omophub

1.8.1

R Client for the 'OMOPHub' Medical Vocabulary API

0packages depend

3.1Kdownloads / year

95.2%test coverage

13/13checks pass

Overview

About

Maintained by Alex ChenFirst published 2025-12-178 releasesCRAN page ↗GitHub ↗

Provides an R interface to the 'OMOPHub' API for accessing 'OHDSI ATHENA' standardized medical vocabularies. Supports concept search, semantic search using neural embeddings, concept similarity, vocabulary exploration, hierarchy navigation, relationship queries, concept mappings, and FHIR-to-OMOP concept resolution with automatic pagination.

Install

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

install.packages("omophub", 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("omopHub/omophub-R")

Development version from omopHub/omophub-R. 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-omophub

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

# 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-omophub

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13OK

Slowest check: 2.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 2.02

95.2%

Coverage · measured lines

100%

Documentation · exports

Dependencies · direct

Check history

OK2026-06-08
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-06-07
12 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 858 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 14%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

3.1K

CRAN downloads in the past year

Rank #7,885 · ~8/day · ~258/mo

Releases R versions

Daily download trend is not available in this view yet.

30130 days

1.3K90 days

3.1K1 year

Compare downloads with other packages →

Also on85 r2u39 autocran

Repository

GitHub ↗ omophub/omophub-r

5Stars

0Forks

0Open issues

0Open PRs

9Releases

57Commits

3Contributors

api-clientathenabioinformaticscdmclinical-researchhealthcare-dataicd10medical-vocabularies

57 commits · Last activity 2026-06-01 · 0% stars, 30d

Stars over time

2026-01-08 · 32026-07-07 · 5

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/omophub/omophub-r on 2026-07-19.

Continuous integration (1)

GitHub Actions

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1

Imports (8)

httr2 R6 rlang cli tibble purrr glue checkmate

LinkingTo (0)

none

Suggests (7)

testthat httptest2 webmockr knitr rmarkdown keyring withr

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (2)

Maintainer (1)

Alex Chen

Author, Maintainer, Copyright holder

Authors (1)

Alex Chen

Author, Maintainer, Copyright holder

Alex Chen

Author, Maintainer, Copyright holder

Observational Health Data Science and Informatics

Package Timeline

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

1.8.1Latest
2026-06-01 · current release · diff ↗
1.8.0
2026-05-25 · diff ↗
1.7.0
2026-04-30 · diff ↗
R
R 4.6.0 released · 2026-04-24
1.6.0
2026-04-14 · diff ↗
1.5.0
2026-03-27 · diff ↗
1.4.0
2026-02-23 · diff ↗
1.3.0
2026-01-08 · diff ↗
1.1.0
2025-12-17
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-12-17
Total releases: 8 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 4.1
Download size: 68 KB
Installed size: not tracked yet
With dependencies: not tracked yet

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