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Biology subjects

Elith, J.

Publications and source records attributed to Elith, J..

3 recordsLinked to original sources

A novel method accounting for predictor uncertainty and model transferability of invasive species distribution models

Predicting novel ranges of non-native species is a critical component to understanding the biosecurity threat posed by pests and diseases on economic, environmental and social assets. Species distribution models (SDMs) are often employed to predict the potential ranges of exotic pests and diseases in novel environments and geographic space. To date, researchers have focused on model complexity, data available for model fitting, the size of the geographic area to be considered and how the choice of model impacts results. These investigations are coupled with considerable examination of how model evaluation methods and test scores are influenced by these choices. An area that remains under-discussed is how to account for uncertainty in predictor selection while also selecting variables that increase a models ability to predict to novel environments (model transferability). Here we propose a novel method to finesse this problem by using multiple simple (bivariate) models to search for the candidate sets of predictor variables that are likely to produce transferable models. Once identified, each set is then used to construct 2-dimensional niche envelopes of pest presence/absence. This process ultimately results in a number of possible models that can be used to predict pest potential distributions, however, rather than relying on a single model, we ensemble these models in an attempt to account for predictor uncertainty. We apply this method to both virtual species and real species data, and find that it generally performs well against conventional approaches for statistically fitting numerous variables in a single model. While our methods only consider simple ecological relationships of species to environmental predictors, they allow for increased model transferability because they reduce the likelihood of over-fitting and collinearity issues. Simple models are also likely to be more conservative (over-predict potential distributions) relative to complex models containing many covariates - making them more appropriate for risk-averse applications such as biosecurity. The approach we have explored transforms a model selection problem, for which there is no true correct answer amongst the typically distal covariates on offer, to one of model uncertainty. We argue that increased model transferability at the expense of model interpretation is perhaps more important for effective rapid predictions and management of non-native species and biological invasions.

ecology↗

Modelling species presence-only data with random forests

O_LIThe Random Forest (RF) algorithm is an ensemble of classification or regression trees, and is a widely used and high-performing machine learning technique. It is increasingly used for species distribution modelling (SDM). Many researchers use implementations of RF in the R programming language with default parameters to analyse species presence-only data together with background samples. However, there is good evidence that RF with default parameters does not perform well with such species "presence-background" data. This is often attributed to the typical disparity between the number of presence and background samples also known as class imbalance, and several solutions have been proposed. C_LIO_LIHere, we first set the context: the background sample should be large enough to represent all environments in the region. We then aim to understand the drivers of poor performance of RF with presence-background data, and explain, test and evaluate suggested solutions. Using simulated and real species data, we compare performance of default RF with other weighting and sampling approaches. C_LIO_LIWe show that class overlap is an important driver of poor performance, alongside class imbalance. The results demonstrate clear evidence of improvement in the performance of RFs when class imbalance is explicitly managed by sampling methods or when the overfitting commonly associated with overlapping classes is avoided by forcing shallow trees. C_LIO_LIPresence-background data is a particular version of class imbalance in which class overlap is highly likely and extreme imbalance exists. Without compromising the environmental representativeness of the sampled background, we show several approaches to fitting RF that ameliorate the effects of imbalance and overlap, and allow excellent predictive performance. Understanding the problems of RF in presence-background data allows new insights into how best to fit models, and should guide future efforts to best deal with such data. C_LI

ecology↗

blockCV: an R package for generating spatially or environmentally separated folds for k-fold cross-validation of species distribution models

O_LIWhen applied to structured data, conventional random cross-validation techniques can lead to underestimation of prediction error, and may result in inappropriate model selection.\nC_LIO_LIWe present the R package blockCV, a new toolbox for cross-validation of species distribution modelling.\nC_LIO_LIThe package can generate spatially or environmentally separated folds. It includes tools to measure spatial autocorrelation ranges in candidate covariates, providing the user with insights into the spatial structure in these data. It also offers interactive graphical capabilities for creating spatial blocks and exploring data folds.\nC_LIO_LIPackage blockCV enables modellers to more easily implement a range of evaluation approaches. It will help the modelling community learn more about the impacts of evaluation approaches on our understanding of predictive performance of species distribution models.\nC_LI

ecology↗