# ADaM in R Asset Library

## Documentation for package ‘admiral’ version 0.12.3

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I L M N P Q R S T U V Y misc

## -- A --

admiral_adlb | Lab Analysis Dataset
admiral_adsl | Subject Level Analysis Dataset
ae_event | Pre-Defined Time-to-Event Source Objects
ae_gr1_event | Pre-Defined Time-to-Event Source Objects
ae_gr2_event | Pre-Defined Time-to-Event Source Objects
ae_gr35_event | Pre-Defined Time-to-Event Source Objects
ae_gr3_event | Pre-Defined Time-to-Event Source Objects
ae_gr4_event | Pre-Defined Time-to-Event Source Objects
ae_gr5_event | Pre-Defined Time-to-Event Source Objects
ae_ser_event | Pre-Defined Time-to-Event Source Objects
ae_sev_event | Pre-Defined Time-to-Event Source Objects
ae_wd_event | Pre-Defined Time-to-Event Source Objects
assert_db_requirements | Check required parameters for a basket
assert_terms | Asserts Requirements for Terms for Queries
assert_valid_queries | Verify if a Dataset Has the Required Format as Queries Dataset.
atoxgr_criteria_ctcv4 | Metadata Holding Grading Criteria for NCI-CTCAEv4
atoxgr_criteria_ctcv5 | Metadata Holding Grading Criteria for NCI-CTCAEv5
atoxgr_criteria_daids | Metadata Holding Grading Criteria for DAIDs

## -- B --

basket_select | Create a 'basket_select' object

## -- C --

call_derivation | Call a Single Derivation Multiple Times
call_user_fun | Calls a Function Provided by the User
censor_source | Create a 'censor_source' Object
chr2vars | Turn a Character Vector into a List of Expressions
compute_age_years | Compute Age in Years
compute_bmi | Compute Body Mass Index (BMI)
compute_bsa | Compute Body Surface Area (BSA)
compute_dtf | Derive the Date Imputation Flag
compute_duration | Compute Duration
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
compute_tmf | Derive the Time Imputation Flag
consolidate_metadata | Consolidate Multiple Meta Datasets Into a Single One
convert_blanks_to_na | Convert Blank Strings Into NAs
convert_blanks_to_na.character | Convert Blank Strings Into NAs
convert_blanks_to_na.data.frame | Convert Blank Strings Into NAs
convert_blanks_to_na.default | Convert Blank Strings Into NAs
convert_blanks_to_na.list | Convert Blank Strings Into NAs
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
convert_na_to_blanks | Convert NAs Into Blank Strings
convert_na_to_blanks.character | Convert NAs Into Blank Strings
convert_na_to_blanks.data.frame | Convert NAs Into Blank Strings
convert_na_to_blanks.default | Convert NAs Into Blank Strings
convert_na_to_blanks.list | Convert NAs Into Blank Strings
count_vals | Count Number of Observations Where a Variable Equals a Value
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

## -- D --

date_source | Create a 'date_source' object
death_event | Pre-Defined Time-to-Event Source Objects
default_qtc_paramcd | Get Default Parameter Code for Corrected QT
derivation_slice | Create a 'derivation_slice' Object
derive_basetype_records | Derive Basetype Variable
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_extreme_event | Add an Extreme Event Parameter
derive_param_extreme_record | Adds a Parameter Based on First or Last Record from Multiple Sources
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_tte | Derive a Time-to-Event Parameter
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
derive_vars_aage | Derive Analysis Age
derive_vars_atc | Derive ATC Class Variables
derive_vars_dt | Derive/Impute a Date from a Date Character Vector
derive_vars_dtm | Derive/Impute a Datetime from a Date Character Vector
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_last_dose | Derive Last Dose
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_period | Add Subperiod, Period, or Phase Variables to ADSL
derive_vars_query | Derive Query Variables
derive_vars_transposed | Derive Variables by Transposing and Merging a Second Dataset
derive_var_age_years | Derive Age in Years
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_basetype | Derive Basetype Variable
derive_var_chg | Derive Change from Baseline
derive_var_confirmation_flag | Derive Confirmation Flag
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
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_last_dose_amt | Derive Last Dose Amount
derive_var_last_dose_date | Derive Last Dose Date-Time
derive_var_last_dose_grp | Derive Last Dose with User-Defined Groupings
derive_var_merged_cat | Merge a Categorization Variable
derive_var_merged_character | Merge a Character Variable
derive_var_merged_exist_flag | Merge an Existence Flag
derive_var_merged_summary | Merge a Summary Variable
derive_var_obs_number | Adds a Variable Numbering the Observations Within Each By Group
derive_var_ontrtfl | Derive On-Treatment Flag Variable
derive_var_pchg | Derive Percent Change from Baseline
derive_var_relative_flag | Flag Observations Before or After a Condition is Fulfilled
derive_var_shift | Derive Shift
derive_var_trtdurd | Derive Total Treatment Duration (Days)
derive_var_trtemfl | Derive Treatment-emergent Flag
desc | dplyr desc
dose_freq_lookup | Pre-Defined Dose Frequencies
dthcaus_source | Create a 'dthcaus_source' Object

## -- E --

event | Create a 'event' Object
event_joined | Create a 'event_joined' Object
event_source | Create an 'event_source' Object
example_qs | Example 'QS' Dataset
exprs | rlang exprs
extend_source_datasets | Add By Groups to All Datasets if Necessary
extract_duplicate_records | Extract Duplicate Records
extract_unit | Extract Unit From Parameter Description
ex_single | Single Dose Exposure Dataset

## -- F --

filter_date_sources | Select the First or Last Date from Several Sources
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
format.basket_select | Returns a Character Representation of a 'basket_select()' Object

## -- G --

get_admiral_option | Get the Value of an Admiral Option
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_not_mapped | Get list of records not mapped from the lookup table.
get_one_to_many_dataset | Get One to Many Values that Led to a Prior Error
get_summary_records | Create Summary Records
get_terms_from_db | Get Terms from the Queries Database

## -- I --

impute_dtc_dt | Impute Partial Date Portion of a "-DTC" Variable
impute_dtc_dtm | Impute Partial Date(-time) Portion of a "-DTC" Variable

## -- L --

lastalive_censor | Pre-Defined Time-to-Event Source Objects
list_all_templates | List All Available ADaM Templates
list_tte_source_objects | List all 'tte_source' Objects Available in a Package

## -- M --

max_cond | Maximum Value on a Subset
min_cond | Minimum Value on a Subset

## -- N --

negate_vars | Negate List of Variables

## -- P --

params | Create a Set of Parameters

## -- Q --

queries | Queries Dataset
queries_mh | Queries MH Dataset
query | Create an 'query' object

## -- R --

records_source | Create a 'records_source' Object
restrict_derivation | Execute a Derivation on a Subset of the Input Dataset

## -- S --

set_admiral_options | Set the Value of Admiral Options
signal_duplicate_records | Signal Duplicate Records
slice_derivation | Execute a Derivation with Different Arguments for Subsets of the Input Dataset

## -- T --

tte_source | Create a 'tte_source' Object

## -- U --

use_ad_template | Open an ADaM Template Script

## -- V --

validate_basket_select | Validate an object is indeed a 'basket_select' object
validate_query | Validate an object is indeed a 'query' object

## -- Y --

yn_to_numeric | Map '"Y"' and '"N"' to Numeric Values

## -- misc --

%>% | Pipe operator