R Observatory: Metrics for GSbench version 0.1.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

GSbench

0.1.0Package record

Benchmarking Genomic Selection and Machine-Learning Prediction Models

0packages depend

901downloads / year

75.4%test coverage

13/13flavors OK

Overview

About

Maintained by Muhammad FarooqiCRAN page ↗GitHub ↗Issues ↗

A unified interface to fit, cross-validate and benchmark genomic prediction models from SNP marker data. It implements genomic best linear unbiased prediction (GBLUP) and ridge-regression BLUP in base R, and offers a common interface to machine-learning predictors (elastic net, random forest and gradient boosting) through optional packages, together with a stacked ensemble. Cross-validation uses breeding-relevant schemes and reports prediction accuracy honestly, so models can be compared fairly. The genomic relationship matrix follows VanRaden (2008) doi:10.3168/jds.2007-0980; the mixed-model solver follows Endelman (2011) doi:10.3835/plantgenome2011.08.0024; the genomic-selection framework follows Meuwissen, Hayes and Goddard (2001) doi:10.1093/genetics/157.4.1819.

Changes in 0.1.0

First release.

Core (base R): simulate_population(), qc_markers(), impute_markers(), Gmatrix() (VanRaden), and gblup() (GBLUP by REML, validated against rrBLUP::mixed.solve).
Unified modelling interface gs_fit() / predict() covering GBLUP, elastic net (glmnet), random forest (ranger) and gradient boosting (xgboost).
gs_cv() for breeding-relevant cross-validation (random k-fold and leave-one-group-out).
gs_ensemble(), a stacked super-learner combining base models with non-negative, out-of-fold-fitted weights.
gs_benchmark() with print/summary/plot to compare all available models under one cross-validation.

From NEWS.md in the release

Install

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

install.packages("GSbench", 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("mqfarooqi1/GSbench")

Development version from mqfarooqi1/GSbench. 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-gsbench

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-GSbench

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-GSbench

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: 2.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK7 OK2026-07-01

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.1.0

READMEYes · 505 wordsVignettesYes · 1 · evaluation depends on the environmentNEWSYes · 67% structured · mentions 0.1.0Citation fileNo

Help pages: 15 (1 internal)includes a package overview page
Examples that run: 100%14 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 20%

Vignettes (1)

Benchmarking genomic prediction models with GSbench HTML

How these are measured

Downloads

901

CRAN downloads in the past year

Rank #18,899 · ~2/day · ~75/mo

Releases R versions

Daily download trend is not available in this view yet.

26730 days

68990 days

9011 year

Compare downloads with other packages →

Also on20 r2u2 autocran

How downloads are counted

Repository

mqfarooqi1/gsbench ↗Account: mqfarooqi1

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2026-07-27 · Default branch at 0.1.0.9000, ahead of CRAN 0.1.0 (checked 2026-10-18)

Responsiveness

not measured

How these are measured

PracticesBeta

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

Checks run against github.com/mqfarooqi1/gsbench on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (3)

pkgdown

GitHub Pages site last deployed 2026-07-27 · The repository has a site deploy workflow

Reproducibility and dev environment (1)

Dockerfile

CRAN release process (1)

cran-comments.md

Show all practicesHide 1 practice

Research and citation (1)

CITATION.cff

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

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing GSbench adds 1 package (0 with compiled code, 102 KB of source tarballs). Heaviest: withr 102 KB.

Depends (1)

R >= 4.1.0

Imports (3)

graphicsstatswithr

LinkingTo (0)

none

Suggests (8)

rrBLUP glmnet ranger xgboost testthat knitr rmarkdown spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (1)

Muhammad Farooqi

Author, Maintainer since 0.1.0 (2026)

Releases (1)

0.1.0Latest
record
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: ≥ 4.1.0
Download size: 33 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("GSbench")

Format

Farooqi, M. (2026). GSbench: Benchmarking Genomic Selection and Machine-Learning Prediction Models (Version 0.1.0) [Computer software]. https://doi.org/10.32614/CRAN.package.GSbench

This package has no citation file, so citation() returns this entry built from DESCRIPTION.

The repository also keeps a CITATION.cff.

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 GSbench 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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