Package index • admiral

Derivations for Adding Variables
All ADaMs
`derive_var_extreme_flag()`	Add a Variable Flagging the First or Last Observation Within Each By Group
`derive_var_joined_exist_flag()`	Derives a Flag Based on an Existing Flag
`derive_var_merged_ef_msrc()`	Merge an Existence Flag From Multiple Sources
`derive_var_merged_exist_flag()`	Merge an Existence Flag
`derive_var_merged_summary()`	Merge Summary Variables
`derive_var_obs_number()`	Adds a Variable Numbering the Observations Within Each By Group
`derive_var_relative_flag()`	Flag Observations Before or After a Condition is Fulfilled
`derive_var_trtdurd()`	Derive Total Treatment Duration (Days)
`derive_vars_cat()`	Derive Categorization Variables Like `AVALCATy` and `AVALCAyN`
`derive_vars_computed()`	Adds Variable(s) Computed from the Analysis Value of one or more Parameters
`derive_vars_dt()`	Derive/Impute a Date from a Character Date
`derive_vars_dtm()`	Derive/Impute a Datetime from a Character Date
`derive_vars_dtm_to_dt()`	Derive Date Variables from Datetime Variables
`derive_vars_dtm_to_tm()`	Derive Time Variables from Datetime Variables
`derive_vars_duration()`	Derive Duration
`derive_vars_dy()`	Derive Relative Day Variables
`derive_vars_joined()`	Add Variables from an Additional Dataset Based on Conditions from Both Datasets
`derive_vars_joined_summary()`	Summarize Variables from an Additional Dataset Based on Conditions from Both Datasets
`derive_vars_merged()`	Add New Variable(s) to the Input Dataset Based on Variables from Another Dataset
`derive_vars_merged_lookup()`	Merge Lookup Table with Source Dataset
`derive_vars_transposed()`	Derive Variables by Transposing and Merging a Second Dataset
ADSL-specific Derivation functions helpful for building the ADSL dataset
`derive_var_age_years()`	Derive Age in Years
`derive_vars_aage()`	Derive Analysis Age
`derive_vars_extreme_event()`	Add the Worst or Best Observation for Each By Group as New Variables
`derive_vars_period()`	Add Subperiod, Period, or Phase Variables to ADSL
BDS-specific Derivation functions helpful for building the BDS datasets (e.g. advs, adlb, adeg, adex)
`derive_basetype_records()`	Derive Basetype Variable
`derive_var_analysis_ratio()`	Derive Ratio Variable
`derive_var_anrind()`	Derive Reference Range Indicator
`derive_var_atoxgr()`	Derive Lab High toxicity Grade 0 - 4 and Low Toxicity Grades 0 - (-4)
`derive_var_atoxgr_dir()`	Derive Lab Toxicity Grade 0 - 4
`derive_var_base()`	Derive Baseline Variables
`derive_var_chg()`	Derive Change from Baseline
`derive_var_ontrtfl()`	Derive On-Treatment Flag Variable
`derive_var_pchg()`	Derive Percent Change from Baseline
`derive_var_shift()`	Derive Shift
`derive_vars_crit_flag()`	Derive Criterion Flag Variables `CRITy`, `CRITyFL`, and `CRITyFN`
OCCDS-specific Derivation functions helpful for building the OCCDS datasets (e.g. adae, adcm, admh)
`derive_var_trtemfl()`	Derive Treatment-emergent Flag
`derive_vars_atc()`	Derive ATC Class Variables
`derive_vars_query()`	Derive Query Variables
`get_terms_from_db()`	Get Terms from the Queries Database
Derivations for Adding Parameters/Records
BDS-specific
`default_qtc_paramcd()`	Get Default Parameter Code for Corrected QT
`derive_expected_records()`	Derive Expected Records
`derive_extreme_event()`	Add the Worst or Best Observation for Each By Group as New Records
`derive_extreme_records()`	Add the First or Last Observation for Each By Group as New Records
`derive_locf_records()`	Derive LOCF (Last Observation Carried Forward) Records
`derive_param_bmi()`	Adds a Parameter for BMI
`derive_param_bsa()`	Adds a Parameter for BSA (Body Surface Area) Using the Specified Method
`derive_param_computed()`	Adds a Parameter Computed from the Analysis Value of Other Parameters
`derive_param_doseint()`	Adds a Parameter for Dose Intensity
`derive_param_exist_flag()`	Add an Existence Flag Parameter
`derive_param_exposure()`	Add an Aggregated Parameter and Derive the Associated Start and End Dates
`derive_param_framingham()`	Adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score
`derive_param_map()`	Adds a Parameter for Mean Arterial Pressure
`derive_param_qtc()`	Adds a Parameter for Corrected QT (an ECG measurement)
`derive_param_rr()`	Adds a Parameter for Derived RR (an ECG measurement)
`derive_param_wbc_abs()`	Add a parameter for lab differentials converted to absolute values
`derive_summary_records()`	Add New Records Within By Groups Using Aggregation Functions
TTE-specific
`derive_param_tte()`	Derive a Time-to-Event Parameter
Metadata Auxiliary datasets providing definitions as input for derivations, e.g. grading criteria or dose frequencies
`atoxgr_criteria_ctcv4`	Metadata Holding Grading Criteria for NCI-CTCAEv4 using SI unit where applicable
`atoxgr_criteria_ctcv4_uscv`	Metadata Holding Grading Criteria for NCI-CTCAEv4 using USCV unit where applicable
`atoxgr_criteria_ctcv5`	Metadata Holding Grading Criteria for NCI-CTCAEv5 using SI unit where applicable
`atoxgr_criteria_ctcv5_uscv`	Metadata Holding Grading Criteria for NCI-CTCAEv5 using USCV unit where applicable
`atoxgr_criteria_daids`	Metadata Holding Grading Criteria for DAIDs using SI unit where applicable
`atoxgr_criteria_daids_uscv`	Metadata Holding Grading Criteria for DAIDs using USCV unit where applicable
`country_code_lookup`	Country Code Lookup
`dose_freq_lookup`	Pre-Defined Dose Frequencies
Example Datasets You can run `use_ad_template()` to produce additional datasets
`admiral_adlb`	Lab Analysis Dataset
`admiral_adsl`	Subject Level Analysis Dataset
`ex_single`	Single Dose Exposure Dataset
`example_qs`	Example `QS` Dataset
`queries`	Queries Dataset
`queries_mh`	Queries MH Dataset
Advanced Functions
Admiral Options
`get_admiral_option()`	Get the Value of an Admiral Option
`set_admiral_options()`	Set the Value of admiral Options
Higher Order
`call_derivation()`	Call a Single Derivation Multiple Times
`derivation_slice()`	Create a `derivation_slice` Object
`restrict_derivation()`	Execute a Derivation on a Subset of the Input Dataset
`slice_derivation()`	Execute a Derivation with Different Arguments for Subsets of the Input Dataset
Creating Auxiliary Datasets
`consolidate_metadata()`	Consolidate Multiple Meta Datasets Into a Single One
`create_period_dataset()`	Create a Reference Dataset for Subperiods, Periods, or Phases
`create_query_data()`	Creates a queries dataset as input dataset to the `dataset_queries` argument in `derive_vars_query()`
`create_single_dose_dataset()`	Create dataset of single doses
Source Objects
`basket_select()`	Create a `basket_select` object
`censor_source()`	Create a `censor_source` Object
`event()`	Create a `event` Object
`event_joined()`	Create a `event_joined` Object
`event_source()`	Create an `event_source` Object
`flag_event()`	Create a `flag_event` Object
`query()`	Create an `query` object
`records_source()`	Create a `records_source` Object
`tte_source()`	Create a `tte_source` Object
`death_event` `lastalive_censor` `ae_event` `ae_ser_event` `ae_gr1_event` `ae_gr2_event` `ae_gr3_event` `ae_gr4_event` `ae_gr5_event` `ae_gr35_event` `ae_sev_event` `ae_wd_event`	Pre-Defined Time-to-Event Source Objects
Other
`list_tte_source_objects()`	List all `tte_source` Objects Available in a Package
`params()`	Create a Set of Parameters
Computation Functions for Vectors
All ADaMs
`compute_age_years()`	Compute Age in Years
`compute_dtf()`	Derive the Date Imputation Flag
`compute_duration()`	Compute Duration
`compute_tmf()`	Derive the Time Imputation Flag
`convert_date_to_dtm()`	Convert a Date into a Datetime Object
`convert_dtc_to_dt()`	Convert a Date Character Vector into a Date Object
`convert_dtc_to_dtm()`	Convert a Date Character Vector into a Datetime Object
`impute_dtc_dt()`	Impute Partial Date Portion of a `--DTC` Variable
`impute_dtc_dtm()`	Impute Partial Date(-time) Portion of a `--DTC` Variable
BDS-specific
`compute_bmi()`	Compute Body Mass Index (BMI)
`compute_bsa()`	Compute Body Surface Area (BSA)
`compute_egfr()`	Compute Estimated Glomerular Filtration Rate (eGFR) for Kidney Function
`compute_framingham()`	Compute Framingham Heart Study Cardiovascular Disease 10-Year Risk Score
`compute_map()`	Compute Mean Arterial Pressure (MAP)
`compute_qtc()`	Compute Corrected QT
`compute_qual_imputation()`	Function to Impute Values When Qualifier Exists in Character Result
`compute_qual_imputation_dec()`	Compute Factor for Value Imputations When Character Value Contains < or >
`compute_rr()`	Compute RR Interval From Heart Rate
`compute_scale()`	Compute Scale Parameters
`transform_range()`	Transform Range
Utility Functions
Utilities for Formatting Observations
`convert_blanks_to_na()`	Convert Blank Strings Into NAs
`convert_na_to_blanks()`	Convert NAs Into Blank Strings
`yn_to_numeric()`	Map `"Y"` and `"N"` to Numeric Values
Utilities for Dataset Checking
`get_duplicates_dataset()`	Get Duplicate Records that Led to a Prior Error
`get_many_to_one_dataset()`	Get Many to One Values that Led to a Prior Error
`get_one_to_many_dataset()`	Get One to Many Values that Led to a Prior Error
Utilities used within Derivation Functions
`extract_unit()`	Extract Unit From Parameter Description
`get_flagged_records()`	Create an Existence Flag
`get_not_mapped()`	Get list of records not mapped from the lookup table.
`get_vars_query()`	Get Query Variables
Utilities for Filtering Observations
`count_vals()`	Count Number of Observations Where a Variable Equals a Value
`filter_exist()`	Returns records that fit into existing by groups in a filtered source dataset
`filter_extreme()`	Filter the First or Last Observation for Each By Group
`filter_joined()`	Filter Observations Taking Other Observations into Account
`filter_not_exist()`	Returns records that don't fit into existing by groups in a filtered source dataset
`filter_relative()`	Filter the Observations Before or After a Condition is Fulfilled
`max_cond()`	Maximum Value on a Subset
`min_cond()`	Minimum Value on a Subset
Utilities for Quosures
`chr2vars()`	Turn a Character Vector into a List of Expressions
`negate_vars()`	Negate List of Variables
Utilities used for Examples and Template Scripts
`list_all_templates()`	List All Available ADaM Templates
`use_ad_template()`	Open an ADaM Template Script
Objects exported from other packages To maximize the user-friendliness of admiral, functions from other packages are provided without changes made to them, follow the links below to see their documentation.
`%>%`	Pipe operator
`desc`	dplyr desc
`exprs`	rlang exprs
Deprecated Functions and arguments may need to be removed or replaced over time. In such cases, the function or argument will enter a 3 year deprecation cycle. The cycle will be tied as close as sensibly possible to a package release. When a function is deprecated: In Year 1, there will be a message issued if you use the function/argument, but it will still be available to use. In Year 2, a warning will be produced if you use the function/argument, but it will still be available to use. In Year 3, an error will be produced if you use the function/argument and no longer be able to use. Finally, after 3 years, the function/argument and related documentation and tests will be removed from admiral. Note: Guidance on replacement functionality will be found in the message produced as well as in the function’s documentation. Below, you can find a list of functions in the process of being deprecated:
`call_user_fun()`	Calls a Function Provided by the User
`date_source()`	Create a `date_source` object
`derive_param_extreme_record()`	Adds a Parameter Based on First or Last Record from Multiple Sources
`derive_var_dthcaus()`	Derive Death Cause
`derive_var_extreme_dt()`	Derive First or Last Date from Multiple Sources
`derive_var_extreme_dtm()`	Derive First or Last Datetime from Multiple Sources
`dthcaus_source()`	Create a `dthcaus_source` Object
`get_summary_records()`	Create Summary Records

Reference

Derivations for Adding Variables

All ADaMs

ADSL-specific

BDS-specific

OCCDS-specific

Derivations for Adding Parameters/Records

BDS-specific

TTE-specific

Metadata

Example Datasets

Advanced Functions

Admiral Options

Higher Order

Creating Auxiliary Datasets

Source Objects

Other

Computation Functions for Vectors

All ADaMs

BDS-specific

Utility Functions

Utilities for Formatting Observations

Utilities for Dataset Checking

Utilities used within Derivation Functions

Utilities for Filtering Observations

Utilities for Quosures

Utilities used for Examples and Template Scripts

Objects exported from other packages

Deprecated