

• Function derive_param_tte() has been updated such that only observations are added for subjects who have both an event or censoring and an observation in dataset_adsl. (#1576)

• Function derive_var_disposition_status() has been deprecated, please use derive_var_merged_cat() instead. (#1681)

• Function derive_var_worst_flag() has been deprecated, in favor of slice_derivation()/derive_var_extreme_flag(). (#1682)

• Function derive_vars_disposition_reason() has been deprecated, in favor of derive_vars_merged(). (#1683)

• The following functions have been deprecated from previous {admiral} versions using the next phase of the deprecation process: (#1712)

• derive_derived_param()

• derive_param_first_event()
• derive_vars_merged_dt()
• derive_vars_merged_dtm()
• derive_var_agegr_ema()

• derive_var_agegr_fda()

• The following functions, which were deprecated in previous {admiral} versions, have been removed: (#1712)

• derive_var_ady()

• derive_var_aendy()
• derive_var_astdy()
• derive_var_atirel()
• derive_vars_suppqual()
• smq_select()

• sdg_select()

• The following parameters, which were deprecated in previous {admiral} versions, have been removed: (#1712)

• meddra_version, whodd_version, get_smq_fun and get_sdg_fun from the create_query_data() function

• date_imputation, time_imputation and preserve parameters from date_source() function

• filter parameter from derive_var_extreme_flag()

• ADLB metadata data set called atoxgr_criteria_ctcv5 updated to remove unit check for HYPERURICEMIA as grade criteria based on ANRHI only. This metadata holds criteria for lab grading based on Common Terminology Criteria for Adverse Events (CTCAE) v5.0. (#1650)

• Renamed derive_var_confirmation_flag() and filter_confirmation() to derive_var_joined_exist_flag() and filter_joined() respectively. (#1738)

Documentation

• New vignette "Creating a PK NCA ADaM (ADPC/ADNCA)". (#1639)

• New vignette "Hy's Law Implementation". (#1637)

• New vignette "Creating Questionnaire ADaMs". (#1715)

• The expected value for the derivation argument of restrict_derivation(), slice_derivation(), and call_derivation() is described now. (#1698)

• Removed authors from function documentation, as we will now only be tracking an overall list of authors for admiral. (#1673)

• Added an imputation example for create_single_source_dataset() in function documentation. (#1408, #1760)

• Updates to examples for derive_var_age_years() and derive_vars_duration(). (#1620, #1634)

• Increased the level of documentation for derive_var_age_years() to describe the data type of the newly created new_var column. (#970)

Various

• Functions derive_vars_dtm() and derive_vars_dt() had a bug pertaining to imputations associated with NA values that has now been fixed. (#1646)

admiral 0.9.1

• Implement changes to if_else() from the release of dplyr version 1.1.0, which affects derive_vars_dtm() and and compute_tmf(). (#1641)

admiral 0.9.0

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

• Function derive_param_tte() had a bug that set ADT to NA when start_date was missing, which has now been fixed. (#1540)

• Function derive_vars_merged() had an improperly formatted error message which has been corrected. (#1473)

• Templates now save datasets as .rds instead of .rda. (#1501)

• Function create_single_dose_dataset() no longer fails if the input dataset contains observations with dose frequency "ONCE". (#1375)

admiral 0.8.4

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

admiral 0.8.3

• 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

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

admiral 0.8.1

• derive_var_extreme_dt() and derive_var_extreme_dtm() were updated such that source observations where the date is NA are excluded (#1419)

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.

• 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

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

• 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)

• 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:

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

admiral documentation built on Oct. 19, 2023, 1:08 a.m.