R Observatory: Metrics for MUGS version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MUGS

0.1.0Package record

Multisource Graph Synthesis with EHR Data

0packages depend

5.6Kdownloads / year

58.0%test coverage

13/13flavors OK

Overview

About

Maintained by Mengyan LiCRAN page ↗GitHub ↗Website ↗

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.

Changes in 0.1.0

Initial CRAN release.
Implements Multisource Graph Synthesis (MUGS) for embedding pediatric EHR codes using multi-source graph data.
Includes core functions for generating and evaluating embeddings.
Provides simulated datasets and detailed vignettes demonstrating package usage.

From NEWS.md in the release

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. 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-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). 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: 11.6 min · r-oldrel-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 560 wordsVignettesYes · 7 · dynamicNEWSYes · 67% structured · mentions 0.1.0Citation fileNoWebsiteYes · pkgdown

Help pages: 16
Examples that run: no examples
Exported functions with examples: 0%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 0%

Vignettes (7)

CodeEff_Matrix_usage HTML
CodeSiteEff_I2_par_usage HTML
DataGen_rare_group_usage HTML
Evaluation_sim_usage HTML
get_embed_usage HTML
GroupEff_par_usage HTML
Multisource Graph Synthesis with EHR Data HTML

How these are measured

Downloads

5.6K

CRAN downloads in the past year

Rank #13,311 · ~15/day · ~463/mo

Releases R versions

Daily download trend is not available in this view yet.

30030 days

85990 days

5.6K1 year

Compare downloads with other packages →

Also on68 r2u3 autocran

How downloads are counted

Repository

celehs/mugs ↗Account: celehs

1Stars

1Forks

0Open issues

0Open PRs

0Releases

37Commits

3Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: not measured
Median days to close, 50 most recently updated closed PRs: 4

Stars over time

2026-05-20 · 12026-07-07 · 1

How these are measured

PracticesBeta

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

Checks run against github.com/celehs/mugs on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2025-05-08

pkgdown site last built 2025-05-08, before release 0.1.0 (2025-05-19)

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

15 external dependencies (excludes base and recommended)

Installing MUGS adds 34 packages (18 with compiled code, 35 MB of source tarballs). Heaviest: stringi 11 MB, data.table 5.7 MB, rsvd 3.3 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (6)

Mengyan Li

Maintainer since 0.1.0 (2025), Author

Author

Author

Author

Author

Contributor

Releases (1)

R
R 4.6.0 released · 2026-04-24
0.1.0Latest
record
2025-05-19 · 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

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 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 MUGS version 0.1.0 [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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