# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "dartR" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'dartR: Importing and Analysing ''SNP'' and ''Silicodart'' Data Generated by
  Genome-Wide Restriction Fragment Analysis'
version: 2.9.7
doi: 10.1111/1755-0998.12745
identifiers:
- type: doi
  value: 10.32614/CRAN.package.dartR
- type: url
  value: https://green-striped-gecko.github.io/dartR/
abstract: 'Functions are provided that facilitate the import and analysis of ''SNP''
  (single nucleotide polymorphism) and ''silicodart'' (presence/absence) data. The
  main focus is on data generated by ''DarT'' (Diversity Arrays Technology), however,
  data from other sequencing platforms can be used once ''SNP'' or related fragment
  presence/absence data from any source is imported. Genetic datasets are stored in
  a derived ''genlight'' format (package ''adegenet''), that allows for a very compact
  storage of data and metadata. Functions are available for importing and exporting
  of ''SNP'' and ''silicodart'' data, for reporting on and filtering on various criteria
  (e.g. ''CallRate'', heterozygosity, reproducibility, maximum allele frequency).
  Additional functions are available for visualization (e.g. Principle Coordinate
  Analysis) and creating a spatial representation using maps. ''dartR'' supports also
  the analysis of 3rd party software package such as ''newhybrid'', ''structure'',
  ''NeEstimator'' and ''blast''. Since version 2.0.3 we also implemented simulation
  functions, that allow to forward simulate ''SNP'' dynamics under different population
  and evolutionary dynamics. Comprehensive tutorials and support can be found at our
  ''github'' repository: github.com/green-striped-gecko/dartR/. If you want to cite
  ''dartR'', you find the information by typing citation(''dartR'') in the console.'
authors:
- family-names: Gruber
  given-names: Bernd
  email: bernd.gruber@canberra.edu.au
- family-names: Georges
  given-names: Arthur
  email: georges@aerg.edu.au
- family-names: Mijangos
  given-names: Jose L.
  email: Luis.MijangosAraujo@canberra.edu.au
- family-names: Pacioni
  given-names: Carlo
  email: carlo.pacioni@delwp.vic.gov.au
preferred-citation:
  type: article
  title: 'dartr: An r package to facilitate analysis of SNP data generated from reduced
    representation genome sequencing'
  authors:
  - family-names: Gruber
    given-names: Bernd
    email: bernd.gruber@canberra.edu.au
  - family-names: Unmack
    given-names: Peter J
  - family-names: Berry
    given-names: Oliver F
  - family-names: Georges
    given-names: Arthur
    email: georges@aerg.edu.au
  doi: 10.1111/1755-0998.12745
  journal: Molecular Ecology Resources
  keywords:
  - bioinformatics
  - next-generation-sequencing
  - phylogenomics
  - SNPs
  - population genomics
  - R package
  - RADSeq
  volume: '18'
  year: '2018'
  start: '691'
  end: '699'
repository: https://cranhaven.r-universe.dev
commit: 05e1376d8d854994f881b379651500d7ef0cfde4
url: https://groups.google.com/g/dartr?pli=1
date-released: '2023-06-07'
contact:
- family-names: Gruber
  given-names: Bernd
  email: bernd.gruber@canberra.edu.au
references:
- type: article
  title: 'dartR v2: An accessible genetic analysis platform for conservation, ecology
    and agriculture'
  authors:
  - family-names: Mijangos
    given-names: Jose Luis
  - family-names: Berry
    given-names: Oliver F
  - family-names: Pacioni
    given-names: Carlo
  - family-names: Georges
    given-names: Arthur
  journal: Methods in Ecology and Evolution
  year: '2022'
  doi: 10.1111/2041-210X.13918