CITATION.cff

# -----------------------------------------------------------
# CITATION file created with {cffr} R package, v0.2.2
# See also: https://docs.ropensci.org/cffr/
# -----------------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "bioregion" in publications use:'
type: software
license: GPL-3.0-only
title: 'bioregion: Bioregionalisation Methods in R'
version: 0.1.0
abstract: bioregion provides multiple methods to delineate bioregions. Use methods based
  on projected or bipartite networks.
authors:
- family-names: Denelle
  given-names: Pierre
  email: pierre.denelle@gmail.com
  orcid: https://orcid.org/0000-0001-5037-2281
- family-names: Lenormand
  given-names: Maxime
  email: maxime.lenormand@inrae.fr
  orcid: https://orcid.org/0000-0001-6362-3473
- family-names: Leroy
  given-names: Boris
  email: boris.leroy@gmail.com
  orcid: https://orcid.org/0000-0002-7686-4302
preferred-citation:
  type: manual
  title: 'bioregion: Bioregionalisation Methods in R'
  authors:
  - family-names: Denelle
    given-names: Pierre
    email: pierre.denelle@gmail.com
    orcid: https://orcid.org/0000-0001-5037-2281
  - family-names: Lenormand
    given-names: Maxime
    email: maxime.lenormand@inrae.fr
    orcid: https://orcid.org/0000-0001-6362-3473
  - family-names: Leroy
    given-names: Boris
    email: boris.leroy@gmail.com
    orcid: https://orcid.org/0000-0002-7686-4302
  version: 0.1.0
  abstract: bioregion provides multiple methods to delineate bioregions. Use methods
    based on projected or bipartite networks.
  repository-code: https://github.com/bioRgeo/bioregion
  url: https://github.com/bioRgeo/bioregion
  contact:
  - family-names: Lenormand
    given-names: Maxime
    email: maxime.lenormand@inrae.fr
    orcid: https://orcid.org/0000-0001-6362-3473
  license: GPL-3.0-only
  year: '2022'
repository-code: https://github.com/bioRgeo/bioregion
url: https://github.com/bioRgeo/bioregion
contact:
- family-names: Lenormand
  given-names: Maxime
  email: maxime.lenormand@inrae.fr
  orcid: https://orcid.org/0000-0001-6362-3473
references:
- type: software
  title: 'R: A Language and Environment for Statistical Computing'
  notes: Depends
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
  version: '>= 4.0.0'
- type: software
  title: ape
  abstract: 'ape: Analyses of Phylogenetics and Evolution'
  notes: Imports
  authors:
  - family-names: Paradis
    given-names: Emmanuel
    email: Emmanuel.Paradis@ird.fr
    orcid: https://orcid.org/0000-0003-3092-2199
  - family-names: Blomberg
    given-names: Simon
    orcid: https://orcid.org/0000-0003-1062-0839
  - family-names: Bolker
    given-names: Ben
    orcid: https://orcid.org/0000-0002-2127-0443
  - family-names: Brown
    given-names: Joseph
    orcid: https://orcid.org/0000-0002-3835-8062
  - family-names: Claramunt
    given-names: Santiago
    orcid: https://orcid.org/0000-0002-8926-5974
  - family-names: Claude
    given-names: Julien
    orcid: https://orcid.org/0000-0002-9267-1228
  - family-names: Cuong
    given-names: Hoa Sien
  - family-names: Desper
    given-names: Richard
  - family-names: Didier
    given-names: Gilles
    orcid: https://orcid.org/0000-0003-0596-9112
  - family-names: Durand
    given-names: Benoit
  - family-names: Dutheil
    given-names: Julien
    orcid: https://orcid.org/0000-0001-7753-4121
  - family-names: Ewing
    given-names: RJ
  - family-names: Gascuel
    given-names: Olivier
  - family-names: Guillerme
    given-names: Thomas
    orcid: https://orcid.org/0000-0003-4325-1275
  - family-names: Heibl
    given-names: Christoph
    orcid: https://orcid.org/0000-0002-7655-3299
  - family-names: Ives
    given-names: Anthony
    orcid: https://orcid.org/0000-0001-9375-9523
  - family-names: Jones
    given-names: Bradley
    orcid: https://orcid.org/0000-0003-4498-1069
  - family-names: Krah
    given-names: Franz
    orcid: https://orcid.org/0000-0001-7866-7508
  - family-names: Lawson
    given-names: Daniel
    orcid: https://orcid.org/0000-0002-5311-6213
  - family-names: Lefort
    given-names: Vincent
  - family-names: Legendre
    given-names: Pierre
    orcid: https://orcid.org/0000-0002-3838-3305
  - family-names: Lemon
    given-names: Jim
  - family-names: Louvel
    given-names: Guillaume
    orcid: https://orcid.org/0000-0002-7745-0785
  - family-names: Marcon
    given-names: Eric
    orcid: https://orcid.org/0000-0002-5249-321X
  - family-names: McCloskey
    given-names: Rosemary
    orcid: https://orcid.org/0000-0002-9772-8553
  - family-names: Nylander
    given-names: Johan
  - family-names: Opgen-Rhein
    given-names: Rainer
  - family-names: Popescu
    given-names: Andrei-Alin
  - family-names: Royer-Carenzi
    given-names: Manuela
  - family-names: Schliep
    given-names: Klaus
    orcid: https://orcid.org/0000-0003-2941-0161
  - family-names: Strimmer
    given-names: Korbinian
    orcid: https://orcid.org/0000-0001-7917-2056
  - family-names: de Vienne
    given-names: Damien
    orcid: https://orcid.org/0000-0001-9532-5251
  year: '2022'
  url: https://CRAN.R-project.org/package=ape
- type: software
  title: bipartite
  abstract: 'bipartite: Visualising Bipartite Networks and Calculating Some (Ecological)
    Indices'
  notes: Imports
  authors:
  - family-names: Dormann
    given-names: Carsten F.
  - family-names: Fruend
    given-names: Jochen
  - family-names: Gruber
    given-names: Bernd
  - family-names: Beckett
    given-names: with additional code from Stephen
  - family-names: Devoto
    given-names: Mariano
  - family-names: Felix
    given-names: Gabriel
  - family-names: Iriondo
    given-names: Jose
  - family-names: Opsahl
    given-names: Tove
  - family-names: Pinheiro
    given-names: Rafael
  - family-names: Strauss
    given-names: Rouven
  - family-names: Vazquez
    given-names: Diego
  - family-names: Bluethgen
    given-names: also based on C-code developed by Nils
  - family-names: Strauss
    given-names: Aaron Clauset/Rouven
  - family-names: Rodriguez-Girones
    given-names: Miguel
  year: '2022'
  url: https://CRAN.R-project.org/package=bipartite
- type: software
  title: cluster
  abstract: 'cluster: "Finding Groups in Data": Cluster Analysis Extended Rousseeuw
    et al.'
  notes: Imports
  authors:
  - family-names: Maechler
    given-names: Martin
    email: maechler@stat.math.ethz.ch
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Rousseeuw
    given-names: Peter
    email: peter.rousseeuw@kuleuven.be
    orcid: https://orcid.org/0000-0002-3807-5353
  - family-names: Struyf
    given-names: Anja
  - family-names: Hubert
    given-names: Mia
    email: Mia.Hubert@uia.ua.ac.be
    orcid: https://orcid.org/0000-0001-6398-4850
  year: '2022'
  url: https://CRAN.R-project.org/package=cluster
- type: software
  title: dbscan
  abstract: 'dbscan: Density-Based Spatial Clustering of Applications with Noise (DBSCAN)
    and Related Algorithms'
  notes: Imports
  authors:
  - family-names: Hahsler
    given-names: Michael
    email: mhahsler@lyle.smu.edu
  - family-names: Piekenbrock
    given-names: Matthew
  year: '2022'
  url: https://CRAN.R-project.org/package=dbscan
- type: software
  title: dendextend
  abstract: 'dendextend: Extending ''dendrogram'' Functionality in R'
  notes: Imports
  authors:
  - family-names: Galili
    given-names: Tal
    email: tal.galili@gmail.com
  - family-names: Jefferis
    given-names: Gregory
    email: jefferis@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=dendextend
- type: software
  title: dynamicTreeCut
  abstract: 'dynamicTreeCut: Methods for Detection of Clusters in Hierarchical Clustering
    Dendrograms'
  notes: Imports
  authors:
  - family-names: Langfelder
    given-names: Peter
    email: Peter.Langfelder@gmail.com
  - family-names: Zhang
    given-names: Bin
    email: binzhang.ucla@gmail.com
  - family-names: Horvath
    given-names: with contributions from Steve
    email: SHorvath@mednet.ucla.edu
  year: '2022'
  url: https://CRAN.R-project.org/package=dynamicTreeCut
- type: software
  title: earth
  abstract: 'earth: Multivariate Adaptive Regression Splines'
  notes: Imports
  authors:
  - family-names: Hastie
    given-names: Stephen Milborrow. Derived from mda:mars by Trevor
  - family-names: wrapper.
    given-names: Rob Tibshirani. Uses Alan Miller's Fortran utilities with Thomas
      Lumley's leaps
  year: '2022'
  url: https://CRAN.R-project.org/package=earth
- type: software
  title: fastcluster
  abstract: 'fastcluster: Fast Hierarchical Clustering Routines for R and ''Python'''
  notes: Imports
  authors:
  - family-names: Müllner
    given-names: Daniel
    email: daniel@danifold.net
  year: '2022'
  url: https://CRAN.R-project.org/package=fastcluster
- type: software
  title: ggplot2
  abstract: 'ggplot2: Create Elegant Data Visualisations Using the Grammar of Graphics'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
    orcid: https://orcid.org/0000-0003-4757-117X
  - family-names: Chang
    given-names: Winston
    orcid: https://orcid.org/0000-0002-1576-2126
  - family-names: Henry
    given-names: Lionel
  - family-names: Pedersen
    given-names: Thomas Lin
    email: thomas.pedersen@rstudio.com
    orcid: https://orcid.org/0000-0002-5147-4711
  - family-names: Takahashi
    given-names: Kohske
  - family-names: Wilke
    given-names: Claus
    orcid: https://orcid.org/0000-0002-7470-9261
  - family-names: Woo
    given-names: Kara
    orcid: https://orcid.org/0000-0002-5125-4188
  - family-names: Yutani
    given-names: Hiroaki
    orcid: https://orcid.org/0000-0002-3385-7233
  - family-names: Dunnington
    given-names: Dewey
    orcid: https://orcid.org/0000-0002-9415-4582
  year: '2022'
  url: https://CRAN.R-project.org/package=ggplot2
- type: software
  title: igraph
  abstract: 'igraph: Network Analysis and Visualization'
  notes: Imports
  authors:
  - family-names: file.
    given-names: See AUTHORS
  year: '2022'
  url: https://CRAN.R-project.org/package=igraph
- type: software
  title: MASS
  abstract: 'MASS: Support Functions and Datasets for Venables and Ripley''s MASS'
  notes: Imports
  authors:
  - family-names: Ripley
    given-names: Brian
    email: ripley@stats.ox.ac.uk
  year: '2022'
  url: https://CRAN.R-project.org/package=MASS
- type: software
  title: mathjaxr
  abstract: 'mathjaxr: Using ''Mathjax'' in Rd Files'
  notes: Imports
  authors:
  - family-names: Viechtbauer
    given-names: Wolfgang
    email: wvb@wvbauer.com
    orcid: https://orcid.org/0000-0003-3463-4063
  year: '2022'
  url: https://CRAN.R-project.org/package=mathjaxr
- type: software
  title: Matrix
  abstract: 'Matrix: Sparse and Dense Matrix Classes and Methods'
  notes: Imports
  authors:
  - family-names: Bates
    given-names: Douglas
  - family-names: Maechler
    given-names: Martin
    email: mmaechler+Matrix@gmail.com
    orcid: https://orcid.org/0000-0002-8685-9910
  - family-names: Jagan
    given-names: Mikael
  year: '2022'
  url: https://CRAN.R-project.org/package=Matrix
- type: software
  title: mclust
  abstract: 'mclust: Gaussian Mixture Modelling for Model-Based Clustering, Classification,
    and Density Estimation'
  notes: Imports
  authors:
  - family-names: Fraley
    given-names: Chris
  - family-names: Raftery
    given-names: Adrian E.
    orcid: https://orcid.org/0000-0002-6589-301X
  - family-names: Scrucca
    given-names: Luca
    email: luca.scrucca@unipg.it
    orcid: https://orcid.org/0000-0003-3826-0484
  year: '2022'
  url: https://CRAN.R-project.org/package=mclust
- type: software
  title: Rcpp
  abstract: 'Rcpp: Seamless R and C++ Integration'
  notes: Imports
  authors:
  - family-names: Eddelbuettel
    given-names: Dirk
  - family-names: Francois
    given-names: Romain
  - family-names: Allaire
    given-names: JJ
  - family-names: Ushey
    given-names: Kevin
  - family-names: Kou
    given-names: Qiang
  - family-names: Russell
    given-names: Nathan
  - family-names: Ucar
    given-names: Inaki
  - family-names: Bates
    given-names: Douglas
  - family-names: Chambers
    given-names: John
  year: '2022'
  url: https://CRAN.R-project.org/package=Rcpp
- type: software
  title: Rdpack
  abstract: 'Rdpack: Update and Manipulate Rd Documentation Objects'
  notes: Imports
  authors:
  - family-names: Boshnakov
    given-names: Georgi N.
    email: georgi.boshnakov@manchester.ac.uk
  year: '2022'
  url: https://CRAN.R-project.org/package=Rdpack
- type: software
  title: reshape2
  abstract: 'reshape2: Flexibly Reshape Data: A Reboot of the Reshape Package'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: h.wickham@gmail.com
  year: '2022'
  url: https://CRAN.R-project.org/package=reshape2
- type: software
  title: rmarkdown
  abstract: 'rmarkdown: Dynamic Documents for R'
  notes: Imports
  authors:
  - family-names: Allaire
    given-names: JJ
    email: jj@rstudio.com
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  - family-names: McPherson
    given-names: Jonathan
    email: jonathan@rstudio.com
  - family-names: Luraschi
    given-names: Javier
    email: javier@rstudio.com
  - family-names: Ushey
    given-names: Kevin
    email: kevin@rstudio.com
  - family-names: Atkins
    given-names: Aron
    email: aron@rstudio.com
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Cheng
    given-names: Joe
    email: joe@rstudio.com
  - family-names: Chang
    given-names: Winston
    email: winston@rstudio.com
  - family-names: Iannone
    given-names: Richard
    email: rich@rstudio.com
    orcid: https://orcid.org/0000-0003-3925-190X
  year: '2022'
  url: https://CRAN.R-project.org/package=rmarkdown
- type: software
  title: stats
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: tidyr
  abstract: 'tidyr: Tidy Messy Data'
  notes: Imports
  authors:
  - family-names: Wickham
    given-names: Hadley
    email: hadley@rstudio.com
  - family-names: Girlich
    given-names: Maximilian
  year: '2022'
  url: https://CRAN.R-project.org/package=tidyr
- type: software
  title: utils
  abstract: 'R: A Language and Environment for Statistical Computing'
  notes: Imports
  authors:
  - name: R Core Team
  location:
    name: Vienna, Austria
  year: '2022'
  url: https://www.R-project.org/
  institution:
    name: R Foundation for Statistical Computing
- type: software
  title: knitr
  abstract: 'knitr: A General-Purpose Package for Dynamic Report Generation in R'
  notes: Suggests
  authors:
  - family-names: Xie
    given-names: Yihui
    email: xie@yihui.name
    orcid: https://orcid.org/0000-0003-0645-5666
  year: '2022'
  url: https://CRAN.R-project.org/package=knitr