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
CONICET Digital (CONICET)
Institución
Consejo Nacional de Investigaciones Científicas y Técnicas
OAI Identificador
oai:ri.conicet.gov.ar:11336/263723

id CONICETDig_dcba876b555218c965cf1a64ca62bf6d
oai_identifier_str oai:ri.conicet.gov.ar:11336/263723
network_acronym_str CONICETDig
repository_id_str 3498
network_name_str CONICET Digital (CONICET)
spelling 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 Técnicas2025-09-29T10:31:59Zoai: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:34982025-09-29 10:31:59.516CONICET 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
dc.date.none.fl_str_mv 2024-11
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv 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
dc.language.none.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv info:eu-repo/semantics/altIdentifier/url/https://nsojournals.onlinelibrary.wiley.com/doi/10.1111/ecog.07346
info:eu-repo/semantics/altIdentifier/doi/10.1111/ecog.07346
dc.rights.none.fl_str_mv info:eu-repo/semantics/openAccess
https://creativecommons.org/licenses/by/2.5/ar/
eu_rights_str_mv openAccess
rights_invalid_str_mv https://creativecommons.org/licenses/by/2.5/ar/
dc.format.none.fl_str_mv application/pdf
application/pdf
dc.publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
publisher.none.fl_str_mv Wiley Blackwell Publishing, Inc
dc.source.none.fl_str_mv reponame:CONICET Digital (CONICET)
instname:Consejo Nacional de Investigaciones Científicas y Técnicas
reponame_str CONICET Digital (CONICET)
collection CONICET Digital (CONICET)
instname_str Consejo Nacional de Investigaciones Científicas y Técnicas
repository.name.fl_str_mv CONICET Digital (CONICET) - Consejo Nacional de Investigaciones Científicas y Técnicas
repository.mail.fl_str_mv dasensio@conicet.gov.ar; lcarlino@conicet.gov.ar
_version_ 1844614332035366912
score 13.070432