Achieving higher standards in species distribution modeling by leveraging the diversity of available software
- Autores
- Kass, Jamie M.; Smith, Adam B.; Warren, Dan L.; Vignali, Sergio; Schmitt, Sylvain; Aiello Lammens, Matthew E.; Arlé, Eduardo; Márcia Barbosa, Ana; Broennimann, Olivier; Cobos, Marlon E.; Guéguen, Maya; Guisan, Antoine; Merow, Cory; Naimi, Babak; Nobis, Michael P.; Ondo, Ian; Osorio Olvera, Luis Alfredo; Owens, Hannah L.; Pinilla Buitrago, Gonzalo E.; Sánchez Tapia, Andrea; Thuiller, Wilfried; Valavi, Roozbeh; Velazco, Santiago José Elías; Zizka, Alexander; Zurell, Damaris
- Año de publicación
- 2024
- Idioma
- inglés
- Tipo de recurso
- artículo
- Estado
- versión publicada
- Descripción
- The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.
Fil: Kass, Jamie M.. Tohoku University; Japón. Okinawa Institute of Science and Technology Graduate University; Japón
Fil: Smith, Adam B.. Missouri Botanical Garden; Estados Unidos
Fil: Warren, Dan L.. Charles Sturt University; Australia. Okinawa Institute of Science and Technology Graduate University; Japón
Fil: Vignali, Sergio. University of Bern; Suiza
Fil: Schmitt, Sylvain. Philipps-university Marburg; Alemania. Université Montpellier II; Francia
Fil: Aiello Lammens, Matthew E.. Pace University; Estados Unidos
Fil: Arlé, Eduardo. German Centre for Integrative Biodiversity Research; Alemania. Universitat Tel Aviv; Israel
Fil: Márcia Barbosa, Ana. Universidad de Porto; Portugal
Fil: Broennimann, Olivier. Universite de Lausanne; Suiza
Fil: Cobos, Marlon E.. University of Kansas; Estados Unidos
Fil: Guéguen, Maya. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; Francia
Fil: Guisan, Antoine. Universite de Lausanne; Suiza
Fil: Merow, Cory. University of Connecticut; Estados Unidos
Fil: Naimi, Babak. University of Utrecht; Países Bajos
Fil: Nobis, Michael P.. Swiss Federal Research Institute; Suiza
Fil: Ondo, Ian. Royal Botanic Gardens; Reino Unido. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido
Fil: Osorio Olvera, Luis Alfredo. Universidad Nacional Autónoma de México; México. Consejo Nacional de Humanidades, Ciencias y Tecnologías; México
Fil: Owens, Hannah L.. Universidad de Copenhagen; Dinamarca. University of Florida; Estados Unidos
Fil: Pinilla Buitrago, Gonzalo E.. City University of New York; Estados Unidos
Fil: Sánchez Tapia, Andrea. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil
Fil: Thuiller, Wilfried. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; Francia
Fil: Valavi, Roozbeh. Commonwealth Scientific And Industrial Research Organisation (csiro);
Fil: Velazco, Santiago José Elías. San Diego State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina
Fil: Zizka, Alexander. Philipps-University Marburg; Alemania
Fil: Zurell, Damaris. Universitat Potsdam; Alemania - Materia
-
Code
Habitat
Niche
Programming
R package
Reproducibility - Nivel de accesibilidad
- acceso abierto
- Condiciones de uso
- https://creativecommons.org/licenses/by/2.5/ar/
- Repositorio
.jpg)
- Institución
- Consejo Nacional de Investigaciones Científicas y Técnicas
- OAI Identificador
- oai:ri.conicet.gov.ar:11336/263723
Ver los metadatos del registro completo
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Achieving higher standards in species distribution modeling by leveraging the diversity of available softwareKass, Jamie M.Smith, Adam B.Warren, Dan L.Vignali, SergioSchmitt, SylvainAiello Lammens, Matthew E.Arlé, EduardoMárcia Barbosa, AnaBroennimann, OlivierCobos, Marlon E.Guéguen, MayaGuisan, AntoineMerow, CoryNaimi, BabakNobis, Michael P.Ondo, IanOsorio Olvera, Luis AlfredoOwens, Hannah L.Pinilla Buitrago, Gonzalo E.Sánchez Tapia, AndreaThuiller, WilfriedValavi, RoozbehVelazco, Santiago José ElíasZizka, AlexanderZurell, DamarisCodeHabitatNicheProgrammingR packageReproducibilityhttps://purl.org/becyt/ford/1.6https://purl.org/becyt/ford/1The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs.Fil: Kass, Jamie M.. Tohoku University; Japón. Okinawa Institute of Science and Technology Graduate University; JapónFil: Smith, Adam B.. Missouri Botanical Garden; Estados UnidosFil: Warren, Dan L.. Charles Sturt University; Australia. Okinawa Institute of Science and Technology Graduate University; JapónFil: Vignali, Sergio. University of Bern; SuizaFil: Schmitt, Sylvain. Philipps-university Marburg; Alemania. Université Montpellier II; FranciaFil: Aiello Lammens, Matthew E.. Pace University; Estados UnidosFil: Arlé, Eduardo. German Centre for Integrative Biodiversity Research; Alemania. Universitat Tel Aviv; IsraelFil: Márcia Barbosa, Ana. Universidad de Porto; PortugalFil: Broennimann, Olivier. Universite de Lausanne; SuizaFil: Cobos, Marlon E.. University of Kansas; Estados UnidosFil: Guéguen, Maya. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; FranciaFil: Guisan, Antoine. Universite de Lausanne; SuizaFil: Merow, Cory. University of Connecticut; Estados UnidosFil: Naimi, Babak. University of Utrecht; Países BajosFil: Nobis, Michael P.. Swiss Federal Research Institute; SuizaFil: Ondo, Ian. Royal Botanic Gardens; Reino Unido. United Nations Environment Programme World Conservation Monitoring Centre; Reino UnidoFil: Osorio Olvera, Luis Alfredo. Universidad Nacional Autónoma de México; México. Consejo Nacional de Humanidades, Ciencias y Tecnologías; MéxicoFil: Owens, Hannah L.. Universidad de Copenhagen; Dinamarca. University of Florida; Estados UnidosFil: Pinilla Buitrago, Gonzalo E.. City University of New York; Estados UnidosFil: Sánchez Tapia, Andrea. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; BrasilFil: Thuiller, Wilfried. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; FranciaFil: Valavi, Roozbeh. Commonwealth Scientific And Industrial Research Organisation (csiro);Fil: Velazco, Santiago José Elías. San Diego State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; ArgentinaFil: Zizka, Alexander. Philipps-University Marburg; AlemaniaFil: Zurell, Damaris. Universitat Potsdam; AlemaniaWiley Blackwell Publishing, Inc2024-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfapplication/pdfhttp://hdl.handle.net/11336/263723Kass, Jamie M.; Smith, Adam B.; Warren, Dan L.; Vignali, Sergio; Schmitt, Sylvain; et al.; Achieving higher standards in species distribution modeling by leveraging the diversity of available software; Wiley Blackwell Publishing, Inc; Ecography; 2025; 2; 11-2024; 1-140906-7590CONICET DigitalCONICETenginfo:eu-repo/semantics/altIdentifier/url/https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/ecog.07346info:eu-repo/semantics/altIdentifier/doi/10.1111/ecog.07346info:eu-repo/semantics/openAccesshttps://creativecommons.org/licenses/by/2.5/ar/reponame:CONICET Digital (CONICET)instname:Consejo Nacional de Investigaciones Científicas y Técnicas2025-10-22T12:04:25Zoai:ri.conicet.gov.ar:11336/263723instacron:CONICETInstitucionalhttp://ri.conicet.gov.ar/Organismo científico-tecnológicoNo correspondehttp://ri.conicet.gov.ar/oai/requestdasensio@conicet.gov.ar; lcarlino@conicet.gov.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:34982025-10-22 12:04:25.527CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicasfalse |
| dc.title.none.fl_str_mv |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| title |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| spellingShingle |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software Kass, Jamie M. Code Habitat Niche Programming R package Reproducibility |
| title_short |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| title_full |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| title_fullStr |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| title_full_unstemmed |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| title_sort |
Achieving higher standards in species distribution modeling by leveraging the diversity of available software |
| dc.creator.none.fl_str_mv |
Kass, Jamie M. Smith, Adam B. Warren, Dan L. Vignali, Sergio Schmitt, Sylvain Aiello Lammens, Matthew E. Arlé, Eduardo Márcia Barbosa, Ana Broennimann, Olivier Cobos, Marlon E. Guéguen, Maya Guisan, Antoine Merow, Cory Naimi, Babak Nobis, Michael P. Ondo, Ian Osorio Olvera, Luis Alfredo Owens, Hannah L. Pinilla Buitrago, Gonzalo E. Sánchez Tapia, Andrea Thuiller, Wilfried Valavi, Roozbeh Velazco, Santiago José Elías Zizka, Alexander Zurell, Damaris |
| author |
Kass, Jamie M. |
| author_facet |
Kass, Jamie M. Smith, Adam B. Warren, Dan L. Vignali, Sergio Schmitt, Sylvain Aiello Lammens, Matthew E. Arlé, Eduardo Márcia Barbosa, Ana Broennimann, Olivier Cobos, Marlon E. Guéguen, Maya Guisan, Antoine Merow, Cory Naimi, Babak Nobis, Michael P. Ondo, Ian Osorio Olvera, Luis Alfredo Owens, Hannah L. Pinilla Buitrago, Gonzalo E. Sánchez Tapia, Andrea Thuiller, Wilfried Valavi, Roozbeh Velazco, Santiago José Elías Zizka, Alexander Zurell, Damaris |
| author_role |
author |
| author2 |
Smith, Adam B. Warren, Dan L. Vignali, Sergio Schmitt, Sylvain Aiello Lammens, Matthew E. Arlé, Eduardo Márcia Barbosa, Ana Broennimann, Olivier Cobos, Marlon E. Guéguen, Maya Guisan, Antoine Merow, Cory Naimi, Babak Nobis, Michael P. Ondo, Ian Osorio Olvera, Luis Alfredo Owens, Hannah L. Pinilla Buitrago, Gonzalo E. Sánchez Tapia, Andrea Thuiller, Wilfried Valavi, Roozbeh Velazco, Santiago José Elías Zizka, Alexander Zurell, Damaris |
| author2_role |
author author author author author author author author author author author author author author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
Code Habitat Niche Programming R package Reproducibility |
| topic |
Code Habitat Niche Programming R package Reproducibility |
| purl_subject.fl_str_mv |
https://purl.org/becyt/ford/1.6 https://purl.org/becyt/ford/1 |
| dc.description.none.fl_txt_mv |
The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs. Fil: Kass, Jamie M.. Tohoku University; Japón. Okinawa Institute of Science and Technology Graduate University; Japón Fil: Smith, Adam B.. Missouri Botanical Garden; Estados Unidos Fil: Warren, Dan L.. Charles Sturt University; Australia. Okinawa Institute of Science and Technology Graduate University; Japón Fil: Vignali, Sergio. University of Bern; Suiza Fil: Schmitt, Sylvain. Philipps-university Marburg; Alemania. Université Montpellier II; Francia Fil: Aiello Lammens, Matthew E.. Pace University; Estados Unidos Fil: Arlé, Eduardo. German Centre for Integrative Biodiversity Research; Alemania. Universitat Tel Aviv; Israel Fil: Márcia Barbosa, Ana. Universidad de Porto; Portugal Fil: Broennimann, Olivier. Universite de Lausanne; Suiza Fil: Cobos, Marlon E.. University of Kansas; Estados Unidos Fil: Guéguen, Maya. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; Francia Fil: Guisan, Antoine. Universite de Lausanne; Suiza Fil: Merow, Cory. University of Connecticut; Estados Unidos Fil: Naimi, Babak. University of Utrecht; Países Bajos Fil: Nobis, Michael P.. Swiss Federal Research Institute; Suiza Fil: Ondo, Ian. Royal Botanic Gardens; Reino Unido. United Nations Environment Programme World Conservation Monitoring Centre; Reino Unido Fil: Osorio Olvera, Luis Alfredo. Universidad Nacional Autónoma de México; México. Consejo Nacional de Humanidades, Ciencias y Tecnologías; México Fil: Owens, Hannah L.. Universidad de Copenhagen; Dinamarca. University of Florida; Estados Unidos Fil: Pinilla Buitrago, Gonzalo E.. City University of New York; Estados Unidos Fil: Sánchez Tapia, Andrea. Instituto de Pesquisas Jardim Botânico do Rio de Janeiro; Brasil Fil: Thuiller, Wilfried. Universite Grenoble Alpes; Francia. Centre National de la Recherche Scientifique; Francia Fil: Valavi, Roozbeh. Commonwealth Scientific And Industrial Research Organisation (csiro); Fil: Velazco, Santiago José Elías. San Diego State University; Estados Unidos. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Nordeste. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú | Universidad Nacional de Misiones. Instituto de Biología Subtropical. Instituto de Biología Subtropical - Nodo Puerto Iguazú; Argentina Fil: Zizka, Alexander. Philipps-University Marburg; Alemania Fil: Zurell, Damaris. Universitat Potsdam; Alemania |
| description |
The increasing online availability of biodiversity data and advances in ecological modeling have led to a proliferation of open-source modeling tools. In particular, R packages for species distribution modeling continue to multiply without guidance on how they can be employed together, resulting in high fidelity of researchers to one or several packages. Here, we assess the wide variety of software for species distribution models (SDMs) and highlight how packages can work together to diversify and expand analyses in each step of a modeling workflow. We also introduce the new R package ‘sdmverse' to catalog metadata for packages, cluster them based on their methodological functions, and visualize their relationships. To demonstrate how pluralism of software use helps improve SDM workflows, we provide three extensive and fully documented analyses that utilize tools for modeling and visualization from multiple packages, then score these tutorials according to recent methodological standards. We end by identifying gaps in the capabilities of current tools and highlighting outstanding challenges in the development of software for SDMs. |
| publishDate |
2024 |
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2024-11 |
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info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion http://purl.org/coar/resource_type/c_6501 info:ar-repo/semantics/articulo |
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article |
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publishedVersion |
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http://hdl.handle.net/11336/263723 Kass, Jamie M.; Smith, Adam B.; Warren, Dan L.; Vignali, Sergio; Schmitt, Sylvain; et al.; Achieving higher standards in species distribution modeling by leveraging the diversity of available software; Wiley Blackwell Publishing, Inc; Ecography; 2025; 2; 11-2024; 1-14 0906-7590 CONICET Digital CONICET |
| url |
http://hdl.handle.net/11336/263723 |
| identifier_str_mv |
Kass, Jamie M.; Smith, Adam B.; Warren, Dan L.; Vignali, Sergio; Schmitt, Sylvain; et al.; Achieving higher standards in species distribution modeling by leveraging the diversity of available software; Wiley Blackwell Publishing, Inc; Ecography; 2025; 2; 11-2024; 1-14 0906-7590 CONICET Digital CONICET |
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eng |
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eng |
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Wiley Blackwell Publishing, Inc |
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Wiley Blackwell Publishing, Inc |
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Consejo Nacional de Investigaciones Científicas y Técnicas |
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dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar |
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