README.md

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ENMeval

R package for automated runs and evaluations of ecological niche models.

ENMeval is an R package that performs automated runs and evaluations of ecological niche models, and currently implements Maxent using the either (now by default) the 'maxnet' algoritm developed by Phillips et al. (2017) using the 'maxnet' R package or [the original java program (https://biodiversityinformatics.amnh.org/open_source/maxent/). ENMeval was made for those who want to "tune" their models to maximize predictive ability and avoid overfitting, or in other words, optimize model complexity to balance goodness-of-fit and predictive ability. The primary function, ENMevaluate, does all the heavy lifting and returns several items including a table of evaluation statistics and, for each setting combination, a model object and a raster layer showing the model prediction across the study extent. There are also options for calculating niche overlap between predictions, running in parallel to speed up computation, and more. For a more detailed description of the package, check out the open-access publication:

Muscarella, R., Galante, P. J., Soley-Guardia, M., Boria, R. A., Kass, J. M., Uriarte, M. and Anderson, R. P. (2014), ENMeval: An R package for conducting spatially independent evaluations and estimating optimal model complexity for Maxent ecological niche models. Methods in Ecology and Evolution, 5: 1198–1205.

Also see the vignette for examples of implementation.

Note that as of version 0.3.0, the default implementation uses the 'maxnet' R package. The output from this differs from that of the original java program and so some features are not compatible (e.g., variable importance, the old html output). Our team has done some fairly extensive testing to ensure this implementation gives the expected results but the maxnet implementation is relatively new (at the time of writing this) and we encourage users to scrutinize their results.



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ENMeval documentation built on Jan. 13, 2021, 8:08 p.m.