R Observatory: Metrics for ldsep version 2.1.6

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

ldsep

2.1.6

Linkage Disequilibrium Shrinkage Estimation for Polyploids

0packages depend

3.2Kdownloads / year

72.5%test coverage

13/13checks pass

Overview

About

Maintained by David GerardFirst published 2020-08-029 releasesCRAN page ↗GitHub ↗

Estimate haplotypic or composite pairwise linkage disequilibrium (LD) in polyploids, using either genotypes or genotype likelihoods. Support is provided to estimate the popular measures of LD: the LD coefficient D, the standardized LD coefficient D', and the Pearson correlation coefficient r. All estimates are returned with corresponding standard errors. These estimates and standard errors can then be used for shrinkage estimation. The main functions are ldfast(), ldest(), mldest(), sldest(), plot.lddf(), format_lddf(), and ldshrink(). Details of the methods are available in Gerard (2021a) doi:10.1111/1755-0998.13349 and Gerard (2021b) doi:10.1038/s41437-021-00462-5.

Install

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

install.packages("ldsep", 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("dcgerard/ldsep")

Development version from dcgerard/ldsep. 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-ldsep

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-ldsep

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-ldsep

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

Health

CRAN checks

13OK

Slowest check: 5.9 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.40

72.5%

Coverage · measured lines

100%

Documentation · exports

9

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
OK2026-04-25
12 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
NOTE2026-04-22
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
11 OK · 2 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 1 earlier snapshots

NOTE2026-03-10
12 OK · 2 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMEYes · 375 wordsVignettesYes · dynamicpkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 38%

Downloads

3.2K

CRAN downloads in the past year

Rank #12,442 · ~9/day · ~266/mo

Releases R versions

Daily download trend is not available in this view yet.

21130 days

80190 days

3.2K1 year

Compare downloads with other packages →

Also on389 r2u18 autocran

Repository

GitHub ↗ dcgerard/ldsep

13Stars

2Forks

2Open issues

1Open PRs

0Releases

150Commits

2Contributors

License GPL-3.0 · 150 commits · Last activity 2025-09-18 · 0% stars, 30d

Stars over time

2025-07-04 · 102026-07-09 · 13

Repository practices

Upstream repositoryBeta

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

Checks run against github.com/dcgerard/ldsep on 2026-08-16.

Continuous integration (1)

GitHub Actions

Docs source (1)

README.Rmd

Coverage (1)

Codecov

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

Dependencies

Declared dependencies

17 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (9)

Rcpp foreach doParallel ashr corrplot lpSolve abind modeest matrixStats

LinkingTo (2)

Rcpp RcppArmadillo

Suggests (6)

testthat covr knitr rmarkdown updog VariantAnnotation

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

People & History

People (1)

Maintainer (1)

David Gerard

Author, Maintainer

Authors (1)

David Gerard

Author, Maintainer

Package Timeline

9 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
2.1.6Latest
2025-09-18 · current release · diff ↗
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
2.1.5
2022-10-19 · diff ↗
R
R 4.2.0 released · 2022-04-22
2.1.4
2022-02-11 · diff ↗
2.1.2
2021-08-10 · diff ↗
2.1.0
2021-06-11 · diff ↗
R
R 4.1.0 released · 2021-05-18
2.0.2
2021-02-17 · diff ↗
2.0.1
2021-02-12 · diff ↗
1.1.0
2020-11-14 · diff ↗
1.0.0
2020-08-02
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2020-08-02
Total releases: 9 / 6 yrs
License: GPL (>= 3) OSI
Minimum R: ≥ 2.10
Bundled data: 119 KB / 3 files
Download size: 494 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("ldsep")

Format

Gerard, D. (2025). ldsep: Linkage Disequilibrium Shrinkage Estimation for Polyploids (Version 2.1.6) [Computer software]. https://doi.org/10.32614/CRAN.package.ldsep

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 ldsep version 2.1.6 [Data set]. HJJB, LLC. Data release v2026-08-18. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-18, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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