R Observatory: Metrics for qgg version 1.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

qgg

1.1.6Package record

Statistical Tools for Quantitative Genetic Analyses

0packages depend

4.1Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Peter SoerensenCRAN page ↗GitHub ↗Issues ↗

Provides an infrastructure for efficient processing of large-scale genetic and phenotypic data including core functions for: 1) fitting linear mixed models, 2) constructing marker-based genomic relationship matrices, 3) estimating genetic parameters (heritability and correlation), 4) performing genomic prediction and genetic risk profiling, and 5) single or multi-marker association analyses. Rohde et al. (2019) doi:10.1101/503631.

Install

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

install.packages("qgg", 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("psoerensen/qgg")

Development version from psoerensen/qgg. 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-qgg

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-qgg

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-qgg

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: 5.3 min · r-devel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK12 OK2026-04-25
NOTE12 OK, 2 NOTE2026-04-22
ERROR11 OK, 2 NOTE, 1 ERROR2026-04-18

Show 1 earlier changeHide 1 earlier change

NOTE12 OK, 2 NOTE2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.6

READMEYes · 997 wordsVignettesNoNEWSYes · 33% structured · does not mention 1.1.6Citation fileNo

Help pages: 55 (36 internal)
Examples that run: 73%8 run in a plain check · 1 only when donttest examples are enabled (R CMD check --as-cran) · 2 hold no code
Exported functions with examples: 21%
Documented parameters: 98%
Return-value docs: 71%
Help pages citing references: 4%

How these are measured

Downloads

4.1K

CRAN downloads in the past year

Rank #9,692 · ~11/day · ~345/mo

Releases R versions

Daily download trend is not available in this view yet.

36530 days

1K90 days

4.1K1 year

Compare downloads with other packages →

Also on354 r2u6 autocran5.8K conda_forge91 c2d4u

How downloads are counted

Repository

psoerensen/qgg ↗Account: psoerensen

41Stars

8Forks

1Open issues

0Open PRs

0Releases

2,485Commits

8Commit identities

2,485 commits · Last activity 2026-04-16 · 0% stars, 30d

Responsiveness

How these are sampled

PRs merged (all time): 50%
Median days to close, 50 most recently updated closed issues: 62
Median days to close, 50 most recently updated closed PRs: 429

Stars over time

2025-07-14 · 382026-09-09 · 41

How these are measured

PracticesBeta

7 development-tooling and community-health practices detected across 4 families in the upstream repository

Checks run against github.com/psoerensen/qgg on 2026-10-18.

Continuous integration (1)

GitHub Actions

Docs source (3)

README.Rmdpkgdown

GitHub Pages site last deployed 2026-04-16

CRAN release process (2)

cran-comments.mdCRAN-SUBMISSION

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Installing qgg adds 11 packages (8 with compiled code, 12 MB of source tarballs). Heaviest: data.table 5.7 MB, Rcpp 1.8 MB, mcmc 1.5 MB.

Depends (1)

R >= 3.3.0

Imports (11)

Rcpp data.tableparallelstatmodstatsMCMCpackMASScoda corpcorMatrixmethods

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

How these are counted

Code & Tests

People & History

People (3)

Peter Soerensen

Author, Maintainer since 1.0.0 (2019)

Palle Duun Rohde

Author

Izel Fourie Soerensen

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
1.1.6Latest
record
2024-12-16 · current release · diff ↗
1.1.3
record
2024-12-11 · diff ↗ ·
removed 1 export
qcStat

added 9 exports
checkStat, createLDsets, getLDscores, gsimC, gsimR, magma, pops, vegas, writeBED
R
R 4.4.0 released · 2024-04-24
1.1.2
record
2023-09-07 · diff ↗ ·
added 16 exports
adjustB, adjustMapLD, getMap, getPos, getSparseLD, gmap, ldscore, mapSets, plotForest, plotLD, predict_auc_mt_cc, predict_auc_mt_continuous, predict_auc_st, predict_r2_mt, predict_r2_st, splitWithOverlap
R
R 4.3.0 released · 2023-04-21
unarchivedReturned to CRAN
2022-08-08
1.1.1
record
2022-08-08 · diff ↗
archivedRemoved from CRAN
2022-07-20
check issues were not corrected in time Declares 'fread' with 'int' not 'size_t' in 'iso_c_binding'
1.1.0
record
2022-06-27 · diff ↗ ·
removed 2 exports
getW, lma

added 17 exports
acc, adjLDStat, adjStat, computeROC, getG, getLD, getLDsets, getMarkers, gfilter, glma, gsim, ldsc, mapStat, mtadj, plotBayes, plotROC, qcStat
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.0.4
record
2020-06-29 · diff ↗
R
R 4.0.0 released · 2020-04-24
unarchivedReturned to CRAN
2020-04-21

Show 8 earlier eventsHide 8 earlier events

1.0.3
record
2020-04-21 · diff ↗
archivedRemoved from CRAN
2020-03-31
installation problems were not corrected in time Hardcodes '-fopenmp' which is not recognized by Apple clang
unarchivedReturned to CRAN
2020-01-08
1.0.2
record
2020-01-08 · diff ↗
archivedRemoved from CRAN
2019-12-20
reported installation issues were ignored in update
1.0.1
record
2019-12-17 · diff ↗
1.0.0
record
2019-12-13
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-12-13
Total releases: 10 / 7 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.3.0
Download size: 243 KB

Appears in task views

Agricultural Science

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("qgg")

Format

Soerensen, P., Duun Rohde, P., & Fourie Soerensen, I. (2024). qgg: Statistical Tools for Quantitative Genetic Analyses (Version 1.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.qgg

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 qgg version 1.1.6 [Data set]. HJJB, LLC. Data release v2026-10-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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