R Observatory: Metrics for Ghat version 0.2.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

Ghat

0.2.0

Quantifying Evolution and Selection on Complex Traits

0packages depend

2.6Kdownloads / year

–test coverage

13/13checks pass

Overview

About

Maintained by Tim BeissingerFirst published 2019-08-022 releasesCRAN page ↗GitHub ↗

Functions are provided for quantifying evolution and selection on complex traits. The package implements effective handling and analysis algorithms scaled for genome-wide data and calculates a composite statistic, denoted Ghat, which is used to test for selection on a trait. The package provides a number of simple examples for handling and analysing the genome data and visualising the output and results. Beissinger et al., (2018) doi:10.1534/genetics.118.300857.

Install

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

install.packages("Ghat", 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("Medhat86/Ghat")

Development version from Medhat86/Ghat. 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-ghat

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-Ghat

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-Ghat

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

Health

CRAN checks

13OK

Slowest check: 51 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
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 307 wordsVignettesNopkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 67%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

2.6K

CRAN downloads in the past year

Rank #17,457 · ~7/day · ~218/mo

Releases R versions

Daily download trend is not available in this view yet.

15730 days

61090 days

2.6K1 year

Compare downloads with other packages →

Also on112 r2u10 autocran

Repository

GitHub ↗ medhat86/ghat

0Stars

0Forks

0Open issues

0Open PRs

0Releases

Last activity 2023-11-16

Repository practices

Upstream repositoryBeta

1 development-tooling and community-health practice detected across 1 family in the upstream repository

Checks run against github.com/medhat86/ghat on 2026-08-03.

Lint, format, editor (1)

RStudio project

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

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.0.0

Imports (1)

rrBLUP

LinkingTo (0)

none

Suggests (2)

knitr rmarkdown

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (3)

Maintainer (1)

Tim Beissinger

Author, Maintainer · added in 0.2.0

Authors (3)

Tim Beissinger

Author, Maintainer · added in 0.2.0

Ngoc-Thuy Ha

Author

Medhat Mahmoud

Author

Listed in earlier versions (1)

Timothy Beissinger

no longer listed · 0.1.0

Package Timeline

2 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
0.2.0Latest
2022-12-14 · current release · diff ↗
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
0.1.0
2019-08-02
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-02
Total releases: 2 / 7 yrs
License: MIT + file LICENSE OSI
Minimum R: ≥ 3.0.0
Bundled data: 924 KB / 1 file
Download size: 934 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("Ghat")

Format

Beissinger, T., Ha, N., & Mahmoud, M. (2022). Ghat: Quantifying Evolution and Selection on Complex Traits (Version 0.2.0) [Computer software]. https://doi.org/10.32614/CRAN.package.Ghat

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 Ghat version 0.2.0 [Data set]. HJJB, LLC. Data release v2026-08-08. https://doi.org/10.5281/zenodo.21843040

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

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