allofus

1.2.0

Interface for 'All of Us' Researcher Workbench

0packages depend

10Kdownloads / year

2.8%test coverage

12/13checks pass

Overview

About

Maintained by Rob CavanaughFirst published 2023-12-213 releasesCRAN page ↗GitHub ↗

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'.

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.

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).

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.19

2.8%

Coverage · measured lines

94%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-06-09
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-08
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-05-12
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
WARNING2026-05-11
12 OK · 0 NOTE · 1 WARNING · 0 ERROR · 0 FAILURE

Show 3 earlier snapshots

OK2026-04-14
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-16
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 281 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

10K

CRAN downloads in the past year

Rank #4,251 · ~27/day · ~832/mo

Releases R versions

Daily download trend is not available in this view yet.

40030 days

2.1K90 days

10K1 year

Compare downloads with other packages →

Also on176 r2u3 autocran

Repository

GitHub ↗ roux-ohdsi/allofus

19Stars

5Forks

5Open issues

3Open PRs

3Releases

380Commits

4Contributors

380 commits · Last activity 2026-07-02 · 0% stars, 30d

Stars over time

2025-07-11 · 172026-07-07 · 19

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/roux-ohdsi/allofus on 2026-07-31.

Continuous integration (1)

GitHub Actions

Reproducibility and dev environment (1)

data-raw/

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Docs source (1)

README.Rmd

Show all practices

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

24 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (16)

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

LinkingTo (0)

none

Suggests (10)

knitr rmarkdown testthat kableExtra DT googlesheets4 tibble forcats gh SqlRender

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Rob Cavanaugh

Author, Maintainer, Copyright holder

Authors (2)

Rob Cavanaugh

Author, Maintainer, Copyright holder

Louisa Smith

Author, Copyright holder

Rob Cavanaugh

Author, Maintainer, Copyright holder

Louisa Smith

Author, Copyright holder

Package Timeline

3 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
1.2.0Latest
2024-11-06 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
1.1.0
2024-04-04 · diff ↗
1.0.0
2023-12-21
R
R 4.3.0 released · 2023-04-21

Package metadata

First published: 2023-12-21
Total releases: 3 / 3 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 2.10
Bundled data: 75 KB / 5 files
Download size: 3.3 MB
Installed size: not tracked yet
With dependencies: not tracked yet

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