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 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_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

atoxgr_criteria_ctcv5: Metadata Holding Grading Criteria for NCI-CTCAEv5

atoxgr_criteria_daids: Metadata Holding Grading Criteria for DAIDs

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

call_user_fun(): Calls a Function Provided by the User

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

Superseded

Superseded functions have been replaced with better functions. However, we will not be removing these functions from admiral. We do strongly encourage you to make the switch over.

date_source() superseded: Create a date_source object

derive_param_extreme_record() superseded: Adds a Parameter Based on First or Last Record from Multiple Sources

derive_var_dthcaus() superseded: Derive Death Cause

derive_var_extreme_dt() superseded: Derive First or Last Date from Multiple Sources

derive_var_extreme_dtm() superseded: Derive First or Last Datetime from Multiple Sources

dthcaus_source() superseded: Create a dthcaus_source Object

get_summary_records() superseded: Create Summary Records