R Observatory: Metrics for IPLGP version 2.0.5

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

IPLGP

2.0.5Package record

Identification of Parental Lines via Genomic Prediction

0packages depend

2.9Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Ping-Yuan ChungCRAN page ↗GitHub ↗Issues ↗

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. 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-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). 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: 1.6 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-04-10
ERROR13 OK, 1 ERROR2026-04-09
OK14 OK2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 2.0.5

READMENoVignettesNoNEWSNoCitation fileNoWebsitenot declared in DESCRIPTION

Help pages: 10
Examples that run: 100%10 run in a plain check
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 90%

How these are measured

Downloads

2.9K

CRAN downloads in the past year

Rank #16,252 · ~8/day · ~241/mo

Releases R versions

Daily download trend is not available in this view yet.

33030 days

76190 days

2.9K1 year

Compare downloads with other packages →

Also on65 r2u4 autocran

How downloads are counted

Repository

py-chung/iplgp ↗Account: py-chung

2Stars

1Forks

0Open issues

0Open PRs

0Releases

53Commits

1Commit identities

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

Responsiveness

How these are sampled

PRs merged (all time): not measured
Median days to close, 50 most recently updated closed issues: 3
Median days to close, 50 most recently updated closed PRs: not measured

Stars over time

2025-08-11 · 22026-07-07 · 2

How these are measured

PracticesBeta

Checks run against github.com/py-chung/iplgp on 2026-10-18.

No development-tooling practices detected in the upstream repository.

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

Dependencies

Declared dependencies

2 external dependencies (excludes base and recommended)

Installing IPLGP adds 24 packages (11 with compiled code, 22 MB of source tarballs). Heaviest: ggplot2 6.0 MB, enhancer 2.3 MB, Rcpp 1.8 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (2)

Ping-Yuan Chung

Maintainer since 0.1.0 (2021)

Chen-Tuo Liao

Author

Releases (10)

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
2.0.5Latest
record
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
record
2023-04-06 · diff ↗
2.0.3
record
2022-09-02 · diff ↗
2.0.2
record
2022-06-21 · diff ↗
2.0.1
record
2022-06-10 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.0.0
record
2021-12-13 · diff ↗ ·
added 1 export
geno.d
1.3.0
record
2021-09-08 · diff ↗
R
R 4.1.0 released · 2021-05-18
1.2.0
record
2021-04-23 · diff ↗
1.1.0
record
2021-04-20 · diff ↗
0.1.0
record
2021-02-17

Show 1 earlier eventHide 1 earlier event

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

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

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 v2026-10-20. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-20, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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