ecospat: an R package to support spatial analyses and modeling of species niches and distributions

Ecography - Tập 40 Số 6 - Trang 774-787 - 2017
Valeria Di Cola1, Olivier Broennimann1, Blaise Petitpierre1, Frank T. Breiner2,1, Manuela D’Amen1, Christophe F. Randin3,2,1, Robin Engler4, Antoine Guisan5, Dorothea Pio6,1, Luigi Maiorano1, Loïc Pellissier7,2, Rubén G. Mateo1, Wim Hordijk8,1, Nicolas Salamin9,1
1Université de Lausanne = University of Lausanne
2Swiss Federal Institute for Forest, Snow and Landscape Research WSL
3Centre de Recherches sur les Ecosystèmes d'Altitude
4Swiss Institute of Bioinformatics [Lausanne]
5Unité Mixte de Recherche sur l'Ecosystème Prairial - UMR
6Fauna and Flora International [Cambridge, UK]
7Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
8Konrad Lorenz Institute for Evolution and Cognition Research
9Genopode

Tóm tắt

The aim of the ecospat package is to make available novel tools and methods to support spatial analyses and modeling of species niches and distributions in a coherent workflow. The package is written in the R language (R Development Core Team) and contains several features, unique in their implementation, that are complementary to other existing R packages. Pre‐modeling analyses include species niche quantifications and comparisons between distinct ranges or time periods, measures of phylogenetic diversity, and other data exploration functionalities (e.g. extrapolation detection, ExDet). Core modeling brings together the new approach of ensemble of small models (ESM) and various implementations of the spatially‐explicit modeling of species assemblages (SESAM) framework. Post‐modeling analyses include evaluation of species predictions based on presence‐only data (Boyce index) and of community predictions, phylogenetic diversity and environmentally‐constrained species co‐occurrences analyses. The ecospat package also provides some functions to supplement the ‘biomod2’ package (e.g. data preparation, permutation tests and cross‐validation of model predictive power). With this novel package, we intend to stimulate the use of comprehensive approaches in spatial modelling of species and community distributions.

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Ecography

Tập 40 Số 6

774-787

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