paper.bib

@article{leroy2016virtualspecies,
  title={{virtualspecies, an R package to generate virtual species distributions}},
  author={Leroy, Boris and Meynard, Christine N and Bellard, C{\'e}line and Courchamp, Franck},
  journal={Ecography},
  volume={39},
  number={6},
  pages={599--607},
  year={2016},
  doi={10.1111/ecog.01388}
}

@software{langeraert2024gcube,
  author = {Langeraert, Ward},
  license = {MIT},
  title = {{gcube: Simulating Biodiversity Data Cubes}},
  url = {https://github.com/b-cubed-eu/gcube/},
  version = {0.4.0},
  year={2024}
}

@misc{huybrechts2024guidelines,
  title={{B-Cubed software development guide}},
  author={Huybrechts, P and Trekels, M and Abraham, L and Desmet, P},
  howpublished={\url{https://docs.b-cubed.eu/dev-guide/}},
  year={2024}
}

@Manual{R2024lang,
  title = {{R: A Language and Environment for Statistical Computing}},
  author = {{R Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2024},
  url = {https://www.R-project.org/},
}

@Manual{pkgdown2024wickham,
  title = {{pkgdown: Make Static HTML Documentation for a Package}},
  author = {Hadley Wickham and Jay Hesselberth and Maëlle Salmon and Olivier Roy and Salim Brüggemann},
  year = {2024},
  url = {https://CRAN.R-project.org/package=pkgdown},
}

@Article{gstat2016Graler,
  title = {{Spatio-Temporal Interpolation using gstat}},
  author = {Benedikt Gräler and Edzer Pebesma and Gerard Heuvelink},
  year = {2016},
  journal = {The R Journal},
  volume = {8},
  issue = {1},
  pages = {204-218},
  url = {https://journal.r-project.org/archive/2016/RJ-2016-014/index.html},
}

@Manual{terra2024hijmans,
  title = {{terra: Spatial Data Analysis}},
  author = {Robert J. Hijmans},
  year = {2024},
  url = {https://CRAN.R-project.org/package=terra},
}

@Manual{cli2024csardi,
  title = {{cli: Helpers for Developing Command Line Interfaces}},
  author = {Gábor Csárdi},
  year = {2024},
  url = {https://CRAN.R-project.org/package=cli},
}

@Manual{dplyr2023wickham,
  title = {{dplyr: A Grammar of Data Manipulation}},
  author = {Hadley Wickham and Romain François and Lionel Henry and Kirill Müller and Davis Vaughan},
  year = {2023},
  url = {https://CRAN.R-project.org/package=dplyr},
}

@Manual{magrittr2022bache,
  title = {{magrittr: A Forward-Pipe Operator for R}},
  author = {Stefan Milton Bache and Hadley Wickham},
  year = {2022},
  url = {https://CRAN.R-project.org/package=magrittr},
}

@Manual{mnormt2022azzalini,
  title = {The {R} package \texttt{mnormt}: The multivariate normal and $t$ distributions (version 2.1.1)},
  author = {Adelchi Azzalini and Alan Genz},
  year = {2022},
  url = {http://azzalini.stat.unipd.it/SW/Pkg-mnormt/},
}

@Manual{rlang2024henry,
  title = {{rlang: Functions for Base Types and Core R and 'Tidyverse' Features}},
  author = {Lionel Henry and Hadley Wickham},
  year = {2024},
  url = {https://CRAN.R-project.org/package=rlang},
}

@Book{sf2023pebesma,
  author = {Edzer Pebesma and Roger Bivand},
  title = {{Spatial Data Science: With applications in R}},
  year = {2023},
  publisher = {{Chapman and Hall/CRC}},
  url = {https://r-spatial.org/book/},
  doi = {10.1201/9780429459016},
}


@Article{sf2018pebesma,
  author = {Edzer Pebesma},
  title = {{Simple Features for R: Standardized Support for Spatial Vector Data}},
  year = {2018},
  journal = {{The R Journal}},
  doi = {10.32614/RJ-2018-009},
  pages = {439--446},
  volume = {10},
  number = {1},
}

@Manual{vegan2024oskanen,
  title = {{vegan: Community Ecology Package}},
  author = {Jari Oksanen and Gavin L. Simpson and F. Guillaume Blanchet and Roeland Kindt and Pierre Legendre and Peter R. Minchin and R.B. O'Hara and Peter Solymos and M. Henry H. Stevens and Eduard Szoecs and Helene Wagner and Matt Barbour and Michael Bedward and Ben Bolker and Daniel Borcard and Gustavo Carvalho and Michael Chirico and Miquel {De Caceres} and Sebastien Durand and Heloisa Beatriz Antoniazi Evangelista and Rich FitzJohn and Michael Friendly and Brendan Furneaux and Geoffrey Hannigan and Mark O. Hill and Leo Lahti and Dan McGlinn and Marie-Helene Ouellette and Eduardo {Ribeiro Cunha} and Tyler Smith and Adrian Stier and Cajo J.F. {Ter Braak} and James Weedon},
  year = {2024},
  url = {https://CRAN.R-project.org/package=vegan},
}

@Manual{withr2024hester,
  title = {{withr: Run Code 'With' Temporarily Modified Global State}},
  author = {Jim Hester and Lionel Henry and Kirill Müller and Kevin Ushey and Hadley Wickham and Winston Chang},
  year = {2024},
  url = {https://CRAN.R-project.org/package=withr},
}

@Book{ggplot2016wickham,
  author = {Hadley Wickham},
  title = {ggplot2: Elegant Graphics for Data Analysis},
  publisher = {Springer-Verlag New York},
  year = {2016},
  isbn = {978-3-319-24277-4},
  doi = {10.1007/978-3-319-24277-4},
}

@Article{testthat2011wickham,
  author = {Hadley Wickham},
  title = {testthat: Get Started with Testing},
  journal = {The R Journal},
  year = {2011},
  volume = {3},
  pages = {5--10},
  url = {https://journal.r-project.org/archive/2011-1/RJournal_2011-1_Wickham.pdf},
}

@article{zurell2010virtualecologist,
	title = {The virtual ecologist approach: simulating data and observers},
	volume = {119},
	copyright = {http://doi.wiley.com/10.1002/tdm\_license\_1.1},
	issn = {00301299, 16000706},
	shorttitle = {The virtual ecologist approach},
	url = {https://onlinelibrary.wiley.com/doi/10.1111/j.1600-0706.2009.18284.x},
	doi = {10.1111/j.1600-0706.2009.18284.x},
	language = {en},
	number = {4},
	urldate = {2024-08-07},
	journal = {Oikos},
	author = {Zurell, Damaris and Berger, Uta and Cabral, Juliano S. and Jeltsch, Florian and Meynard, Christine N. and Münkemüller, Tamara and Nehrbass, Nana and Pagel, Jörn and Reineking, Björn and Schröder, Boris and Grimm, Volker},
	month = feb,
	year = {2010},
	pages = {622--635}
}

@article{may2018mobsim,
	title = {{mobsim: An R package for the simulation and measurement of biodiversity across spatial scales}},
	volume = {9},
	copyright = {http://onlinelibrary.wiley.com/termsAndConditions\#vor},
	issn = {2041-210X, 2041-210X},
	shorttitle = {mobsim},
	url = {https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.12986},
	doi = {10.1111/2041-210X.12986},
	language = {en},
	number = {6},
	urldate = {2024-08-20},
	journal = {Methods in Ecology and Evolution},
	author = {May, Felix and Gerstner, Katharina and McGlinn, Daniel J. and Xiao, Xiao and Chase, Jonathan M.},
	editor = {Goslee, Sarah},
	month = jun,
	year = {2018},
	pages = {1401--1408}
}

@article{sokol2015linking,
	title = {Linking management to biodiversity in built ponds using metacommunity simulations},
	volume = {296},
	issn = {03043800},
	url = {https://linkinghub.elsevier.com/retrieve/pii/S0304380014004918},
	doi = {10.1016/j.ecolmodel.2014.10.022},
	language = {en},
	urldate = {2024-08-20},
	journal = {Ecological Modelling},
author={Sokol, Eric R and Brown, Bryan L and Carey, Cayelan C and Tornwall, Brett M and Swan, Christopher M and Barrett, JE},
	month = jan,
	year = {2015},
	pages = {36--45},
}

@article{grimm2017next,
  title={Next-generation individual-based models integrate biodiversity and ecosystems: yes we can, and yes we must},
  author={Grimm, Volker and Ayll{\'o}n, Daniel and Railsback, Steven F},
  journal={Ecosystems},
  volume={20},
  pages={229--236},
  year={2017},
  publisher={Springer},
  doi = {10.1007/s10021-016-0071-2}
}

@article{grimm1996pattern,
  title={Pattern-oriented modelling in population ecology},
  author={Grimm, Volker and Frank, Karin and Jeltsch, Florian and Brandl, Roland and Uchma{\'n}ski, Janusz and Wissel, Christian},
  journal={Science of the Total Environment},
  volume={183},
  number={1-2},
  pages={151--166},
  year={1996},
  publisher={Elsevier},
  doi = {10.1016/0048-9697(95)04966-5}
}

@article{sokol2017simulation,
  title={A simulation‐based approach to understand how metacommunity characteristics influence emergent biodiversity patterns},
  author={Sokol, Eric R and Brown, Bryan L and Barrett, JE},
  journal={Oikos},
  year={2017},
  volume={126},
  pages={723-737},
  doi={10.1111/OIK.03690}
}

@article{munkemüller2012fromindices,
  title={From diversity indices to community assembly processes: a test with simulated data},
  author={T. Münkemüller and F. Bello and C. Meynard and D. Gravel and S. Lavergne and D. Mouillot and N. Mouquet and W. Thuiller},
  journal={Ecography},
  year={2012},
  volume={35},
  pages={468-480},
  doi={10.1111/J.1600-0587.2011.07259.X}
}

@article{christie2019simple,
  title={Simple study designs in ecology produce inaccurate estimates of biodiversity responses},
  author={Alec P. Christie and Tatsuya Amano and Philip A. Martin and Gorm E. Shackelford and Benno I. Simmons and William J. Sutherland},
  journal={Journal of Applied Ecology},
  year={2019},
  doi={10.1111/1365-2664.13499}
}

@article{oldoni2020cubesconf,
	author = {Damiano Oldoni and Quentin Groom and Peter Desmet},
	title = {{Occurrence Cubes: A new way of aggregating heterogeneous species occurrence data}},
	volume = {4},
	year = {2020},
	doi = {10.3897/biss.4.59154},
	publisher = {Pensoft Publishers},
	pages = {e59154},
	journal = {Biodiversity Information Science and Standards}
}

@article{oldoni2020cubes,
	author = {Oldoni, Damiano and Groom, Quentin and Adriaens, Tim and Davis, Amy J.S. and Reyserhove, Lien and Strubbe, Diederik and Vanderhoeven, Sonia and Desmet, Peter},
	title = {Occurrence cubes: a new paradigm for aggregating species occurrence data},
	elocation-id = {2020.03.23.983601},
	year = {2020},
	doi = {10.1101/2020.03.23.983601},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2020/03/25/2020.03.23.983601},
	eprint = {https://www.biorxiv.org/content/early/2020/03/25/2020.03.23.983601.full.pdf},
	journal = {bioRxiv}
}

@incollection{grimm2013individual,
  title={Individual-based modeling and ecology},
  author={Grimm, Volker and Railsback, Steven F},
  booktitle={Individual-based modeling and ecology},
  year={2013},
  publisher={Princeton university press},
  doi={10.1515/9781400850624}
}

@Article{inlabru,
  title = {{inlabru}: an {R} package for {Bayesian} spatial modelling from ecological survey data},
  author = {Fabian E. Bachl and Finn Lindgren and David L. Borchers and Janine B. Illian},
  year = {2019},
  journal = {Methods in Ecology and Evolution},
  volume = {10},
  pages = {760--766},
  doi = {10.1111/2041-210X.13168},
  publisher = {British Ecological Society}
}

@Article{sdmTMB,
  title = {sdmTMB: an R package for fast, flexible, and user-friendly generalized linear mixed effects models with spatial and spatiotemporal random fields},
  author = {Sean C. Anderson and Eric J. Ward and Philina A. English and Lewis A. K. Barnett and James T. Thorson},
  year = {2024},
  journal = {bioRxiv},
  volume = {2022.03.24.485545},
  doi = {10.1101/2022.03.24.485545}
}

@Book{spatstat,
  title = {Spatial Point Patterns: Methodology and Applications with {R}},
  author = {Adrian Baddeley and Ege Rubak and Rolf Turner},
  year = {2015},
  publisher = {Chapman and Hall/CRC Press},
  address = {London},
  isbn = {9781482210200},
  doi = {10.1201/b19708},
}

@article{wilkinson2016fair,
  title={{The FAIR Guiding Principles for scientific data management and stewardship}},
  author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and {da Silva Santos}, Luiz Bonino and Bourne, Philip E and Bouwman, J and Brookes, A J and Clark, T and Crosas, M and Dillo, I and Dumon, O and Edmunds, S and Evelo, C T and Finkers, R and Gonzalez-Beltran, A and Gray, A J G and Groth, P and Goble, C and Grethe, J S and Heringa, J and {'t Hoen}, P A C and Jooft, R and Kuhn, T and Kok, R and Kok J, and Lusher, S J and Martone, M E and Mons, A and Packer, A L and Persson, B and Rocca-Serra, P and Roos, M and {van Schaik}, R and Sansone, Susanna-Asunta and and Schultes, E and Sengstag, T and Slater, T and Strawn, G and Swertz, M A and Thompson, M and {van der Lei}, J and {van Mulligen}, E and Velterop, J and Waagmeester, A and Wittenburg, P and Wolstencroft, Katherine and Zhao, J and Mons, Barend},
  journal={Scientific data},
  volume={3},
  number={1},
  pages={1--9},
  year={2016},
  publisher={Nature Publishing Group},
  doi = {10.1038/sdata.2016.18}
}