R Observatory: Metrics for IPLGP version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

IPLGP

2.0.5

Identification of Parental Lines via Genomic Prediction

0packages depend

2.7Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Ping-Yuan ChungFirst published 2021-02-1710 releasesCRAN page ↗GitHub ↗

Combining genomic prediction with Monte Carlo simulation, three different strategies are implemented to select parental lines for multiple traits in plant breeding. The selection strategies include (i) GEBV-O considers only genomic estimated breeding values (GEBVs) of the candidate individuals; (ii) GD-O considers only genomic diversity (GD) of the candidate individuals; and (iii) GEBV-GD considers both GEBV and GD. The above method can be seen in Chung PY, Liao CT (2020) doi:10.1371/journal.pone.0243159. Multi-trait genomic best linear unbiased prediction (MT-GBLUP) model is used to simultaneously estimate GEBVs of the target traits, and then a selection index is adopted to evaluate the composite performance of an individual.

Install

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

install.packages("IPLGP", 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("py-chung/IPLGP")

Development version from py-chung/IPLGP. 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-iplgp

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-IPLGP

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-IPLGP

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

Health

CRAN checks

13OK

Slowest check: 1.6 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

4

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
OK2026-04-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-09
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 90%

Downloads

2.7K

CRAN downloads in the past year

Rank #16,144 · ~8/day · ~229/mo

Releases R versions

Daily download trend is not available in this view yet.

14330 days

67290 days

2.7K1 year

Compare downloads with other packages →

Also on89 r2u27 autocran

Repository

GitHub ↗ py-chung/iplgp

2Stars

1Forks

0Open issues

0Open PRs

0Releases

53Commits

1Contributors

53 commits · Last activity 2025-03-21 · 0% stars, 30d

Stars over time

2025-08-11 · 22026-07-07 · 2

Repository practices

Upstream repositoryBeta

Checks run against github.com/py-chung/iplgp on 2026-08-23.

No development-tooling practices detected in the upstream repository.

How this is detected·Detection ruleset v1 (2026-07-18)

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (4)

ggplot2 sommergrDevicesstats

LinkingTo (0)

none

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Ping-Yuan Chung

Maintainer

Authors (1)

Chen-Tuo Liao

Author

Package Timeline

10 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
2.0.5Latest
2024-08-01 · current release · diff ↗
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
2.0.4
2023-04-06 · diff ↗
2.0.3
2022-09-02 · diff ↗
2.0.2
2022-06-21 · diff ↗
2.0.1
2022-06-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.0
2021-12-13 · diff ↗
1.3.0
2021-09-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.0
2021-04-23 · diff ↗
1.1.0
2021-04-20 · diff ↗
0.1.0
2021-02-17

Show 1 earlier events

R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-17
Total releases: 10 / 5 yrs
License: GPL-2 OSI
Download size: 623 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("IPLGP")

Format

Chung, P., & Liao, C. (2024). IPLGP: Identification of Parental Lines via Genomic Prediction (Version 2.0.5) [Computer software]. https://doi.org/10.32614/CRAN.package.IPLGP

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 IPLGP version 2.0.5 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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