PopVar

1.3.2

Genomic Breeding Tools: Genetic Variance Prediction and Cross-Validation

0packages depend

3Kdownloads / year

–test coverage

12/13checks pass

Overview

About

Maintained by Jeffrey NeyhartFirst published 2015-04-017 releasesCRAN page ↗GitHub ↗

The main attribute of 'PopVar' is the prediction of genetic variance in bi-parental populations, from which the package derives its name. 'PopVar' contains a set of functions that use phenotypic and genotypic data from a set of candidate parents to 1) predict the mean, genetic variance, and superior progeny value of all, or a defined set of pairwise bi-parental crosses, and 2) perform cross-validation to estimate genome-wide prediction accuracy of multiple statistical models. More details are available in Mohammadi, Tiede, and Smith (2015, doi:10.2135/cropsci2015.01.0030). A dataset 'think_barley.rda' is included for reference and examples.

Install

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

install.packages("PopVar", 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("UMN-BarleyOatSilphium/PopVar")

Development version from UMN-BarleyOatSilphium/PopVar. 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-popvar

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

# 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-PopVar

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

Health

CRAN checks

1NOTE12OK

Failing flavors

NOTE r-devel-linux-x86_64-debian-gcc

Slowest check: 4.1 min · r-oldrel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Check history

NOTE2026-08-01
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 482 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 67% structuredCode of conductNoContributing guideNo

Examples that run: 25%
Documented parameters: 98%
Return-value docs: 100%
References docs: 57%

Downloads

CRAN downloads in the past year

Rank #16,464 · ~8/day · ~250/mo

Releases R versions

Daily download trend is not available in this view yet.

16530 days

63990 days

3K1 year

Compare downloads with other packages →

Also on113 r2u5 autocran52 c2d4u

Repository

GitHub ↗ umn-barleyoatsilphium/popvar

0Stars

0Forks

1Open issues

0Open PRs

1Releases

32Commits

3Contributors

License GPL-3.0 · 32 commits · Last activity 2026-03-09

Releases over time

2024-01-23 · 12026-07-07 · 1

Repository practices

Upstream repositoryBeta

6 development-tooling and community-health practices detected across 3 families in the upstream repository

Checks run against github.com/umn-barleyoatsilphium/popvar on 2026-08-03.

Continuous integration (2)

GitHub ActionsTravis CI

CRAN release process (3)

cran-comments.mdrevdep/CRAN-SUBMISSION

Docs source (1)

README.Rmd

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (7)

BGLR qtl rrBLUPstatsutilsmethodsparallel

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Jeffrey Neyhart

Author, Contributor, Maintainer · added in 1.3.0

Authors (2)

Jeffrey Neyhart

Author, Contributor, Maintainer · added in 1.3.0

Tyler Tiede

Author

Contributors (3)

Jeffrey Neyhart

Author, Contributor, Maintainer · added in 1.3.0

Mohsen Mohammadi

Contributor

Kevin Smith

Contributor · added in 1.3.0

Listed in earlier versions (1)

Kevin P. Smith

no longer listed · 1.0 to 1.2.1

Package Timeline

7 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
1.3.2Latest
2024-10-21 · current release · diff ↗
unarchivedReturned to CRAN
2024-10-21
archivedRemoved from CRAN
2024-09-05
issues were not corrected in time
R
R 4.4.0 released · 2024-04-24
1.3.1
2024-01-29 · diff ↗
unarchivedReturned to CRAN
2024-01-29
archivedRemoved from CRAN
2024-01-12
issues were not corrected despite reminders
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
1.3.0
2021-02-07 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
R
R 3.5.0 released · 2018-04-23

Show 8 earlier events

R
R 3.4.0 released · 2017-04-21
R
R 3.3.0 released · 2016-05-03
1.2.1
2015-07-08 · diff ↗
1.2
2015-06-17 · diff ↗
1.1
2015-04-28 · diff ↗
R
R 3.2.0 released · 2015-04-16
1.0
2015-04-01
R
R 3.1.0 released · 2014-04-10

Package metadata

First published: 2015-04-01
Total releases: 7 / 11 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 109 KB / 1 file
Download size: 241 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Agricultural Science

Report a problem with this page →