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RZooRoH

0.4.1

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

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4.1Kdownloads / year
–test coverage
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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>.

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Health

CRAN checks
13OK
Code health
Yes
Tests · ratio 0.04
not tracked
Coverage
100%
Documentation · exports
Yes
Vignettes
No
README
7
Dependencies · direct
Check history
  • 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

Downloads

4.1K
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Rank #11,841 · ~11/day · ~341/mo
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44630 days
89390 days
4.1K1 year
Also on414 r2u16 autocran
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Repository stars, issues, and contributor activity are not tracked yet.

Dependencies

Declared dependencies
8 external dependencies (excludes base and recommended)
Depends (2)
R >= 3.5.0methods base
Imports (6)
foreachdoParallelparallel basedata.tableRColorBreweriterators
LinkingTo (0)
none
Suggests (3)
knitrrmarkdowntestthat
Enhances (0)
none
Reverse dependencies
0direct
–indirect (not tracked)

Nothing depends on this yet.

Code

12,545Lines of code
16Exported functions

Code & tests

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Line coverage

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Expression

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Tests / Examples

–

Functions

49 16 exported

Complexity

12.5 avg / 52 max

Call network

49 nodes / 26 edges

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Lowest coverage

Per-function coverage is not measured for this package yet.

People & History

People (4)
Maintainer (1)
Tom Druet
Author, Maintainer
Authors (2)
Mathieu Gautier
Author
Naveen Kumar Kadri
Author
Contributors (1)
Amandine Bertrand
Contributor
Release 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
  • 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 4 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

Package metadata

First published
2018-06-19
Total releases
12 / 8 yrs
License
GPL-3 OSI
Download size
not tracked yet
Installed size
not tracked yet
With dependencies
not tracked yet