ADaM in R Asset Library

Documentation for package ‘admiral’ version 0.9.1

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-- A --

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

-- 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 Quosures
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_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_tmf	Derive the Time Imputation Flag
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_derived_param	Adds a Parameter Computed from the Analysis Value of Other Parameters
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_first_event	Add a First Event Parameter
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_disposition_reason	Derive a Disposition Reason at a Specific Timepoint
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_dt	Merge a (Imputed) Date Variable
derive_vars_merged_dtm	Merge a (Imputed) Datetime Variable
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_suppqual	Join Supplementary Qualifier Variables into the Parent SDTM Domain
derive_vars_transposed	Derive Variables by Transposing and Merging a Second Dataset
derive_var_ady	Derive Analysis Study Day
derive_var_aendy	Derive Analysis End Relative Day
derive_var_agegr_ema	Derive Age Groups
derive_var_agegr_fda	Derive Age Groups
derive_var_age_years	Derive Age in Years
derive_var_analysis_ratio	Derive Ratio Variable
derive_var_anrind	Derive Reference Range Indicator
derive_var_astdy	Derive Analysis Start Relative Day
derive_var_atirel	Derive Time Relative to Reference
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_disposition_status	Derive a Disposition Status at a Specific Timepoint
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_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
derive_var_worst_flag	Adds a Variable Flagging the Maximal / Minimal Value Within a Group of Observations
dose_freq_lookup	Pre-Defined Dose Frequencies
dthcaus_source	Create a 'dthcaus_source' Object
dtm_level	Create a 'dtm_level' object
dt_level	Create a 'dt_level' object

-- E --

event_source	Create an 'event_source' Object
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_confirmation	Filter Confirmed Observations
filter_date_sources	Select the First or Last Date from Several Sources
filter_extreme	Filter the First or Last Observation for Each By Group
filter_relative	Filter the Observations Before or After a Condition is Fulfilled
format.basket_select	Returns a Character Representation of a 'basket_select()' Object
format_eoxxstt_default	Default Format for Disposition Status
format_reason_default	Default Format for the Disposition Reason

-- G --

get_admiral_option	Get the Value of an Admiral Option
get_duplicates_dataset	Get Duplicate Records that Led to a Prior Error
get_imputation_target_date	Get Date Imputation Targets
get_imputation_target_time	Get Time Imputation Targets
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_partialdatetime	Parse DTC variable and Determine Components
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
print.adam_templates	Print 'adam_templates' Objects
print.source	Print 'source' Objects
print_named_list	Print Named List

-- Q --

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

-- R --

restrict_derivation	Execute a Derivation on a Subset of the Input Dataset
restrict_imputed_dtc_dt	Restrict Imputed DTC date to Minimum/Maximum Dates
restrict_imputed_dtc_dtm	Restrict Imputed DTC date to Minimum/Maximum Dates

-- S --

sdg_select	Create an 'sdg_select' object
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
smq_select	Create an 'smq_select' object

-- 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