ADaM in R Asset Library

[Up] [Top]

Documentation for package ‘admiral’ version 0.12.3

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