Package: admiral 1.1.1.9008

Ben Straub

admiral: ADaM in R Asset Library

A toolbox for programming Clinical Data Interchange Standards Consortium (CDISC) compliant Analysis Data Model (ADaM) datasets in R. ADaM datasets are a mandatory part of any New Drug or Biologics License Application submitted to the United States Food and Drug Administration (FDA). Analysis derivations are implemented in accordance with the "Analysis Data Model Implementation Guide" (CDISC Analysis Data Model Team, 2021, <https://www.cdisc.org/standards/foundational/adam>).

Authors:Ben Straub [aut, cre], Stefan Bundfuss [aut], Jeffrey Dickinson [aut], Ross Farrugia [aut], Fanny Gautier [aut], G Gayatri [aut], Asha Chakma [aut], Dinakar Kulkarni [aut], Edoardo Mancini [aut], Sadchla Mascary [aut], Gordon Miller [aut], Lina Patil [aut], Sophie Shapcott [aut], Eric Simms [aut], Daniel Sjoberg [aut], Stefan Thoma [aut], Phillip Webster [aut], Kangjie Zhang [aut], Zelos Zhu [aut], F. Hoffmann-La Roche AG [cph, fnd], GlaxoSmithKline LLC [cph, fnd]

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admiral.pdf |admiral.html✨
admiral/json (API)
NEWS

# Install 'admiral' in R:

install.packages('admiral', repos = c('https://pharmaverse.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/pharmaverse/admiral/issues

Datasets:

admiral_adlb - Lab Analysis Dataset
admiral_adsl - Subject Level Analysis 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
ex_single - Single Dose Exposure Dataset
example_qs - Example 'QS' Dataset
queries - Queries Dataset
queries_mh - Queries MH Dataset

On CRAN:

cdisc clinical-trials open-source

144 exports 219 stars 6.52 score 25 dependencies 5 dependents 556 scripts 1.4k downloads

Last updated 5 days agofrom:0beb82dd82. Checks:OK: 1 NOTE: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Sep 03 2024
R-4.5-win	NOTE	Sep 03 2024
R-4.5-linux	NOTE	Sep 03 2024
R-4.4-win	NOTE	Sep 03 2024
R-4.4-mac	NOTE	Sep 03 2024
R-4.3-win	NOTE	Sep 03 2024
R-4.3-mac	NOTE	Sep 03 2024

Exports:%>%ae_event ae_gr1_event ae_gr2_event ae_gr3_event ae_gr35_event ae_gr4_event ae_gr5_event ae_ser_event ae_sev_event ae_wd_event basket_select call_derivation call_user_fun censor_source chr2vars compute_age_years compute_bmi compute_bsa compute_dtf compute_duration compute_egfr compute_framingham compute_map compute_qtc compute_qual_imputation compute_qual_imputation_dec compute_rr compute_scale compute_tmf consolidate_metadata convert_blanks_to_na convert_date_to_dtm convert_dtc_to_dt convert_dtc_to_dtm convert_na_to_blanks count_vals country_code_lookup create_period_dataset create_query_data create_single_dose_dataset date_source death_event default_qtc_paramcd derivation_slice derive_basetype_records derive_expected_records derive_extreme_event derive_extreme_records derive_locf_records derive_param_bmi derive_param_bsa derive_param_computed derive_param_doseint derive_param_exist_flag derive_param_exposure derive_param_extreme_record derive_param_framingham derive_param_map derive_param_qtc derive_param_rr derive_param_tte derive_param_wbc_abs derive_summary_records derive_var_age_years derive_var_analysis_ratio derive_var_anrind derive_var_atoxgr derive_var_atoxgr_dir derive_var_base derive_var_chg derive_var_dthcaus derive_var_extreme_dt derive_var_extreme_dtm derive_var_extreme_flag derive_var_joined_exist_flag derive_var_merged_ef_msrc derive_var_merged_exist_flag derive_var_merged_summary derive_var_obs_number derive_var_ontrtfl derive_var_pchg derive_var_relative_flag derive_var_shift derive_var_trtdurd derive_var_trtemfl derive_vars_aage derive_vars_atc derive_vars_computed derive_vars_crit_flag derive_vars_dt derive_vars_dtm derive_vars_dtm_to_dt derive_vars_dtm_to_tm derive_vars_duration derive_vars_dy derive_vars_extreme_event derive_vars_joined derive_vars_merged derive_vars_merged_lookup derive_vars_period derive_vars_query derive_vars_transposed desc dose_freq_lookup dthcaus_source event event_joined event_source exprs extract_duplicate_records extract_unit filter_exist filter_extreme filter_joined filter_not_exist filter_relative flag_event get_admiral_option get_duplicates_dataset get_flagged_records get_many_to_one_dataset get_not_mapped get_one_to_many_dataset get_summary_records get_vars_query impute_dtc_dt impute_dtc_dtm lastalive_censor list_all_templates list_tte_source_objects max_cond min_cond negate_vars params print_named_list query records_source restrict_derivation set_admiral_options signal_duplicate_records slice_derivation use_ad_template yn_to_numeric

Dependencies:admiraldev cli cpp11 dplyr fansi generics glue hms lifecycle lubridate magrittr pillar pkgconfig purrr R6 rlang stringi stringr tibble tidyr tidyselect timechange utf8 vctrs withr

Creating a BDS Exposure ADaM

Rendered frombds_exposure.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-02-05
Started: 2021-09-08

Creating a BDS Finding ADaM

Rendered frombds_finding.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-07-09
Started: 2021-07-05

Creating a BDS Time-to-Event ADaM

Rendered frombds_tte.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-03-06
Started: 2021-11-17

Creating a PK NCA or Population PK ADaM

Rendered frompk_adnca.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-09-03
Started: 2023-03-07

Creating ADSL

Rendered fromadsl.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-06-06
Started: 2021-07-05

Creating an OCCDS ADaM

Rendered fromoccds.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-01-26
Started: 2021-07-05

Creating Questionnaire ADaMs

Rendered fromquestionnaires.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-09-03
Started: 2023-03-07

Date and Time Imputation

Rendered fromimputation.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2023-09-11
Started: 2021-09-08

Generic Derivations

Rendered fromgeneric.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2023-11-30
Started: 2022-12-06

Higher Order Functions

Rendered fromhigher_order.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2023-09-11
Started: 2022-09-06

Hy's Law Implementation

Rendered fromhys_law.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-07-09
Started: 2023-03-07

Lab Grading

Rendered fromlab_grading.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-07-09
Started: 2022-09-06

Programming Concepts and Conventions

Rendered fromconcepts_conventions.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-06-07
Started: 2024-05-16

Queries Dataset Documentation

Rendered fromqueries_dataset.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2023-12-04
Started: 2021-11-17

Visit and Period Variables

Rendered fromvisits_periods.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2024-05-21
Started: 2022-12-06

Help page	Topics
Pipe operator	%>%
Lab Analysis Dataset	admiral_adlb
Subject Level Analysis Dataset	admiral_adsl
Metadata Holding Grading Criteria for NCI-CTCAEv4	atoxgr_criteria_ctcv4
Metadata Holding Grading Criteria for NCI-CTCAEv5	atoxgr_criteria_ctcv5
Metadata Holding Grading Criteria for DAIDs	atoxgr_criteria_daids
Create a 'basket_select' object	basket_select
Call a Single Derivation Multiple Times	call_derivation
Calls a Function Provided by the User	call_user_fun
Create a 'censor_source' Object	censor_source
Turn a Character Vector into a List of Expressions	chr2vars
Compute Age in Years	compute_age_years
Compute Body Mass Index (BMI)	compute_bmi
Compute Body Surface Area (BSA)	compute_bsa
Derive the Date Imputation Flag	compute_dtf
Compute Duration	compute_duration
Compute Estimated Glomerular Filtration Rate (eGFR) for Kidney Function	compute_egfr
Compute Framingham Heart Study Cardiovascular Disease 10-Year Risk Score	compute_framingham
Compute Mean Arterial Pressure (MAP)	compute_map
Compute Corrected QT	compute_qtc
Function to Impute Values When Qualifier Exists in Character Result	compute_qual_imputation
Compute Factor for Value Imputations When Character Value Contains < or >	compute_qual_imputation_dec
Compute RR Interval From Heart Rate	compute_rr
Compute Scale Parameters	compute_scale
Derive the Time Imputation Flag	compute_tmf
Consolidate Multiple Meta Datasets Into a Single One	consolidate_metadata
Convert Blank Strings Into NAs	convert_blanks_to_na convert_blanks_to_na.character convert_blanks_to_na.data.frame convert_blanks_to_na.default convert_blanks_to_na.list
Convert a Date into a Datetime Object	convert_date_to_dtm
Convert a Date Character Vector into a Date Object	convert_dtc_to_dt
Convert a Date Character Vector into a Datetime Object	convert_dtc_to_dtm
Convert NAs Into Blank Strings	convert_na_to_blanks convert_na_to_blanks.character convert_na_to_blanks.data.frame convert_na_to_blanks.default convert_na_to_blanks.list
Count Number of Observations Where a Variable Equals a Value	count_vals
Country Code Lookup	country_code_lookup
Create a Reference Dataset for Subperiods, Periods, or Phases	create_period_dataset
Creates a queries dataset as input dataset to the 'dataset_queries' argument in 'derive_vars_query()'	create_query_data
Create dataset of single doses	create_single_dose_dataset
Create a 'date_source' object	date_source
Pre-Defined Time-to-Event Source Objects	ae_event ae_gr1_event ae_gr2_event ae_gr35_event ae_gr3_event ae_gr4_event ae_gr5_event ae_ser_event ae_sev_event ae_wd_event death_event lastalive_censor
Get Default Parameter Code for Corrected QT	default_qtc_paramcd
Create a 'derivation_slice' Object	derivation_slice
Derive Basetype Variable	derive_basetype_records
Derive Expected Records	derive_expected_records
Add the Worst or Best Observation for Each By Group as New Records	derive_extreme_event
Add the First or Last Observation for Each By Group as New Records	derive_extreme_records
Derive LOCF (Last Observation Carried Forward) Records	derive_locf_records
Adds a Parameter for BMI	derive_param_bmi
Adds a Parameter for BSA (Body Surface Area) Using the Specified Method	derive_param_bsa
Adds a Parameter Computed from the Analysis Value of Other Parameters	derive_param_computed
Adds a Parameter for Dose Intensity	derive_param_doseint
Add an Existence Flag Parameter	derive_param_exist_flag
Add an Aggregated Parameter and Derive the Associated Start and End Dates	derive_param_exposure
Adds a Parameter Based on First or Last Record from Multiple Sources	derive_param_extreme_record
Adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Score	derive_param_framingham
Adds a Parameter for Mean Arterial Pressure	derive_param_map
Adds a Parameter for Corrected QT (an ECG measurement)	derive_param_qtc
Adds a Parameter for Derived RR (an ECG measurement)	derive_param_rr
Derive a Time-to-Event Parameter	derive_param_tte
Add a parameter for lab differentials converted to absolute values	derive_param_wbc_abs
Add New Records Within By Groups Using Aggregation Functions	derive_summary_records
Derive Age in Years	derive_var_age_years
Derive Ratio Variable	derive_var_analysis_ratio
Derive Reference Range Indicator	derive_var_anrind
Derive Lab High toxicity Grade 0 - 4 and Low Toxicity Grades 0 - (-4)	derive_var_atoxgr
Derive Lab Toxicity Grade 0 - 4	derive_var_atoxgr_dir
Derive Baseline Variables	derive_var_base
Derive Change from Baseline	derive_var_chg
Derive Death Cause	derive_var_dthcaus
Derive First or Last Date from Multiple Sources	derive_var_extreme_dt
Derive First or Last Datetime from Multiple Sources	derive_var_extreme_dtm
Add a Variable Flagging the First or Last Observation Within Each By Group	derive_var_extreme_flag
Derives a Flag Based on an Existing Flag	derive_var_joined_exist_flag
Merge an Existence Flag From Multiple Sources	derive_var_merged_ef_msrc
Merge an Existence Flag	derive_var_merged_exist_flag
Merge Summary Variables	derive_var_merged_summary
Adds a Variable Numbering the Observations Within Each By Group	derive_var_obs_number
Derive On-Treatment Flag Variable	derive_var_ontrtfl
Derive Percent Change from Baseline	derive_var_pchg
Flag Observations Before or After a Condition is Fulfilled	derive_var_relative_flag
Derive Shift	derive_var_shift
Derive Total Treatment Duration (Days)	derive_var_trtdurd
Derive Treatment-emergent Flag	derive_var_trtemfl
Derive Analysis Age	derive_vars_aage
Derive ATC Class Variables	derive_vars_atc
Adds Variable(s) Computed from the Analysis Value of one or more Parameters	derive_vars_computed
Derive Criterion Flag Variables 'CRITy', 'CRITyFL', and 'CRITyFLN'	derive_vars_crit_flag
Derive/Impute a Date from a Date Character Vector	derive_vars_dt
Derive/Impute a Datetime from a Date Character Vector	derive_vars_dtm
Derive Date Variables from Datetime Variables	derive_vars_dtm_to_dt
Derive Time Variables from Datetime Variables	derive_vars_dtm_to_tm
Derive Duration	derive_vars_duration
Derive Relative Day Variables	derive_vars_dy
Add the Worst or Best Observation for Each By Group as New Variables	derive_vars_extreme_event
Add Variables from an Additional Dataset Based on Conditions from Both Datasets	derive_vars_joined
Add New Variable(s) to the Input Dataset Based on Variables from Another Dataset	derive_vars_merged
Merge Lookup Table with Source Dataset	derive_vars_merged_lookup
Add Subperiod, Period, or Phase Variables to ADSL	derive_vars_period
Derive Query Variables	derive_vars_query
Derive Variables by Transposing and Merging a Second Dataset	derive_vars_transposed
dplyr desc	desc
Pre-Defined Dose Frequencies	dose_freq_lookup
Create a 'dthcaus_source' Object	dthcaus_source
Create a 'event' Object	event
Create a 'event_joined' Object	event_joined
Create an 'event_source' Object	event_source
Single Dose Exposure Dataset	ex_single
Example 'QS' Dataset	example_qs
rlang exprs	exprs
Extract Unit From Parameter Description	extract_unit
Returns records that fit into existing by groups in a filtered source dataset	filter_exist
Filter the First or Last Observation for Each By Group	filter_extreme
Filter Observations Taking Other Observations into Account	filter_joined
Returns records that don't fit into existing by groups in a filtered source dataset	filter_not_exist
Filter the Observations Before or After a Condition is Fulfilled	filter_relative
Create a 'flag_event' Object	flag_event
Get the Value of an Admiral Option	get_admiral_option
Get Duplicate Records that Led to a Prior Error	get_duplicates_dataset
Create an Existence Flag	get_flagged_records
Get Many to One Values that Led to a Prior Error	get_many_to_one_dataset
Get list of records not mapped from the lookup table.	get_not_mapped
Get One to Many Values that Led to a Prior Error	get_one_to_many_dataset
Create Summary Records	get_summary_records
Get Terms from the Queries Database	get_terms_from_db
Get Query Variables	get_vars_query
Impute Partial Date Portion of a ''--DTC'' Variable	impute_dtc_dt
Impute Partial Date(-time) Portion of a ''--DTC'' Variable	impute_dtc_dtm
List All Available ADaM Templates	list_all_templates
List all 'tte_source' Objects Available in a Package	list_tte_source_objects
Maximum Value on a Subset	max_cond
Minimum Value on a Subset	min_cond
Negate List of Variables	negate_vars
Create a Set of Parameters	params
Queries Dataset	queries
Queries MH Dataset	queries_mh
Create an 'query' object	query
Create a 'records_source' Object	records_source
Execute a Derivation on a Subset of the Input Dataset	restrict_derivation
Set the Value of Admiral Options	set_admiral_options
Execute a Derivation with Different Arguments for Subsets of the Input Dataset	slice_derivation
Create a 'tte_source' Object	tte_source
Open an ADaM Template Script	use_ad_template
Map '"Y"' and '"N"' to Numeric Values	yn_to_numeric