Package: admiral 1.1.1.9032

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'))

Peer review:

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

Pkgdown:https://pharmaverse.github.io

Datasets:

On CRAN:

cdiscclinical-trialsopen-source

13.60 score 227 stars 4 packages 574 scripts 1.2k downloads 145 exports 25 dependencies

Last updated 3 hours agofrom:6b77c1a303. Checks:OK: 3 NOTE: 4. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 03 2024
R-4.5-winOKDec 03 2024
R-4.5-linuxOKDec 03 2024
R-4.4-winNOTEDec 03 2024
R-4.4-macNOTEDec 03 2024
R-4.3-winNOTEDec 03 2024
R-4.3-macNOTEDec 03 2024

Exports:%>%ae_eventae_gr1_eventae_gr2_eventae_gr3_eventae_gr35_eventae_gr4_eventae_gr5_eventae_ser_eventae_sev_eventae_wd_eventbasket_selectcall_derivationcall_user_funcensor_sourcechr2varscompute_age_yearscompute_bmicompute_bsacompute_dtfcompute_durationcompute_egfrcompute_framinghamcompute_mapcompute_qtccompute_qual_imputationcompute_qual_imputation_deccompute_rrcompute_scalecompute_tmfconsolidate_metadataconvert_blanks_to_naconvert_date_to_dtmconvert_dtc_to_dtconvert_dtc_to_dtmconvert_na_to_blankscount_valscountry_code_lookupcreate_period_datasetcreate_query_datacreate_single_dose_datasetdate_sourcedeath_eventdefault_qtc_paramcdderivation_slicederive_basetype_recordsderive_expected_recordsderive_extreme_eventderive_extreme_recordsderive_locf_recordsderive_param_bmiderive_param_bsaderive_param_computedderive_param_doseintderive_param_exist_flagderive_param_exposurederive_param_extreme_recordderive_param_framinghamderive_param_mapderive_param_qtcderive_param_rrderive_param_ttederive_param_wbc_absderive_summary_recordsderive_var_age_yearsderive_var_analysis_ratioderive_var_anrindderive_var_atoxgrderive_var_atoxgr_dirderive_var_basederive_var_chgderive_var_dthcausderive_var_extreme_dtderive_var_extreme_dtmderive_var_extreme_flagderive_var_joined_exist_flagderive_var_merged_ef_msrcderive_var_merged_exist_flagderive_var_merged_summaryderive_var_obs_numberderive_var_ontrtflderive_var_pchgderive_var_relative_flagderive_var_shiftderive_var_trtdurdderive_var_trtemflderive_vars_aagederive_vars_atcderive_vars_catderive_vars_computedderive_vars_crit_flagderive_vars_dtderive_vars_dtmderive_vars_dtm_to_dtderive_vars_dtm_to_tmderive_vars_durationderive_vars_dyderive_vars_extreme_eventderive_vars_joinedderive_vars_mergedderive_vars_merged_lookupderive_vars_periodderive_vars_queryderive_vars_transposeddescdose_freq_lookupdthcaus_sourceeventevent_joinedevent_sourceexprsextract_duplicate_recordsextract_unitfilter_existfilter_extremefilter_joinedfilter_not_existfilter_relativeflag_eventget_admiral_optionget_duplicates_datasetget_flagged_recordsget_many_to_one_datasetget_not_mappedget_one_to_many_datasetget_summary_recordsget_vars_queryimpute_dtc_dtimpute_dtc_dtmlastalive_censorlist_all_templateslist_tte_source_objectsmax_condmin_condnegate_varsparamsprint_named_listqueryrecords_sourcerestrict_derivationset_admiral_optionssignal_duplicate_recordsslice_derivationuse_ad_templateyn_to_numeric

Dependencies:admiraldevclicpp11dplyrfansigenericsgluehmslifecyclelubridatemagrittrpillarpkgconfigpurrrR6rlangstringistringrtibbletidyrtidyselecttimechangeutf8vctrswithr

Creating a BDS Exposure ADaM

Rendered frombds_exposure.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-11-13
Started: 2021-09-08

Creating a BDS Finding ADaM

Rendered frombds_finding.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-11-15
Started: 2021-07-05

Creating a BDS Time-to-Event ADaM

Rendered frombds_tte.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-09-20
Started: 2021-11-17

Creating a PK NCA or Population PK ADaM

Rendered frompk_adnca.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-09-20
Started: 2023-03-07

Creating ADSL

Rendered fromadsl.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-09-30
Started: 2021-07-05

Creating an OCCDS ADaM

Rendered fromoccds.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-11-13
Started: 2021-07-05

Creating Questionnaire ADaMs

Rendered fromquestionnaires.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-09-30
Started: 2023-03-07

Date and Time Imputation

Rendered fromimputation.Rmdusingknitr::rmarkdownon Dec 03 2024.

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

Generic Derivations

Rendered fromgeneric.Rmdusingknitr::rmarkdownon Dec 03 2024.

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

Higher Order Functions

Rendered fromhigher_order.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-09-20
Started: 2022-09-06

Hy's Law Implementation

Rendered fromhys_law.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-10-03
Started: 2023-03-07

Lab Grading

Rendered fromlab_grading.Rmdusingknitr::rmarkdownon Dec 03 2024.

Last update: 2024-11-25
Started: 2022-09-06

Programming Concepts and Conventions

Rendered fromconcepts_conventions.Rmdusingknitr::rmarkdownon Dec 03 2024.

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

Queries Dataset Documentation

Rendered fromqueries_dataset.Rmdusingknitr::rmarkdownon Dec 03 2024.

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

Visit and Period Variables

Rendered fromvisits_periods.Rmdusingknitr::rmarkdownon Dec 03 2024.

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

Readme and manuals

Help Manual

Help pageTopics
Pipe operator%>%
Lab Analysis Datasetadmiral_adlb
Subject Level Analysis Datasetadmiral_adsl
Metadata Holding Grading Criteria for NCI-CTCAEv4atoxgr_criteria_ctcv4
Metadata Holding Grading Criteria for NCI-CTCAEv5atoxgr_criteria_ctcv5
Metadata Holding Grading Criteria for DAIDsatoxgr_criteria_daids
Create a 'basket_select' objectbasket_select
Call a Single Derivation Multiple Timescall_derivation
Calls a Function Provided by the Usercall_user_fun
Create a 'censor_source' Objectcensor_source
Turn a Character Vector into a List of Expressionschr2vars
Compute Age in Yearscompute_age_years
Compute Body Mass Index (BMI)compute_bmi
Compute Body Surface Area (BSA)compute_bsa
Derive the Date Imputation Flagcompute_dtf
Compute Durationcompute_duration
Compute Estimated Glomerular Filtration Rate (eGFR) for Kidney Functioncompute_egfr
Compute Framingham Heart Study Cardiovascular Disease 10-Year Risk Scorecompute_framingham
Compute Mean Arterial Pressure (MAP)compute_map
Compute Corrected QTcompute_qtc
Function to Impute Values When Qualifier Exists in Character Resultcompute_qual_imputation
Compute Factor for Value Imputations When Character Value Contains < or >compute_qual_imputation_dec
Compute RR Interval From Heart Ratecompute_rr
Compute Scale Parameterscompute_scale
Derive the Time Imputation Flagcompute_tmf
Consolidate Multiple Meta Datasets Into a Single Oneconsolidate_metadata
Convert Blank Strings Into NAsconvert_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 Objectconvert_date_to_dtm
Convert a Date Character Vector into a Date Objectconvert_dtc_to_dt
Convert a Date Character Vector into a Datetime Objectconvert_dtc_to_dtm
Convert NAs Into Blank Stringsconvert_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 Valuecount_vals
Country Code Lookupcountry_code_lookup
Create a Reference Dataset for Subperiods, Periods, or Phasescreate_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 dosescreate_single_dose_dataset
Create a 'date_source' objectdate_source
Pre-Defined Time-to-Event Source Objectsae_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 QTdefault_qtc_paramcd
Create a 'derivation_slice' Objectderivation_slice
Derive Basetype Variablederive_basetype_records
Derive Expected Recordsderive_expected_records
Add the Worst or Best Observation for Each By Group as New Recordsderive_extreme_event
Add the First or Last Observation for Each By Group as New Recordsderive_extreme_records
Derive LOCF (Last Observation Carried Forward) Recordsderive_locf_records
Adds a Parameter for BMIderive_param_bmi
Adds a Parameter for BSA (Body Surface Area) Using the Specified Methodderive_param_bsa
Adds a Parameter Computed from the Analysis Value of Other Parametersderive_param_computed
Adds a Parameter for Dose Intensityderive_param_doseint
Add an Existence Flag Parameterderive_param_exist_flag
Add an Aggregated Parameter and Derive the Associated Start and End Datesderive_param_exposure
Adds a Parameter Based on First or Last Record from Multiple Sourcesderive_param_extreme_record
Adds a Parameter for Framingham Heart Study Cardiovascular Disease 10-Year Risk Scorederive_param_framingham
Adds a Parameter for Mean Arterial Pressurederive_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 Parameterderive_param_tte
Add a parameter for lab differentials converted to absolute valuesderive_param_wbc_abs
Add New Records Within By Groups Using Aggregation Functionsderive_summary_records
Derive Age in Yearsderive_var_age_years
Derive Ratio Variablederive_var_analysis_ratio
Derive Reference Range Indicatorderive_var_anrind
Derive Lab High toxicity Grade 0 - 4 and Low Toxicity Grades 0 - (-4)derive_var_atoxgr
Derive Lab Toxicity Grade 0 - 4derive_var_atoxgr_dir
Derive Baseline Variablesderive_var_base
Derive Change from Baselinederive_var_chg
Derive Death Causederive_var_dthcaus
Derive First or Last Date from Multiple Sourcesderive_var_extreme_dt
Derive First or Last Datetime from Multiple Sourcesderive_var_extreme_dtm
Add a Variable Flagging the First or Last Observation Within Each By Groupderive_var_extreme_flag
Derives a Flag Based on an Existing Flagderive_var_joined_exist_flag
Merge an Existence Flag From Multiple Sourcesderive_var_merged_ef_msrc
Merge an Existence Flagderive_var_merged_exist_flag
Merge Summary Variablesderive_var_merged_summary
Adds a Variable Numbering the Observations Within Each By Groupderive_var_obs_number
Derive On-Treatment Flag Variablederive_var_ontrtfl
Derive Percent Change from Baselinederive_var_pchg
Flag Observations Before or After a Condition is Fulfilledderive_var_relative_flag
Derive Shiftderive_var_shift
Derive Total Treatment Duration (Days)derive_var_trtdurd
Derive Treatment-emergent Flagderive_var_trtemfl
Derive Analysis Agederive_vars_aage
Derive ATC Class Variablesderive_vars_atc
Derive Categorization Variables Like 'AVALCATy' and 'AVALCAyN'derive_vars_cat
Adds Variable(s) Computed from the Analysis Value of one or more Parametersderive_vars_computed
Derive Criterion Flag Variables 'CRITy', 'CRITyFL', and 'CRITyFLN'derive_vars_crit_flag
Derive/Impute a Date from a Date Character Vectorderive_vars_dt
Derive/Impute a Datetime from a Date Character Vectorderive_vars_dtm
Derive Date Variables from Datetime Variablesderive_vars_dtm_to_dt
Derive Time Variables from Datetime Variablesderive_vars_dtm_to_tm
Derive Durationderive_vars_duration
Derive Relative Day Variablesderive_vars_dy
Add the Worst or Best Observation for Each By Group as New Variablesderive_vars_extreme_event
Add Variables from an Additional Dataset Based on Conditions from Both Datasetsderive_vars_joined
Add New Variable(s) to the Input Dataset Based on Variables from Another Datasetderive_vars_merged
Merge Lookup Table with Source Datasetderive_vars_merged_lookup
Add Subperiod, Period, or Phase Variables to ADSLderive_vars_period
Derive Query Variablesderive_vars_query
Derive Variables by Transposing and Merging a Second Datasetderive_vars_transposed
dplyr descdesc
Pre-Defined Dose Frequenciesdose_freq_lookup
Create a 'dthcaus_source' Objectdthcaus_source
Create a 'event' Objectevent
Create a 'event_joined' Objectevent_joined
Create an 'event_source' Objectevent_source
Single Dose Exposure Datasetex_single
Example 'QS' Datasetexample_qs
rlang exprsexprs
Extract Unit From Parameter Descriptionextract_unit
Returns records that fit into existing by groups in a filtered source datasetfilter_exist
Filter the First or Last Observation for Each By Groupfilter_extreme
Filter Observations Taking Other Observations into Accountfilter_joined
Returns records that don't fit into existing by groups in a filtered source datasetfilter_not_exist
Filter the Observations Before or After a Condition is Fulfilledfilter_relative
Create a 'flag_event' Objectflag_event
Get the Value of an Admiral Optionget_admiral_option
Get Duplicate Records that Led to a Prior Errorget_duplicates_dataset
Create an Existence Flagget_flagged_records
Get Many to One Values that Led to a Prior Errorget_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 Errorget_one_to_many_dataset
Create Summary Recordsget_summary_records
Get Terms from the Queries Databaseget_terms_from_db
Get Query Variablesget_vars_query
Impute Partial Date Portion of a ''--DTC'' Variableimpute_dtc_dt
Impute Partial Date(-time) Portion of a ''--DTC'' Variableimpute_dtc_dtm
List All Available ADaM Templateslist_all_templates
List all 'tte_source' Objects Available in a Packagelist_tte_source_objects
Maximum Value on a Subsetmax_cond
Minimum Value on a Subsetmin_cond
Negate List of Variablesnegate_vars
Create a Set of Parametersparams
Queries Datasetqueries
Queries MH Datasetqueries_mh
Create an 'query' objectquery
Create a 'records_source' Objectrecords_source
Execute a Derivation on a Subset of the Input Datasetrestrict_derivation
Set the Value of Admiral Optionsset_admiral_options
Execute a Derivation with Different Arguments for Subsets of the Input Datasetslice_derivation
Create a 'tte_source' Objecttte_source
Open an ADaM Template Scriptuse_ad_template
Map '"Y"' and '"N"' to Numeric Valuesyn_to_numeric