R Observatory: Metrics for MMINP version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

MMINP

0.1.0Package record

Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor

0packages depend

2.5Kdownloads / year

63.8%test coverage

13/13flavors OK

Overview

About

Maintained by Wenli TangCRAN page ↗GitHub ↗Issues ↗

Implements a computational framework to predict microbial community-based metabolic profiles with 'O2PLS' model. It provides procedures of model training and prediction. Paired microbiome and metabolome data are needed for modeling, and the trained model can be applied to predict metabolites of analogous environments using new microbial feature abundances.

Install

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

install.packages("MMINP", 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("YuLab-SMU/MMINP")

Development version from YuLab-SMU/MMINP. 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-mminp

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-MMINP

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-MMINP

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: 3.6 min · r-release-macos-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 23 wordsVignettesYes · 1 · dynamicNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 14
Examples that run: 100%9 run in a plain check
Exported functions with examples: 57%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 29%

Vignettes (1)

MMINP

How these are measured

Downloads

2.5K

CRAN downloads in the past year

Rank #18,141 · ~7/day · ~210/mo

Releases R versions

Daily download trend is not available in this view yet.

26930 days

71390 days

2.5K1 year

Compare downloads with other packages →

Also on100 r2u5 autocran

How downloads are counted

Repository

yulab-smu/mminp ↗Organization: YuLab-SMU

17Stars

4Forks

0Open issues

0Open PRs

0Releases

34Commits

2Commit identities

microbesmetabolitesmetabolite-prediction

34 commits · Last activity 2023-03-17 · +6.3% stars, 30d · Default branch at 0.1.1, ahead of CRAN 0.1.0 (checked 2026-10-21)

Responsiveness

not measured

Stars over time

2025-04-07 · 152026-07-07 · 16

How these are measured

PracticesBeta

2 development-tooling and community-health practices detected across 2 families in the upstream repository

Checks run against github.com/yulab-smu/mminp on 2026-10-21.

Reproducibility and dev environment (1)

Makefile

Lint, format, editor (1)

RStudio project

How this is detected·Detection ruleset v4 (2026-10-20)

Dependencies

Declared dependencies

6 external dependencies (excludes base and recommended)

Installing MMINP adds 27 packages (13 with compiled code, 16 MB of source tarballs). Heaviest: ggplot2 6.0 MB, isoband 1.5 MB, farver 1.2 MB.

Depends (1)

R >= 4.1.0

Imports (4)

magrittr OmicsPLSutilsstats

LinkingTo (0)

none

Suggests (4)

rmarkdown knitr prettydoc 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 (2)

Wenli Tang

Author, Maintainer since 0.1.0 (2022)

Guangchuang Yu

Author, Thesis advisor

Releases (1)

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
0.1.0Latest
record
2022-07-04 · current release
R
R 4.2.0 released · 2022-04-22

Package metadata

First published: 2022-07-04
Total releases: 1 / 4 yrs
License: GPL (>= 3.0)
Minimum R: ≥ 4.1.0
Bundled data: 3.1 MB / 5 files
Download size: 3.4 MB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("MMINP")

Format

Tang, W., & Yu, G. (2022). MMINP: Microbe-Metabolite Interactions-Based Metabolic Profiles Predictor (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.MMINP

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 MMINP version 0.1.0 [Data set]. HJJB, LLC. Data release v2026-10-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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