R Observatory: Metrics for hscovar version 0.4.2

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

hscovar

0.4.2Package record

Calculation of Covariance Between Markers for Half-Sib Families

0packages depend

2.6Kdownloads / year

–test coverage

13/13flavors OK

Overview

About

Maintained by Dörte WittenburgCRAN page ↗

The theoretical covariance between pairs of markers is calculated from either paternal haplotypes and maternal linkage disequilibrium (LD) or vise versa. A genetic map is required. Grouping of markers is based on the correlation matrix and a representative marker is suggested for each group. Employing the correlation matrix, optimal sample size can be derived for association studies based on a SNP-BLUP approach. The implementation relies on paternal half-sib families and biallelic markers. If maternal half-sib families are used, the roles of sire/dam are swapped. Multiple families can be considered. Wittenburg, Bonk, Doschoris, Reyer (2020) "Design of Experiments for Fine-Mapping Quantitative Trait Loci in Livestock Populations" doi:10.1186/s12863-020-00871-1. Carlson, Eberle, Rieder, Yi, Kruglyak, Nickerson (2004) "Selecting a maximally informative set of single-nucleotide polymorphisms for association analyses using linkage disequilibrium" doi:10.1086/381000.

Install

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

install.packages("hscovar", 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-hscovar

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-hscovar

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-hscovar

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

13OK

CRAN check page ↗

Slowest check: 1.8 min · r-oldrel-windows-x86_64

Status changes

OK13 OK2026-08-05
NOTE12 OK, 1 NOTE2026-08-01
OK14 OK2026-03-30
ERROR13 OK, 1 ERROR2026-03-10

Advisories

none known

How this is measured·How advisories are found

Documentation

In release 0.4.2

READMENoVignettesNoNEWSYes · 100% structured · does not mention 0.4.2Citation fileNoWebsitenot declared in DESCRIPTION

Help pages: 19
Examples that run: 93%14 run in a plain check · 1 never run
Exported functions with examples: 100%
Documented parameters: 100%
Return-value docs: 100%
Help pages citing references: 26%

How these are measured

Downloads

2.6K

CRAN downloads in the past year

Rank #16,023 · ~7/day · ~217/mo

Releases R versions

Daily download trend is not available in this view yet.

29030 days

78590 days

2.6K1 year

Compare downloads with other packages →

Also on68 r2u3 autocran

How downloads are counted

Dependencies

Declared dependencies

3 external dependencies (excludes base and recommended)

Installing hscovar adds 8 packages (4 with compiled code, 8.2 MB of source tarballs). Heaviest: data.table 5.7 MB, jsonlite 1.0 MB, XML 937 KB.

Depends (1)

R >= 3.5.0

Imports (5)

parallelMatrixforeach rlist pwr

LinkingTo (0)

none

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 (3)

Dörte Wittenburg

Author, Maintainer since 0.1.2 (2020)

Michael Doschoris

Author

Jan Klosa

Contributor

Releases (4)

Pick two releases to compare their code metrics.

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
R
R 4.2.0 released · 2022-04-22
R
R 4.1.0 released · 2021-05-18
0.4.2Latest
record
2021-04-13 · current release · diff ↗
0.4.0
record
2020-08-06 · diff ↗ ·
removed 1 export
coeff.beta.k
R
R 4.0.0 released · 2020-04-24
0.2.1
record
2020-04-16 · diff ↗ ·
added 8 exports
AR1, calcvar, coeff.beta.k, pwr.normtest, pwr.snpblup, search.best.n.bisection, simpleM, startvalue
0.1.2
record
2020-03-04
R
R 3.6.0 released · 2019-04-26

Package metadata

First published: 2020-03-04
Total releases: 4 / 6 yrs
License: GPL (>= 2) OSI
Minimum R: ≥ 3.5.0
Bundled data: 143 KB / 1 file
Download size: 179 KB

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("hscovar")

Format

Wittenburg, D., Doschoris, M., & Klosa, J. (2021). hscovar: Calculation of Covariance Between Markers for Half-Sib Families (Version 0.4.2) [Computer software]. https://doi.org/10.32614/CRAN.package.hscovar

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 hscovar version 0.4.2 [Data set]. HJJB, LLC. Data release v2026-10-26. https://doi.org/10.5281/zenodo.21843040

From data release v2026-10-26, which the citation names so these numbers can be found later. More on citing and the projects behind them.

Report a problem with this page →