R Observatory: Metrics for allofus version 1.3.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

allofus

1.3.0Package record

Interface for 'All of Us' Researcher Workbench

0packages depend

9.2Kdownloads / year

14.7%test coverage

13/13flavors OK

Overview

About

Maintained by Louisa SmithCRAN page ↗GitHub ↗Website ↗Issues ↗

Streamline use of the 'All of Us' Researcher Workbench (https://www.researchallofus.org/data-tools/workbench/)with tools to extract and manipulate data from the 'All of Us' database. Increase interoperability with the Observational Health Data Science and Informatics ('OHDSI') tool stack by decreasing reliance of 'All of Us' tools and allowing for cohort creation via 'Atlas'. Improve reproducible and transparent research using 'All of Us'.

Changes in 1.3.0

The package now supports All of Us workbench 2.0. In particular, environment variables are resolved on package load. aou_create_bucket() can now be used to create a workspace bucket, as it is no longer automatic.

In addition, this version fixes aou_create_temp_table() on workbench 2.0, where the resulting table could not be joined to a CDR table. The workbench 2.0 CDR lives in a single BigQuery region (us-central1), but a query built entirely from local data references no CDR table, so BigQuery had nothing to infer a location from and ran it in the US multi-region instead. Queries are now run with the CDR as the default dataset, which pins them to the CDR's region.

From NEWS.md in the release

Install

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

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

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

if (!requireNamespace("pak", quietly = TRUE))
  install.packages("pak", repos = "https://cloud.r-project.org/")
pak::pak("roux-ohdsi/allofus")

Development version from roux-ohdsi/allofus. Installs pak first if it is not already available.

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-allofus

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-allofus

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-allofus

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: 2.1 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK13 OK2026-06-09
ERROR12 OK, 1 ERROR2026-06-08
OK13 OK2026-05-12

Show 4 earlier changesHide 4 earlier changes

WARNING12 OK, 1 WARNING2026-05-11
OK14 OK2026-04-14
ERROR13 OK, 1 ERROR2026-03-16
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.3.0

READMEYes · 449 wordsVignettesYes · 4 · dynamicNEWSYes · 100% structured · mentions 1.3.0Citation fileYes · cites a publicationWebsiteYes · pkgdown

Help pages: 35 (14 internal)includes a package overview page
Examples that run: 95%18 run in a plain check (15 of them under a condition) · 1 never run
Exported functions with examples: 100%
Documented parameters: 99%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (4)

All of Us in R HTML
Extracting All of Us survey and EHR data HTML
Managing files on the workbench HTML
Using ATLAS to create a cohort HTML

How these are measured

Downloads

9.2K

CRAN downloads in the past year

Rank #5,292 · ~25/day · ~763/mo

Releases R versions

Daily download trend is not available in this view yet.

54530 days

1.5K90 days

9.2K1 year

Compare downloads with other packages →

Also on137 r2u31 autocran

How downloads are counted

Repository

roux-ohdsi/allofus ↗Organization: roux-ohdsi

19Stars

5Forks

5Open issues

1Open PRs

4Releases

392Commits

5Commit identities

392 commits · Last activity 2026-09-03 · 0% stars, 30d · Default branch at 1.3.0.9000, ahead of CRAN 1.3.0 (checked 2026-10-18) · Discussions: 2 posts

Responsiveness

How these are sampled

PRs merged (all time): 92%
Median days to close, 50 most recently updated closed issues: 46
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2025-09-29 · 182026-07-07 · 19

How these are measured

PracticesBeta

11 development-tooling and community-health practices detected across 5 families in the upstream repository

Checks run against github.com/roux-ohdsi/allofus on 2026-10-18.

Continuous integration (2)

GitHub ActionsR CMD check workflow

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (4)

README.Rmdpkgdownaltdoc

GitHub Pages site last deployed 2026-09-03

pkgdown site last built 2026-09-03

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Show all practicesHide 1 practice

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v3 (2026-09-26)

AI coding toolsBeta

This repository shows signs of AI coding tools.

Claude Codefirst seen 2026-06-10
Commits: at least 2 crediting it in the message

Models named in its commits

Claude Opus 4.82 commits · Jun 2026

Counts are commits, not lines of code. Commits by a tool's accounts count once across all of its accounts. Commits crediting it are the largest count among its credit lines, a minimum.How this is detected·Detection ruleset v4 (updated 2026-09-27)

Dependencies

Declared dependencies

27 external dependencies (excludes base and recommended)

Installing allofus adds 43 packages (27 with compiled code, 27 MB of source tarballs). Heaviest: stringi 11 MB, fs 1.4 MB, nanoparquet 1.1 MB.

Depends (1)

R >= 2.10

Imports (17)

cli tidyr magrittr dplyr glue bigrquery (>= 1.5.1)purrrstatsutilsdbplyr sessioninfo rlang stringr DBI lifecycle bit64 jsonlite

LinkingTo (0)

none

Suggests (12)

knitr rmarkdown testthat kableExtra DT googlesheets4 tibble forcats gh SqlRender duckdb withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Louisa Smith

Rob Cavanaugh

Author, Copyright holder

Previously maintained by Rob Cavanaugh (1.0.0 to 1.2.0).

Releases (4)

Pick two releases to compare their code metrics.

1.3.0Latest
record
2026-09-03 · current release · diff ↗ ·
added 1 export
aou_create_bucket
R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.0
record
2024-11-06 · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.0
record
2024-04-04 · diff ↗ ·
added 3 exports
aou_collect, aou_compute, aou_create_temp_table
1.0.0
record
2023-12-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-21
Total releases: 4 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 75 KB / 5 files
Download size: 3.3 MB

Cite

Cite this package

Run in R for the authors' entry:

citation("allofus")

The package provides a citation file, so citation() returns the authors' own entry.

It points to 10.1093/jamia/ocae198.

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 allofus version 1.3.0 [Data set]. HJJB, LLC. Data release v2026-10-21. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-21, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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