R Observatory: Metrics for BGGE version 0.6.5

Balamuta, James Joseph

BGGE

0.6.5

Bayesian Genomic Linear Models Applied to GE Genome Selection

0packages depend

3.4Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Italo GranatoFirst published 2017-11-305 releasesCRAN page ↗

Application of genome prediction for a continuous variable, focused on genotype by environment (GE) genomic selection models (GS). It consists a group of functions that help to create regression kernels for some GE genomic models proposed by Jarquín et al. (2014) doi:10.1007/s00122-013-2243-1 and Lopez-Cruz et al. (2015) doi:10.1534/g3.114.016097. Also, it computes genomic predictions based on Bayesian approaches. The prediction function uses an orthogonal transformation of the data and specific priors present by Cuevas et al. (2014) doi:10.1534/g3.114.013094.

Install

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

install.packages("BGGE", 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-bgge

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-BGGE

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-BGGE

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

Health

CRAN checks

13OK

Slowest check: 55 s · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

1

Dependencies · direct

Check history

OK2026-08-05
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-03-10
11 OK · 3 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 33% structuredCode of conductNoContributing guideNo

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

Downloads

3.4K

CRAN downloads in the past year

Rank #12,434 · ~9/day · ~285/mo

Releases R versions

Daily download trend is not available in this view yet.

22730 days

79690 days

3.4K1 year

Compare downloads with other packages →

Also on125 r2u3 autocran39 c2d4u

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.1.1

Imports (1)

stats

LinkingTo (0)

none

Suggests (2)

BGLR coda

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Italo Granato

Author, Maintainer

Authors (3)

Italo Granato

Author, Maintainer

Luna-Vázquez Francisco J.

Author

Cuevas Jaime

Author

Package Timeline

5 releases. Pick two to compare their code metrics. R releases are shown for context.

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
R
R 3.6.0 released · 2019-04-26
0.6.5Latest
2018-08-10 · current release · diff ↗
0.6.4
2018-07-23 · diff ↗
0.6.3
2018-05-16 · diff ↗
0.6.2
2018-05-10 · diff ↗
R
R 3.5.0 released · 2018-04-23
0.6.1
2017-11-30
R
R 3.4.0 released · 2017-04-21

Package metadata

First published: 2017-11-30
Total releases: 5 / 9 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.1.1
Download size: 10 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Cite

Cite this package

Start here. This is the citation for the package itself.

citation("BGGE")

CRAN DOI

https://doi.org/10.32614/CRAN.package.BGGE

BibTeX, derived from DESCRIPTION

@Manual{BGGE,
  title  = {BGGE: Bayesian Genomic Linear Models Applied to GE Genome Selection},
  author = {Granato, Italo and Francisco J., Luna-Vázquez and Jaime, Cuevas},
  year   = {2018},
  note   = {R package version 0.6.5},
  doi    = {10.32614/CRAN.package.BGGE},
  url    = {https://CRAN.R-project.org/package=BGGE}
}

Derived from the package DESCRIPTION, not from a citation file the authors wrote. If they publish one later, prefer it.

This is the citation for the package. It is not a citation for the R Observatory.

Cite this page

Use this when the claim is about a measurement on this page.

BibTeX

@misc{robservatoryBGGE,
  author    = {Balamuta, James Joseph},
  title     = {{R} {Observatory}: Metrics for {BGGE} version 0.6.5},
  year      = {2026},
  publisher = {HJJB, LLC},
  url       = {https://r-observatory.thecoatlessprofessor.com/packages/BGGE},
  note      = {Data set. Data release v2026-08-05}
}

APA

Balamuta, J. J. (2026). R Observatory: Metrics for BGGE version 0.6.5 [Data set]. HJJB, LLC. Data release v2026-08-05. https://r-observatory.thecoatlessprofessor.com/packages/BGGE

RIS

TY  - DATA
AU  - Balamuta, James Joseph
TI  - R Observatory: Metrics for BGGE version 0.6.5
PY  - 2026
PB  - HJJB, LLC
N1  - Data release v2026-08-05
UR  - https://r-observatory.thecoatlessprofessor.com/packages/BGGE
ER  -

In prose

These package metrics were obtained from the R Observatory (Balamuta, 2026), data release v2026-08-05, https://r-observatory.thecoatlessprofessor.com/packages/BGGE.

Bound to data release v2026-08-05, which is what makes the numbers on this page reproducible. See how to cite.

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