R Observatory: Metrics for xnet version 0.1.11

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

xnet

0.1.11Package record

Two-Step Kernel Ridge Regression for Network Predictions

0packages depend

2.1Kdownloads / year

71.2%test coverage

11/13flavors OK

Overview

About

Maintained by Joris MeysCRAN page ↗GitHub ↗Issues ↗

Fit a two-step kernel ridge regression model for predicting edges in networks, and carry out cross-validation using shortcuts for swift and accurate performance assessment (Stock et al, 2018 doi:10.1093/bib/bby095 ).

Changes in 0.1.11

Bug fixes

unnecessary mentions of dots argument removed from some help pages.
linear_filter() takes floating point errors into account when checking whether the alpha values sum to 1.

From NEWS.md in the release

Install

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

install.packages("xnet", 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("CenterForStatistics-UGent/xnet")

Development version from CenterForStatistics-UGent/xnet. 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-xnet

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-xnet

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-xnet

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

2NOTE11OK

Check messages

NOTECRAN incoming feasibilityr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Maintainer: ‘Joris Meys <Joris.Meys@UGent.be>’

Found the following URLs which should use \doi (with the DOI name only):
  File ‘drugTargetInteraction.Rd’:
    https://doi.org/10.1093/bioinformatics/btn162
  File ‘loo.Rd’:
    http://doi.org/10.1093/bib/bby095
  File ‘proteinInteraction.Rd’:
    https://doi.org/10.1093/bioinformatics/bth910
  File ‘xnet-package.Rd’:
    http://doi.org/10.1093/bib/bby095

CRAN check page ↗

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.11

README· In the repository, left out of the releaseVignettesYes · 3 · dynamicNEWSYes · 100% structured · mentions 0.1.11Citation fileYes · cites a publication

Help pages: 49includes a package overview page
Examples that run: 100%26 run in a plain check
Exported functions with examples: 88%
Documented parameters: 96%
Return-value docs: 96%
Help pages citing references: 4%

Vignettes (3)

How these are measured

Downloads

2.1K

CRAN downloads in the past year

Rank #22,524 · ~6/day · ~178/mo

Releases R versions

Daily download trend is not available in this view yet.

22130 days

59190 days

2.1K1 year

Compare downloads with other packages →

Also on67 r2u9 autocran

How downloads are counted

Repository

centerforstatistics-ugent/xnet ↗Organization: CenterForStatistics-UGent

11Stars

2Forks

2Open issues

0Open PRs

5Releases

379Commits

2Commit identities

379 commits · Last activity 2021-06-03 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 100%
Median days to close, 50 most recently updated closed issues: 116
Median days to close, 50 most recently updated closed PRs: 0

Stars over time

2023-12-21 · 112026-07-07 · 11

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/centerforstatistics-ugent/xnet on 2026-10-22.

Continuous integration (3)

GitHub ActionsR CMD check workflowTravis CI (config file)

The R CMD check workflow runs on Linux, macOS and Windows, and on R-devel

Docs source (1)

GitHub Pages site last deployed 2021-06-03

Coverage (2)

Coverage reporting (Codecov).covrignore

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 xnet adds no packages beyond those that come with R.

Depends (1)

R >= 3.4.0

Imports (5)

methodsutilsgraphicsstatsgrDevices

LinkingTo (0)

none

Suggests (6)

testthat knitr rmarkdown ChemmineR covr fmcsR

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)

Joris Meys

Maintainer since 0.1.10 (2020), Author

Michiel Stock

Author

Releases (2)

Pick two releases to compare their code metrics.

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
R
R 4.0.0 released · 2020-04-24
0.1.11Latest
record
2020-02-03 · current release · diff ↗
0.1.10
record
2020-01-09
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-01-09
Total releases: 2 / 6 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.4.0
Bundled data: 75 KB / 2 files
Download size: 236 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("xnet")

The package provides a citation file that builds its entry when R runs it. Run citation() to see it.

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 xnet version 0.1.11 [Data set]. HJJB, LLC. Data release v2026-10-25. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-25, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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