# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "RZooRoH" in publications use:'
type: software
license: GPL-3.0-only
title: 'RZooRoH: Partitioning of Individual Autozygosity into Multiple Homozygous-by-Descent
  Classes'
version: 0.4.1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.RZooRoH
abstract: 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) <https://doi.org/10.1111/mec.14324>
  and Druet and Gautier (2022) <https://doi.org/10.1016/j.tpb.2022.03.001>.
authors:
- family-names: Druet
  given-names: Tom
  email: tom.druet@uliege.be
- family-names: Kadri
  given-names: Naveen Kumar
- family-names: Gautier
  given-names: Mathieu
preferred-citation:
  type: article
  title: A model-based approach to characterize individual inbreeding at both global
    and local genomic scales.
  authors:
  - family-names: Druet
    given-names: Tom
    email: tom.druet@uliege.be
  - family-names: Gautier
    given-names: Mathieu
  journal: Molecular Ecology
  year: '2017'
  volume: '26'
  issue: '20'
  start: 5820-5841
repository: https://cran.r-universe.dev
commit: e186115454b500d32d76a967bb0fc55bea2f6408
date-released: '2025-06-08'
contact:
- family-names: Druet
  given-names: Tom
  email: tom.druet@uliege.be
references:
- type: article
  title: 'RZooRoH: an R package to characterize individual genomic autozygosity and
    identify homozygous-by-descent segments.'
  authors:
  - family-names: Bertrand
    given-names: Amandine
  - family-names: Kadri
    given-names: Naveen
  - family-names: Flori
    given-names: Laurence
  - family-names: Gautier
    given-names: Mathieu
  - family-names: Druet
    given-names: Tom
  journal: Methods in Ecology and Evolution
  year: '2019'
- type: article
  title: A hidden Markov model to estimate homozygous-by-descent probabilities associated
    with nested layers of ancestors.
  authors:
  - family-names: Druet
    given-names: Tom
  - family-names: Gautier
    given-names: Mathieu
  journal: Theoretical Population Biology
  year: '2022'
  volume: '145'
  start: 38-51