R Observatory: Metrics for LDlinkR version 1.4.0

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

LDlinkR

1.4.0

Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest

1packages depend

13Kdownloads / year

9.9%test coverage

13/13checks pass

Overview

About

Maintained by Timothy A. MyersFirst published 2019-08-0111 releasesCRAN page ↗GitHub ↗

Provides access to the 'LDlink' API (https://ldlink.nih.gov/?tab=apiaccess) using the R console. This programmatic access facilitates researchers who are interested in performing batch queries in 1000 Genomes Project (2015) doi:10.1038/nature15393 data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying germline variants in human population groups of interest. For more details, please see Machiela et al. (2015) doi:10.1093/bioinformatics/btv402.

Install

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

install.packages("LDlinkR", 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("CBIIT/LDlinkR")

Development version from CBIIT/LDlinkR. 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-ldlinkr

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-LDlinkR

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-LDlinkR

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

Health

CRAN checks

13OK

Slowest check: 1.1 min · r-oldrel-windows-x86_64

Code health

Yes

Tests · ratio 0.21

9.9%

Coverage · measured lines

100%

Documentation · exports

2

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 · 884 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 54%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

13K

CRAN downloads in the past year

Rank #3,659 · ~36/day · ~1.1K/mo

Releases R versions

Daily download trend is not available in this view yet.

70830 days

2.6K90 days

13K1 year

Compare downloads with other packages →

Also on100 r2u21 autocran2.8K conda_forge

Repository

GitHub ↗ cbiit/ldlinkr

65Stars

12Forks

10Open issues

0Open PRs

9Releases

471Commits

5Contributors

linkage-disequilibriumldlink-apildlinkpopulation-geneticsld-calculatorr-packager-statsldlink-webtool

471 commits · Last activity 2026-06-22 · 0% stars, 30d

Stars over time

2025-04-15 · 582026-07-23 · 65

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/cbiit/ldlinkr on 2026-08-16.

Continuous integration (1)

GitHub Actions

CRAN release process (2)

cran-comments.mdrevdep/

Lint, format, editor (1)

RStudio project

Governance and community (1)

Security policy

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

Dependencies

Declared dependencies

5 external dependencies (excludes base and recommended)

Depends (0)

none

Imports (2)

httrutils

LinkingTo (0)

none

Suggests (4)

testthat knitr rmarkdown spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

1direct

0indirect

locuszoomr

Code & Tests

People & History

People (3)

Maintainer (1)

Timothy A. Myers

Author, Maintainer

Authors (3)

Timothy A. Myers

Author, Maintainer

Stephen J. Chanock

Author · added in 1.0.1

Mitchell J. Machiela

Author

Package Timeline

11 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
1.4.0Latest
2024-04-10 · current release · diff ↗
1.3.0
2023-05-31 · diff ↗
R
R 4.3.0 released · 2023-04-21
1.2.3
2022-12-15 · diff ↗
1.2.2
2022-08-08 · diff ↗
1.2.1
2022-06-07 · diff ↗
1.2.0
2022-05-11 · diff ↗
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
1.1.2
2021-02-19 · diff ↗
1.1.1
2021-02-02 · diff ↗
R
R 4.0.0 released · 2020-04-24
1.0.2
2020-03-02 · diff ↗

Show 3 earlier events

1.0.1
2019-10-17 · diff ↗
1.0.0
2019-08-01
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2019-08-01
Total releases: 11 / 7 yrs
License: GPL (>= 2) OSI
Download size: 87 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("LDlinkR")

Format

Myers, T. A., Chanock, S. J., & Machiela, M. J. (2024). LDlinkR: Calculating Linkage Disequilibrium (LD) in Human Population Groups of Interest (Version 1.4.0) [Computer software]. https://doi.org/10.32614/CRAN.package.LDlinkR

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 LDlinkR version 1.4.0 [Data set]. HJJB, LLC. Data release v2026-08-22. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-22, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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