R Observatory: Metrics for RZooRoH version 0.4.1

Balamuta, James Joseph

doi:10.5281/zenodo.21843040

RZooRoH

0.4.1

Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes

0packages depend

3.9Kdownloads / year

21.8%test coverage

13/13checks pass

Overview

About

Maintained by Tom DruetFirst published 2018-06-1912 releasesCRAN page ↗

Functions to identify Homozygous-by-Descent (HBD) segments associated with runs of homozygosity (ROH) and to estimate individual autozygosity (or inbreeding coefficient). HBD segments and autozygosity are assigned to multiple HBD classes with a model-based approach relying on a mixture of exponential distributions. The rate of the exponential distribution is distinct for each HBD class and defines the expected length of the HBD segments. These HBD classes are therefore related to the age of the segments (longer segments and smaller rates for recent autozygosity / recent common ancestor). The functions allow to estimate the parameters of the model (rates of the exponential distributions, mixing proportions), to estimate global and local autozygosity probabilities and to identify HBD segments with the Viterbi decoding. The method is fully described in Druet and Gautier (2017) doi:10.1111/mec.14324 and Druet and Gautier (2022) doi:10.1016/j.tpb.2022.03.001.

Install

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

install.packages("RZooRoH", 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-rzooroh

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-RZooRoH

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-RZooRoH

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

Health

CRAN checks

13OK

Slowest check: 4.4 min · r-devel-windows-x86_64

Code health

Yes

Tests · ratio 0.04

21.8%

Coverage · measured lines

100%

Documentation · exports

7

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
ERROR2026-03-30
13 OK · 0 NOTE · 0 WARNING · 1 ERROR · 0 FAILURE
OK2026-03-10
14 OK · 0 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 99%
Return-value docs: 100%
References docs: 0%

Downloads

3.9K

CRAN downloads in the past year

Rank #10,482 · ~11/day · ~328/mo

Releases R versions

Daily download trend is not available in this view yet.

23830 days

93390 days

3.9K1 year

Compare downloads with other packages →

Also on392 r2u22 autocran

Dependencies

Declared dependencies

8 external dependencies (excludes base and recommended)

Depends (2)

R >= 3.5.0methods

Imports (6)

foreach doParallelparalleldata.table RColorBrewer iterators

LinkingTo (0)

none

Suggests (3)

knitr rmarkdown testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (4)

Maintainer (1)

Tom Druet

Author, Maintainer

Authors (3)

Tom Druet

Author, Maintainer

Mathieu Gautier

Author

Naveen Kumar Kadri

Author

Contributors (1)

Amandine Bertrand

Contributor

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
0.4.1Latest
2025-06-08 · current release · diff ↗
0.4.0
2025-06-06 · diff ↗
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
0.3.2.1
2023-10-27 · diff ↗
0.3.2
2023-09-04 · diff ↗
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.3.1
2021-05-22 · diff ↗
R
R 4.1.0 released · 2021-05-18
0.3.0
2021-01-22 · diff ↗
0.2.4
2021-01-20 · diff ↗
R
R 4.0.0 released · 2020-04-24
R
R 3.6.0 released · 2019-04-26
0.2.3
2019-03-22 · diff ↗

Show 5 earlier events

0.2.2
2018-11-19 · diff ↗
0.2.1
2018-11-15 · diff ↗
0.1.1
2018-06-23 · diff ↗
0.1.0
2018-06-19
R
R 3.5.0 released · 2018-04-23

Package metadata

First published: 2018-06-19
Total releases: 12 / 8 yrs
License: GPL-3 OSI
Minimum R: ≥ 3.5.0
Bundled data: 712 KB / 14 files
Download size: 2.2 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Cite

Cite this package

Run in R for the authors' preferred citation:

citation("RZooRoH")

Format

Druet, T., Bertrand, A., Gautier, M., & Kadri, N. K. (2025). RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent Classes (Version 0.4.1) [Computer software]. https://doi.org/10.32614/CRAN.package.RZooRoH

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 RZooRoH version 0.4.1 [Data set]. HJJB, LLC. Data release v2026-08-23. https://doi.org/10.5281/zenodo.21843040

From data release v2026-08-23, 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 →