R Observatory: Metrics for hsrecombi version 1.1.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hsrecombi

1.1.1Package record

Estimation of Recombination Rate and Maternal LD in Half-Sibs

0packages depend

5Kdownloads / year

–test coverage

11/13flavors OK

Overview

About

Maintained by Dörte WittenburgCRAN 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.

Changes in 1.1.1

vignette removed because an error occurred sporadically when rebuilding the vignette under r-devel-windows-x86_64. The error does not show up with other systems.

From NEWS.md in the release

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. 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-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). 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

2NOTE11OK

Check messages

NOTERd contentsr-devel-linux-x86_64-debian-clang, r-devel-linux-x86_64-debian-gcc

Rd files without \usage:
  ‘countNumbers.Rd’ ‘loglikfun.Rd’
\arguments should not be documented without \usage.

CRAN check page ↗

Slowest check: 3.5 min · r-devel-windows-x86_64

Status changes

NOTE11 OK, 2 NOTENow
NOTE12 OK, 1 NOTE2026-07-11
OK14 OK2026-04-22
ERROR13 OK, 1 ERROR2026-04-18
OK13 OK2026-04-13
ERROR13 OK, 1 ERROR2026-04-11

Show 8 earlier changesHide 8 earlier changes

OK14 OK2026-04-04
ERROR13 OK, 1 ERROR2026-04-02
OK14 OK2026-03-31
ERROR13 OK, 1 ERROR2026-03-28
OK14 OK2026-03-25
ERROR13 OK, 1 ERROR2026-03-15
OK14 OK2026-03-14
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 1.1.1

READMENoVignettesNoNEWSYes · 100% structured · mentions 1.1.1Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 23
Examples that run: 94%15 run in a plain check · 1 never run
Exported functions with examples: 94%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 52%

How these are measured

Downloads

5K

CRAN downloads in the past year

Rank #7,561 · ~14/day · ~414/mo

Releases R versions

Daily download trend is not available in this view yet.

44630 days

1.2K90 days

5K1 year

Compare downloads with other packages →

Also on391 r2u2 autocran

How downloads are counted

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Installing hsrecombi adds 29 packages (19 with compiled code, 18 MB of source tarballs). Heaviest: data.table 5.7 MB, Rcpp 1.8 MB, RcppArmadillo 1.0 MB.

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.

How these are counted

Code & Tests

Datasets

People & History

People (1)

Dörte Wittenburg

Author, Maintainer since 0.1.3 (2020)

Releases (12)

Pick two releases to compare their code metrics.

R
R 4.6.0 released · 2026-04-24
unarchivedReturned to CRAN
2026-04-12
archivedRemoved from CRAN
2026-04-12
issues were not corrected in time
1.1.1Latest
record
2026-04-12 · current release · diff ↗
1.1.0
record
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
record
2023-06-07 · diff ↗
R
R 4.3.0 released · 2023-04-21
0.5.1
record
2022-12-01 · diff ↗ ·
added 1 export
rao.inv
0.5.0
record
2022-11-29 · diff ↗ ·
added 4 exports
felsenstein, haldane, karlin, kosambi
R
R 4.2.0 released · 2022-04-22
0.4.2
record
2022-03-27 · diff ↗
0.4.1
record
2022-03-24 · diff ↗ ·
added 2 exports
bestmapfun, rao
R
R 4.1.0 released · 2021-05-18
0.3.4
record
2021-03-23 · diff ↗

Show 6 earlier eventsHide 6 earlier events

0.3.2
record
2020-10-14 · diff ↗
0.3.1
record
2020-08-27 · diff ↗
0.3.0
record
2020-05-28 · diff ↗ ·
added 3 exports
checkCandidates, geneticPosition, makehappm
R
R 4.0.0 released · 2020-04-24
0.1.3
record
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

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 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 hsrecombi version 1.1.1 [Data set]. HJJB, LLC. Data release v2026-10-24. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-24, which the citation names so these numbers can be found later. More on citing and the projects behind them.

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