R Observatory: Metrics for hsrecombi version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hsrecombi

1.1.1

Estimation of Recombination Rate and Maternal LD in Half-Sibs

0packages depend

4.7Kdownloads / year

–test coverage

11/13checks pass

Overview

About

Maintained by Dörte WittenburgFirst published 2020-03-0412 releasesCRAN page ↗

Paternal recombination rate and maternal linkage disequilibrium (LD) are estimated for pairs of biallelic markers such as single nucleotide polymorphisms (SNPs) from progeny genotypes and sire haplotypes. The implementation relies on paternal half-sib families. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. For parameter estimation, at least one sire has to be double heterozygous at the investigated pairs of SNPs. Based on recombination rates, genetic distances between markers can be estimated. Markers with unusually large recombination rate to markers in close proximity (i.e. putatively misplaced markers) shall be discarded in this derivation. *A pipeline is available at GitHub* https://github.com/wittenburg/hsrecombi Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of recombination rate and maternal linkage disequilibrium in half-sibs" doi:10.3389/fgene.2018.00186. Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium in half-sib families" doi:10.1534/genetics.111.137521.

Install

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

install.packages("hsrecombi", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

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-hsrecombi

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-hsrecombi

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-hsrecombi

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

Health

CRAN checks

2NOTE11OK

Failing flavors

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

Slowest check: 4.3 min · r-devel-windows-x86_64

Code health

None

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

9

Dependencies · direct

Check history

NOTE2026-07-11
12 OK · 1 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
OK2026-04-22
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-18
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-04-13
13 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-11
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Show 8 earlier snapshots

OK2026-04-04
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-04-02
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-31
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-28
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-25
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-15
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-14
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE
ERROR2026-03-10
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE

Documentation

READMENoVignettesNopkgdown siteNoNEWSYes · 100% structuredCode of conductNoContributing guideNo

Examples that run: 94%
Documented parameters: 100%
Return-value docs: 100%
References docs: 52%

Downloads

4.7K

CRAN downloads in the past year

Rank #6,777 · ~13/day · ~390/mo

Releases R versions

Daily download trend is not available in this view yet.

18830 days

1.2K90 days

4.7K1 year

Compare downloads with other packages →

Also on431 r2u15 autocran

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 3.5.0

Imports (9)

Rcpp hsphase dplyr data.table rlist quadprog curlMatrixmagrittr

LinkingTo (1)

Rcpp

Suggests (0)

none

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (1)

Maintainer (1)

Dörte Wittenburg

Author, Maintainer

Authors (1)

Dörte Wittenburg

Author, Maintainer

Package Timeline

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

R
R 4.6.0 released · 2026-04-24
1.1.1Latest
2026-04-12 · current release · diff ↗
unarchivedReturned to CRAN
2026-04-12
archivedRemoved from CRAN
2026-04-12
issues were not corrected in time
1.1.0
2026-03-27 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
1.0.1
2023-06-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.5.1
2022-12-01 · diff ↗
0.5.0
2022-11-29 · diff ↗
R
R 4.2.0 released · 2022-04-22
0.4.2
2022-03-27 · diff ↗
0.4.1
2022-03-24 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.4
2021-03-23 · diff ↗

Show 6 earlier events

0.3.2
2020-10-14 · diff ↗
0.3.1
2020-08-27 · diff ↗
0.3.0
2020-05-28 · diff ↗
R
R 4.0.0 released · 2020-04-24
0.1.3
2020-03-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-04
Total releases: 12 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 12 KB / 1 file
Download size: 38 KB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hsrecombi")

Format

Wittenburg, D. (2026). hsrecombi: Estimation of Recombination Rate and Maternal LD in Half-Sibs (Version 1.1.1) [Computer software]. https://doi.org/10.32614/CRAN.package.hsrecombi

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 hsrecombi version 1.1.1 [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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