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Easy, fast and reproducible Stochastic Cellular Automata with chouca
Indexado
WoS WOS:001347704200010
DOI 10.24072/PCJOURNAL.466
Año 2024
Tipo artículo de investigación

Citas Totales

Autores Afiliación Chile

Instituciones Chile

% Participación
Internacional

Autores
Afiliación Extranjera

Instituciones
Extranjeras


Abstract



Stochastic cellular automata (SCA) are models that describe spatial dynamics using a grid of cells that switch between discrete states over time. They are widely used to understand how small-scale processes scale up to affect ecological dynamics at larger spatial scales, and have been applied to a wide diversity of theoretical and applied problems in all systems, such as arid ecosystems, coral reefs, forests, bacteria, or urban growth. Despite their wide applications, SCA implementations are often ad-hoc, lacking performance, guarantees of correctness and poorly reproducible. De novo implementation of SCA for each specific system and application also represents a major barrier for many practitioners. To provide a unifying, well-tested technical basis to this class of models and facilitate their implementation, we built chouca, an R package that translates definitions of SCA models into compiled code, and runs simulations in an efficient way. chouca supports SCA based on rectangular grids where transition probabilities are defined for each cell, with performance typically two to three orders of magnitude above typical implementations in interpreted languages (e.g. R, Python), all while maintaining an intuitive interface in the R environment. Exact and mean-field simulations can be run, and both numerical and graphical results can be easily exported. Besides providing better reproducibility and accessibility, a fast engine for SCA unlocks novel, computationally intensive statistical approaches, such as simulation-based inference of ecological interactions from field data, which represents by itself an important avenue for research. By providing an easy and efficient entry point to SCAs, chouca lowers the bar to the use of this class of models for ecologists, managers and general practitioners, providing a leveled-off reproducible platform while opening novel methodological approaches.

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Disciplinas de Investigación



WOS
Sin Disciplinas
Scopus
Sin Disciplinas
SciELO
Sin Disciplinas

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Publicaciones WoS (Ediciones: ISSHP, ISTP, AHCI, SSCI, SCI), Scopus, SciELO Chile.

Colaboración Institucional



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Autores - Afiliación



Ord. Autor Género Institución - País
1 Genin, Alexandre - Utrecht Univ Utrecht - Países Bajos
Pontificia Universidad Católica de Chile - Chile
Ctr Natl Rech Sci - Francia
2 Dupont, Guillaume - Pontificia Universidad Católica de Chile - Chile
Univ Ghent - Bélgica
3 Valencia, Daniel - Pontificia Universidad Católica de Chile - Chile
4 Zucconi, Mauro - Pontificia Universidad Católica de Chile - Chile
Universidad de Concepción - Chile
5 Avila-Thiem, M. Isidora - Universidad Mayor - Chile
Pontificia Universidad Católica de Chile - Chile
6 Navarrete, Sergio A. - Pontificia Universidad Católica de Chile - Chile
Universidad de Concepción - Chile
7 Wieters, Evie A. - Pontificia Universidad Católica de Chile - Chile

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Financiamiento



Fuente
FONDECYT
CAPES
Pontificia Universidad Católica de Chile
European Union
Núcleo Milenio
PIA/Basal
SECOS
COPAS Coastal
ICN
Marie Curie Actions (MSCA)
IsBlue program
Nucleo Milenio NUTME
COPAS-COASTAL
NUTME ICM

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Agradecimientos



Agradecimiento
AG has received funding from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement 896159 (INDECOSTAB) . MGZ thanks the Pontificia Universidad Catolica de Chile for the doctoral student support scholarship, and programs COPAS-COASTAL (FB10021) and Nucleo Milenio NUTME NCN2023_004 for the awarded doctoral thesis fellowships. MIAT acknoweldges support from FONDECYT 3220110, GD from the IsBlue program (ANR-17-EURE-0015) , EAW from FONDECYT 1181719, 1241901, and Nucleo Milenio NCN2023_004 (NUTME) , and SAN from NUTME ICM_NCN2023_004, SECOS, ICN 2019-015, CAPES, PIA/BASAL FB0002, COPAS COASTAL FB21002, and FONDECYT 1200636.

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