R Observatory: Metrics for MUGS version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MUGS

0.1.0

Multisource Graph Synthesis with EHR Data

0packages depend

5.9Kdownloads / year

58.0%test coverage

13/13checks pass

Overview

About

Maintained by Mengyan LiFirst published 2025-05-191 releasesCRAN page ↗GitHub ↗

We develop Multi-source Graph Synthesis (MUGS), an algorithm designed to create embeddings for pediatric Electronic Health Record (EHR) codes by leveraging graphical information from three distinct sources: (1) pediatric EHR data, (2) EHR data from the general patient population, and (3) existing hierarchical medical ontology knowledge shared across different patient populations. See Li et al. (2024) doi:10.1038/s41746-024-01320-4 for details.

Install

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

install.packages("MUGS", 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("celehs/MUGS")

Development version from celehs/MUGS. 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-mugs

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-MUGS

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-MUGS

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

Health

CRAN checks

13OK

Slowest check: 11.6 min · r-oldrel-macos-x86_64

Code health

Yes

Tests · ratio 0.40

58.0%

Coverage · measured lines

100%

Documentation · exports

16

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
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 · 560 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: not tracked
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

5.9K

CRAN downloads in the past year

Rank #8,612 · ~16/day · ~489/mo

Releases R versions

Daily download trend is not available in this view yet.

17130 days

1.1K90 days

5.9K1 year

Compare downloads with other packages →

Also on93 r2u16 autocran

Repository

GitHub ↗ celehs/mugs

1Stars

1Forks

0Open issues

0Open PRs

0Releases

37Commits

3Contributors

37 commits · Last activity 2025-05-15 · 0% stars, 30d

Stars over time

2026-05-20 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

5 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/celehs/mugs on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Docs source (1)

README.Rmd

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (16)

MASSMatrixfastDummies doSNOW dplyr grplasso foreach glmnet grpreg inline mvtnorm pROCparallelRcppArmadillo rsvdmethods

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (6)

Maintainer (1)

Mengyan Li

Maintainer, Author

Authors (5)

Maintainer, Author

Author

Author

Author

Author

Contributors (1)

Thomas Charlon

Contributor

Package Timeline

1 release. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
2026-03-10 · current release
R
R 4.5.0 released · 2025-04-11

Package metadata

First published: 2025-05-19
Total releases: 1 / 1 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 125 KB / 8 files
Download size: 514 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MUGS")

Format

Li, M., Cai, T., Charlon, T., LTD, P., Li, X., & Team, C. (2025). MUGS: Multisource Graph Synthesis with EHR Data (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MUGS

This is what citation() produces when a package has no citation file of its own. If it prints something else, use that.

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 MUGS version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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