R Observatory: Metrics for NeighborFinder version 1.0.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

NeighborFinder

1.0.1

Find Neighbor Species of a Bacteria of Interest in the Human Gut Microbiota

0packages depend

454downloads / year

41.3%test coverage

8/13checks pass

Overview

About

Maintained by Mathilde SolaFirst published 2026-06-301 releasesCRAN page ↗

Implementation of the local approach described in Sola et al., 2026 doi:10.64898/2025.12.05.692507 to identify companion species of a bacteria of interest. From several abundance tables of metagenomic data, 'NeighborFinder' suggests a shortlist of companion species based on the integration of results. A visualization via a network is proposed.

Install

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

install.packages("NeighborFinder", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-neighborfinder

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-NeighborFinder

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-NeighborFinder

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

Health

CRAN checks

5NOTE8OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64

Slowest check: 5.0 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.14

41.3%

Coverage · measured lines

96%

Documentation · exports

17

Dependencies · direct

Check history

NOTE2026-07-16
10 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-07-01
7 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 527 wordsVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 95%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

454

CRAN downloads in the past year

Rank #22,967 · ~1/day · ~38/mo

Releases R versions

Daily download trend is not available in this view yet.

19930 days

45490 days

4541 year

Compare downloads with other packages →

Also on15 r2u2 autocran

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (17)

dplyr GGally glmnet glue igraph magrittrMatrixmvtnorm network purrr rlang snastatsstringr tibble tidyrutils

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 (3)

Maintainer (1)

Mathilde Sola

Author, Maintainer

Authors (3)

Mathilde Sola

Author, Maintainer

Magali Berland

Author

Mahendra Mariadassou

Author

Package Timeline

1 release. R releases are shown for context.

1.0.1Latest
2026-06-30 · current release
R
R 4.6.0 released · 2026-04-24

Package metadata

First published: 2026-06-30
Total releases: 1 / 1 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.5.0
Bundled data: 4.0 MB / 5 files
Download size: 7.8 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("NeighborFinder")

Format

Sola, M., Berland, M., & Mariadassou, M. (2026). NeighborFinder: Find Neighbor Species of a Bacteria of Interest in the Human Gut Microbiota (Version 1.0.1) [Computer software]. https://doi.org/10.32614/CRAN.package.NeighborFinder

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 NeighborFinder version 1.0.1 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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