ntbox: An r package with graphical user interface for modelling and evaluating multidimensional ecological niches
Por:
Osorio-Olvera, Luis, Lira-Noriega, Andres, Soberon, Jorge, Peterson, Andrew Townsend, Falconi, Manuel, Contreras-Diaz, Rusby G., Martinez-Meyer, Enrique, Barve, Vijay, Barve, Narayani
Publicada:
1 oct 2020
Ahead of Print:
1 ene 2020
Resumen:
Biodiversity studies rely heavily on estimates of species' distributions often obtained through ecological niche modelling. Numerous software packages exist that allow users to model ecological niches using machine learning and statistical methods. However, no existing package with a graphical user interface allows users to perform model calibration and selection based on convex forms such as ellipsoids, which may match fundamental ecological niche shapes better, incorporating tools for exploring, modelling, and evaluating niches and distributions that are intuitive for both novice and proficient users. Here we describe an r package, NicheToolBox (ntbox), that allows users to conduct all processing steps involved in ecological niche modelling: downloading and curating occurrence data, obtaining and transforming environmental data layers, selecting environmental variables, exploring relationships between geographic and environmental spaces, calibrating and selecting ellipsoid models, evaluating models using binomial and partial ROC tests, assessing extrapolation risk, and performing geographic information system operations via a graphical user interface. A summary of the entire workflow is produced for use as a stand-alone algorithm or as part of research reports. The method is explained in detail and tested via modelling the threatened feline species Leopardus wiedii. Georeferenced occurrence data for this species are queried to display both point occurrences and the IUCN extent of occurrence polygon (IUCN, 2007). This information is used to illustrate tools available for accessing, processing and exploring biodiversity data (e.g. number of occurrences and chronology of collecting) and transforming environmental data (e.g. a summary PCA for 19 bioclimatic layers). Visualizations of three-dimensional ecological niches modelled as minimum volume ellipsoids are developed with ancillary statistics. This niche model is then projected to geographic space, to represent a corresponding potential suitability map. Using ntbox allows a fast and straightforward means by which to retrieve and manipulate occurrence and environmental data, which can then be implemented in model calibration, projection and evaluation for assessing distributions of species in geographic space and their corresponding environmental combinations. © 2020 British Ecological Society
Filiaciones:
Osorio-Olvera, Luis:
Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
Biodiversity Institute, University of Kansas, Lawrence, KS, United States
Univ Nacl Autonoma Mexico, Fac Ciencias, Dept Matemat, Ciudad de Mexico, Mexico
Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA
Lira-Noriega, Andres:
CONACyT Research Fellow, Red de Estudios Moleculares Avanzados-Instituto de Ecología, Veracruz, Mexico
Inst Ecol, Red Estudios Mol Avanzados, Xalapa, Veracruz, Mexico
Soberon, Jorge:
Biodiversity Institute, University of Kansas, Lawrence, KS, United States
Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA
Peterson, Andrew Townsend:
Biodiversity Institute, University of Kansas, Lawrence, KS, United States
Univ Kansas, Biodivers Inst, Lawrence, KS 66045 USA
Falconi, Manuel:
Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
Univ Nacl Autonoma Mexico, Fac Ciencias, Dept Matemat, Ciudad de Mexico, Mexico
Contreras-Diaz, Rusby G.:
Departamento de Matemáticas, Facultad de Ciencias, Universidad Nacional Autónoma de Mexico, Ciudad de Mexico, Mexico
Posgrado en Ciencias Biológicas, Unidad de Posgrado, Edificio A, Circuito de Posgrados, Ciudad Universitaria, Ciudad de México, Mexico
Univ Nacl Autonoma Mexico, Fac Ciencias, Dept Matemat, Ciudad de Mexico, Mexico
Unidad Posgrad, Posgrad Ciencias Biol, Edificio A,Ciudad Univ, Ciudad De Mexico, Mexico
Martinez-Meyer, Enrique:
Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
Centro del Cambio Global y la Sustentabilidad en el Sureste A.C., Villahermosa, Mexico
Univ Nacl Autonoma Mexico, Inst Biol, Mexico City, DF, Mexico
Ctr Cambio Global & Sustentabilidad Sureste AC, Villahermosa, Tabasco, Mexico
Barve, Vijay:
Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA
Barve, Narayani:
Florida Museum of Natural History, University of Florida, Gainesville, FL, United States
Univ Florida, Florida Museum Nat Hist, Gainesville, FL 32611 USA
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