embarcadero: Species distribution modelling with Bayesian additive regression trees in r

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Authors Colin J. Carlson
Journal/Conference Name Methods in Ecology and Evolution
Paper Category , ,
Paper Abstract embarcadero is an r package of convenience tools for species distribution modelling (SDM) with Bayesian additive regression trees (BART), a powerful machine learning approach that has been rarely applied to ecological problems. Like other classification and regression tree methods, BART estimates the probability of a binary outcome based on a set of decision trees. Unlike other methods, BART iteratively generates sets of trees based on a set of priors about tree structure and nodes, and builds a posterior distribution of estimated classification probabilities. So far, BARTs have yet to be applied to SDM. embarcadero is a workflow wrapper for BART species distribution models, and includes functionality for easy spartial prediction, an automated variable selection procedure, several types of partial dependence visualization and other tools for ecological application. The embarcadero package is an open source and available on Github. To show how embarcadero can be used by ecologists, I illustrate a BART workflow for a virtual species distribution model. The supplement includes a more advanced vignette showing how BART can be used for mapping disease transmission risk, using the example of Crimean–Congo haemorrhagic fever in Africa.
Date of publication 2020
Code Programming Language R
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