kuenm: an R package for detailed development of ecological niche models using Maxent

Marlon E. Cobos; A. Townsend Peterson; Narayani Barve; Luis Osorio-Olvera

doi:10.7717/peerj.6281

journal article Open Access Feb 06, 2019

kuenm: an R package for detailed development of ecological niche models using Maxent

Marlon E. Cobos A. Townsend Peterson

Narayani Barve

Luis Osorio-Olvera

PeerJ Vol. 7 pp. e6281 · PeerJ

View at Publisher Save 10.7717/peerj.6281

Abstract

BackgroundEcological niche modeling is a set of analytical tools with applications in diverse disciplines, yet creating these models rigorously is now a challenging task. The calibration phase of these models is critical, but despite recent attempts at providing tools for performing this step, adequate detail is still missing. Here, we present the kuenm R package, a new set of tools for performing detailed development of ecological niche models using the platform Maxent in a reproducible way.ResultsThis package takes advantage of the versatility of R and Maxent to enable detailed model calibration and selection, final model creation and evaluation, and extrapolation risk analysis. Best parameters for modeling are selected considering (1) statistical significance, (2) predictive power, and (3) model complexity. For final models, we enable multiple parameter sets and model transfers, making processing simpler. Users can also evaluate extrapolation risk in model transfers via mobility-oriented parity (MOP) metric.DiscussionUse of this package allows robust processes of model calibration, facilitating creation of final models based on model significance, performance, and simplicity. Model transfers to multiple scenarios, also facilitated in this package, significantly reduce time invested in performing these tasks. Finally, efficient assessments of strict-extrapolation risks in model transfers via the MOP and MESS metrics help to prevent overinterpretation in model outcomes.

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References

Details

Published: Feb 06, 2019
Vol/Issue: 7
Pages: e6281
License: View

Authors

M

Marlon E. Cobos

Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America

A

A. Townsend Peterson

Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America

N

Narayani Barve

Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America; Florida Museum of Natural History, University of Florida, Gainesville, FL, United States of America

L

Luis Osorio-Olvera

Biodiversity Institute and Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America; Facultad de Ciencias, Universidad Nacional Autónoma de México, Ciudad de México, México, Mexico; Centro del Cambio Global y la Sustentabilidad A.C., Villahermosa, Tabasco, Mexico

Funding

PAPIIT UNAM Award: IN116018

CONACyT-FORDECyT Award: 273646

Cite This Article

Marlon E. Cobos, A. Townsend Peterson, Narayani Barve, et al. (2019). kuenm: an R package for detailed development of ecological niche models using Maxent. PeerJ, 7, e6281. https://doi.org/10.7717/peerj.6281

kuenm: an R package for detailed development of ecological niche models using Maxent

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