R Observatory: Metrics for pharmaverseadamjnj version 0.0.8

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

pharmaverseadamjnj

0.0.8Package record

J&J Innovative Medicine ADaM Test Data

0packages dependsuggested by 1

4.3Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by David Munoz TordCRAN page ↗Declared funder: J&J Innovative Medicine

A set of Analysis Data Model (ADaM) datasets constructed by modifying the ADaM datasets in the 'pharmaverseadam' package to meet J&J Innovative Medicine's standard data structure for Clinical and Statistical Programming.

Changes in 0.0.8

Changed

updated adlb code for ANL01FL related to AVALC values

[0.0.7] - 2026-09-30

Added

Added DDPCDTHC and NCTXSDT variables to ADSL
Added AESEVN, EXSTDT, DOSEDT, ADATRES, and NABSTAT variables to ADAE
Added EXSTDT, ADATRES, and NABSTAT variables to ADEX
Added ADATRES and NABSTAT variables to ADEXSUM
Updated ATOXDSCL & ATOXDSCH variables as per latest lbtoxgrade file on ADLB dataset
Updated AVISIT for baseline on ADLB dataset
Added CRITy and CRITyFL on ADLB based on MCRITy and MCRITyML values since details missing on markedlyabnormal file
Added PKRFL variable to ADPC dataset

Show all changes in 0.0.8Hide the rest of the changes in 0.0.8

Added PARCAT3N to ADLB dataset
Added AVALCAT1 for DOSEDAYS parameter in ADEXSUM dataset

Changed

Modified ADSL death-related variable derivations (DTHFL, DTHDT, DTHCAUS, DDPCDTHC)
Modified ADSL to add DCTDT label
Modified ADEXSUM to add DURFUPD parameter
Modified ADLB toxicity grade detail ATOXDSCL and ATOXDSCH
Modified ADLB.PARAM values to display as per paramlookup file to replace x10E with 10^.
Modified MCRITy and MCRITyFL variable values to assign based on PARAM instead of random values.
Modified ADEG for AVAL variable to include "ABNORMAL, CS", "ABNORMAL, NCS", "NORMAL"
Modified ADEG for PARAMCD converted 'msec' to 'ms'
Modified ADPC for CRIT1 variable
Modified ADEX to add ATPT, ATPTN, ADURC, ARSDSDO, ATDPRP, and ATDPRPU variables
Modified ADEX for APERIOD and updated ATPT values
Modified ADEX to add AVAMT, AVAMTU, ADOSFRQP, ADOSDLY, ARSDOSD, ACDOSE, ACDOSU, ASTDY, ALL ANL flags ex. ANL01FL, ANL02FL, ANL03FL, ANL04FL, INTCAT, SKPCAT, DLYCAT variables.
Updated PARAMN values in ADVS domain
Added CRIT6, CRIT6FL, CRIT7 & CRIT7FL on ADILLI for [AST or ALT] PARCAT
Added CRIT2, CRIT2FL, CRIT3, CRIT3FL on ADILLI for TBILI & ALP PARCAT
Modified ADEXSUM to add TRTDURD parameter
Modified ECOCCUR, ADOSE, ACDOSE, ASCHDOSE, AVAMT, ADOSU, ACDOSU. ASCHDOSU and AVAMTU variables
Modified PARAM unit to 'mg' in ADEXSUM dataset
Modified PARAM and PARAMCD to add CUMDOSS1, CUMDOSS2
Modified PARCAT1, PARCAT3 categories tests on ADLB
Modified MCRITyML, MCRITyMN and MCRITy variables as per standards in ADLB
Modified CRITy and CRITYFL variables on ADLB
Modified ADURC values to HH:MM format on ADEX dataset
Modified AVALC, BASE, CHG, PCHG and ATPT on ADLB dataset
Modified ONTRTFL values to consider all non missing visit records on ADDILI dataset
Modified CRIT2FL and CRIT2 on ADDILI dataset

[0.0.6] - 2026-09-24

Added

Added ADISHUM Dataset
Added DDPCDTHC and NCTXSDT variables to ADSL
Added AESEVN, EXSTDT, DOSEDT, ADATRES, and NABSTAT variables to ADAE
Added EXSTDT, ADATRES, and NABSTAT variables to ADEX
Added ADATRES and NABSTAT variables to ADEXSUM
Added vars to ADSL: LASTCTDT, UNBLNDDT, IMFL, SAFEXRS, FASEXRS, PPREXRS, PKEXRES, and IMEXRES
Added restord labels to xpt
Change ONTRFl for ADVS to first dose within 30 days
Added STRAT1D, STRAT2D to ADSL
Added ABODSYS1, ABODSYS2, ADECOD1, and ADECOD2 to ADEX
Added CRITx (1-8) to ADVS
Added VSCLSIG and RACE to ADVS
Added AOCTIFL, AESCAT, SMQzzNAM, and CQzzNAM, AERELSx, AEACNSx, RELGR1, AEDRGSx, DOSSxDY, DOSSxU, DOSSxON to ADAE
Added derived variables AESHOSPP and AESHOSPR
Added ADVS: RESP TEMP and PULSE PARAMCD
Added variables COHORT, GROUP, and EOTDT to ADSL.
Added variables CMSTRTPT and CMSTTPT to ADCM.
Added AOCT01FL, AOCT02FL, AOCT03FL, AOCS01FL, AOCS02FL, AOCS03FL to ADAE
Added ADAECOMP and ADSLCOMP datasets
Added ADDISP dataset
Added RACE variable from ADSL to ADEG dataset
Updated ATOXDSCL & ATOXDSCH variables as per latest lbtoxgrade file on ADLB dataset
Updated AVISIT for baseline on ADLB dataset
Added CRITy and CRITyFL on ADLB based on MCRITy and MCRITyML values since details missing on markedlyabnormal file
Added PKRFL variable to ADPC dataset
Added PARCAT3N to ADLB dataset
Added AVALCAT1 for DOSEDAYS parameter in ADEXSUM dataset

Changed

Modified ADSL death-related variable derivations (DTHFL, DTHDT, DTHCAUS, DDPCDTHC)
Modified ADSL to add DCTDT label
Modified ADEXSUM to add DURFUPD parameter
Removed *_DECODE vars in ADSL, ADLB, ADVS, ADAE, ADCM, ADEG, ADEX
Releveled TRT01P and TRT01A (now Xanomeline Low Dose -> Xanomeline High Dose -> Placebo)
Modified "General disorders and administration site conditions" to "Gastrointestinal disorders" in ADEX
Modified ADVS on ORTHYP, ORTHYPS and ORTHYPD parameters for TSFVIT04
Modified RESCRNFL and assigned 01-701-1240 to Subject refused to sign informed consent
Modified ADVS on RESP parameter for gsfvit02a and gsfvit02b
Modified ADVS on week 20 and week 24 AVISIT derivation
Modified ADVS on AVISITN variable
Modified ADVS on CRIT7/CRIT7FL CRIT8/CRIT8FL values of DIABP parameter
Modified ADVS AVISIT, AVISITN and added ADY derivation
Modified REGION1 to "Northern America"
Added DCSREAS and DCTREAS levels
Modified ADAE to update derivation rules for AEREL, AOCCFL, AOCCPFL, AOCCSFL, TRDISCFL, AESCAT and SMQxxNAM
Modified ADAEOCMQ to update derivation rule for OCMQNAM and AEDECOD
Modified ADAGOCMQ for AEDECOD merge logic, ACAT1, and used conversion factor GLUC, HBA1C for standard units to conventional units.
Modified ADDISP to update labels for SxSDY and SxEDY variables.
Fix adeg CRIT1FL and CRIT2FL factor order
Modified ADLB toxicity grade detail ATOXDSCL and ATOXDSCH
Modified ADLB.PARAM values to display as per paramlookup file to replace x10E with 10^.
Modified MCRITy and MCRITyFL variable values to assign based on PARAM instead of random values.
Modified ADEG for AVAL variable to include "ABNORMAL, CS", "ABNORMAL, NCS", "NORMAL"
Modified ADEG for PARAMCD converted 'msec' to 'ms'
Modified ADPC for CRIT1 variable
Modified ADEX to add ATPT, ATPTN, ADURC, ARSDSDO, ATDPRP, and ATDPRPU variables
Modified ADEX for APERIOD and updated ATPT values
Modified ADEX to add AVAMT, AVAMTU, ADOSFRQP, ADOSDLY, ARSDOSD, ACDOSE, ACDOSU, ASTDY, ALL ANL flags ex. ANL01FL, ANL02FL, ANL03FL, ANL04FL, INTCAT, SKPCAT, DLYCAT variables.
Updated PARAMN values in ADVS domain
Added CRIT6, CRIT6FL, CRIT7 & CRIT7FL on ADILLI for [AST or ALT] PARCAT
Added CRIT2, CRIT2FL, CRIT3, CRIT3FL on ADILLI for TBILI & ALP PARCAT
Modified ADEXSUM to add TRTDURD parameter
Modified ECOCCUR, ADOSE, ACDOSE, ASCHDOSE, AVAMT, ADOSU, ACDOSU. ASCHDOSU and AVAMTU variables
Modified PARAM unit to 'mg' in ADEXSUM dataset
Modified PARAM and PARAMCD to add CUMDOSS1, CUMDOSS2
Modified PARCAT1, PARCAT3 categories tests on ADLB
Modified MCRITyML, MCRITyMN and MCRITy variables as per standards in ADLB
Modified CRITy and CRITYFL variables on ADLB
Modified ADURC values to HH:MM format on ADEX dataset
Modified AVALC, BASE, CHG, PCHG and ATPT on ADLB dataset
Modified ONTRTFL values to consider all non missing visit records on ADDILI dataset
Modified CRIT2FL and CRIT2 on ADDILI dataset

[0.0.5] - 2026-05-25

Added

Add DCTADY to ADSL #32
Add new addili dataset
Add LBNAM variable to adlb
Add REGION1 = "North America"

[0.0.2] - 2025-12-03

Added ADAGOCMQ & ADPC dataset
Added LBSPEC and LBFAST to ADLB dataset

Changed

Update ADSL to have all factor levels of RACE and ETHNIC
Update adsl DTH60TFL to DTHB60FL
Updated adae update to include start/end time.
Updated source file OCMQs to reflect FDA changes to FMQ
Renamed adaefmq to adaeocmq
Fixed ADCM to properly handle uncoded terms
Fixed ADLB to use "BEFORE TREATMENT" for ATPT instead of "00:00"
ADSL: Set RANDFL to "Y" for most subjects with SAFFL="Y", but also for a few with SAFFL="N" and non-NA TRT01P
Updated {pharmaverseadam} released a new version 0.1.2 some variable labels have been added accordingly.

[0.0.1] - 2024-07-02

Added

Initial CRAN release
Provides ADaM datasets that comply with J&J Innovative Medicine standards
Built on top of the 'pharmaverseadam' package
Implements data conversion from pharmaverse format to J&J standards format
Provides reproducible and consistent test data

Implemented ADaM Domains

ADSL (Subject Level Analysis Dataset)
ADAE (Adverse Events Analysis Dataset)
ADCM (Concomitant Medications Analysis Dataset)
ADEG (ECG Analysis Dataset)
ADEX (Exposure Analysis Dataset)
ADESUM (Exposure Analysis Summary Dataset)
ADLB (Laboratory Test Results Analysis Dataset)
ADVS (Vital Signs Analysis Dataset)
ADTTESAF (Time-to-Event Safety Analysis Dataset)
ADAEFMQ (Adverse Events Analysis Dataset FDA Medical Query)

[0.0.2] - 2025-12-03

Added ADAGOCMQ & ADPC dataset
Added LBSPEC and LBFAST to ADLB dataset

Changed

Update ADSL to have all factor levels of RACE and ETHNIC
Update adsl DTH60TFL to DTHB60FL
Updated adae update to include start/end time.
Updated source file OCMQs to reflect FDA changes to FMQ
Renamed adaefmq to adaeocmq
Fixed ADCM to properly handle uncoded terms
Fixed ADLB to use "BEFORE TREATMENT" for ATPT instead of "00:00"
ADSL: Set RANDFL to "Y" for most subjects with SAFFL="Y", but also for a few with SAFFL="N" and non-NA TRT01P
Updated {pharmaverseadam} released a new version 0.1.2 some variable labels have been added accordingly.

[0.0.1] - 2024-07-02

Added

Initial CRAN release
Provides ADaM datasets that comply with J&J Innovative Medicine standards
Built on top of the 'pharmaverseadam' package
Implements data conversion from pharmaverse format to J&J standards format
Provides reproducible and consistent test data

Implemented ADaM Domains

ADSL (Subject Level Analysis Dataset)
ADAE (Adverse Events Analysis Dataset)
ADCM (Concomitant Medications Analysis Dataset)
ADEG (ECG Analysis Dataset)
ADEX (Exposure Analysis Dataset)
ADESUM (Exposure Analysis Summary Dataset)
ADLB (Laboratory Test Results Analysis Dataset)
ADVS (Vital Signs Analysis Dataset)
ADTTESAF (Time-to-Event Safety Analysis Dataset)
ADAEFMQ (Adverse Events Analysis Dataset FDA Medical Query)

From NEWS.md in the release

Install

R (CRAN)Ubuntu (r2u)Fedora (COPR)openSUSE (OBS)

install.packages("pharmaverseadamjnj", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-pharmaverseadamjnj

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled. We list this channel from recorded r2u download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

bspm (used by r2u) also needs make: sudo apt install make

# enable the iucar/cran COPR if it is not already present, then install
ls /etc/yum.repos.d/*iucar*cran*.repo >/dev/null 2>&1 \
  || sudo dnf copr enable -y iucar/cran
sudo dnf install -y R-CRAN-pharmaverseadamjnj

RPMs from the iucar/cran COPR, rebuilt from CRAN.

For install.packages() integration in R, also: sudo dnf install R-CoprManager

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-pharmaverseadamjnj

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed). We list this channel from recorded autoCRAN download activity rather than from a live index of the repository, so treat it as last known rather than guaranteed.

Health

CRAN checks

13OK

CRAN check page ↗

Slowest check: 7.1 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-07-16
WARNING12 OK, 1 WARNING2026-07-15
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.0.8

READMEYes · 201 wordsVignettesNoNEWSYes · 67% structured · mentions 0.0.8Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 18 (1 internal)includes a package overview page
Examples that run: 100%17 run in a plain check
Exported functions with examples: not tracked
Documented parameters: not tracked
Return-value docs: not tracked
Help pages citing references: 0%

How these are measured

Downloads

4.3K

CRAN downloads in the past year

Rank #5,727 · ~12/day · ~355/mo

Releases R versions

Daily download trend is not available in this view yet.

52030 days

1.4K90 days

4.3K1 year

Compare downloads with other packages →

Also on129 r2u8 autocran

How downloads are counted

Dependencies

Declared dependencies

1 external dependency (excludes base and recommended)

Installing pharmaverseadamjnj adds 11 packages (7 with compiled code, 8.1 MB of source tarballs). Heaviest: pharmaverseadam 4.1 MB, vctrs 1.0 MB, rlang 766 KB.

Depends (2)

R >= 3.5pharmaverseadam

Imports (0)

none

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Suggested by 1

Suggests, most downloaded first

junco

How these are counted

Code & Tests

Datasets

People & History

People (7)

David Munoz Tord

Author, Maintainer since 0.0.1 (2025)

Author

Author

Contributor

Contributor · added in 0.0.6

Selvaraj Shanmugam

Contributor · added in 0.0.8

J&J Innovative Medicine

Copyright holder, Funder

Releases (7)

Pick two releases to compare their code metrics.

0.0.8Latest
record
2026-10-09 · current release · diff ↗
0.0.7
record
2026-09-28 · diff ↗
0.0.6
record
2026-09-24 · diff ↗
0.0.5
record
2026-05-08 · diff ↗
0.0.4
record
2026-05-07 · diff ↗
R
R 4.6.0 released · 2026-04-24
0.0.2
record
2025-12-10 · diff ↗
0.0.1
record
2025-07-15
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-07-15
Total releases: 7 / 1 yrs
License: Apache License (>= 2)
Minimum R: ≥ 3.5
Bundled data: 3.5 MB / 17 files
Download size: 3.5 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("pharmaverseadamjnj")

Format

Munoz Tord, D., J&J Innovative Medicine, Divakaran, M., Kovach, J., Mao, R., Masel, N., & Shanmugam, S. (2026). pharmaverseadamjnj: J&J Innovative Medicine ADaM Test Data (Version 0.0.8) [Computer software]. https://doi.org/10.32614/CRAN.package.pharmaverseadamjnj

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

Cite the R Observatory

For a number measured here: a download total, a coverage figure, an archival date.

Format

APA

Balamuta, J. J. (2026). R Observatory: Metrics for pharmaverseadamjnj version 0.0.8 [Data set]. HJJB, LLC. Data release v2026-10-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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