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1. Combining Regional Habitat Selection Models for Large-Scale Prediction: Circumpolar Habitat Selection of Southern Ocean Humpback Whales

   https://doi.org/10.3390/rs13112074  

   Reisinger, Ryan R.; Friedlaender, Ari S.; Zerbini, Alexandre N.; Palacios, Daniel M.; Andrews-Goff, Virginia; Dalla Rosa, Luciano; Double, Mike; Findlay, Ken; Garrigue, Claire; How, Jason; et al (June 2021, Remote Sensing)

   Machine learning algorithms are often used to model and predict animal habitat selection—the relationships between animal occurrences and habitat characteristics. For broadly distributed species, habitat selection often varies among populations and regions; thus, it would seem preferable to fit region- or population-specific models of habitat selection for more accurate inference and prediction, rather than fitting large-scale models using pooled data. However, where the aim is to make range-wide predictions, including areas for which there are no existing data or models of habitat selection, how can regional models best be combined? We propose that ensemble approaches commonly used to combine different algorithms for a single region can be reframed, treating regional habitat selection models as the candidate models. By doing so, we can incorporate regional variation when fitting predictive models of animal habitat selection across large ranges. We test this approach using satellite telemetry data from 168 humpback whales across five geographic regions in the Southern Ocean. Using random forests, we fitted a large-scale model relating humpback whale locations, versus background locations, to 10 environmental covariates, and made a circumpolar prediction of humpback whale habitat selection. We also fitted five regional models, the predictions of which we used as input features for four ensemble approaches: an unweighted ensemble, an ensemble weighted by environmental similarity in each cell, stacked generalization, and a hybrid approach wherein the environmental covariates and regional predictions were used as input features in a new model. We tested the predictive performance of these approaches on an independent validation dataset of humpback whale sightings and whaling catches. These multiregional ensemble approaches resulted in models with higher predictive performance than the circumpolar naive model. These approaches can be used to incorporate regional variation in animal habitat selection when fitting range-wide predictive models using machine learning algorithms. This can yield more accurate predictions across regions or populations of animals that may show variation in habitat selection. 

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2. Probabilistic prediction of algal blooms from basic water quality parameters by Bayesian scale-mixture of skew-normal model

   https://doi.org/10.1088/1748-9326/acaf11  

   Liu, Muyuan; Hu, Jing; Huang, Yuzhou; He, Junyu; Effiong, Kokoette; Tang, Tao; Huang, Shitao; Perianen, Yuvna Devi; Wang, Feier; Li, Ming; et al (January 2023, Environmental Research Letters)

   Abstract The timeliness of monitoring is essential to algal bloom management. However, acquiring algal bio-indicators can be time-consuming and laborious, and bloom biomass data often contain a large proportion of extreme values limiting the predictive models. Therefore, to predict algal blooms from readily water quality parameters (i.e. dissolved oxygen, pH, etc), and to provide a novel solution to the modeling challenges raised by the extremely distributed biomass data, a Bayesian scale-mixture of skew-normal (SMSN) model was proposed. In this study, our SMSN model accurately predicted over-dispersed biomass variations with skewed distributions in both rivers and lakes (in-sample and out-of-sample predictionR²ranged from 0.533 to 0.706 and 0.412 to 0.742, respectively). Moreover, we successfully achieve a probabilistic assessment of algal blooms with the Bayesian framework (accuracy >0.77 and macro-F₁score >0.72), which robustly decreased the classic point-prediction-based inaccuracy by up to 34%. This work presented a promising Bayesian SMSN modeling technique, allowing for real-time prediction of algal biomass variations andin-situprobabilistic assessment of algal bloom. 

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3. Transformed‐Linear Models for Time Series Extremes

   https://doi.org/10.1111/jtsa.12732  

   Mhatre, Nehali; Cooley, Daniel (February 2024, Journal of Time Series Analysis)

   To capture the dependence in the upper tail of a time series, we develop non‐negative regularly varying time series models that are constructed similarly to classical non‐extreme ARMA models. Rather than fully characterizing tail dependence of the time series, we define the concept of weak tail stationarity which allows us to describe a regularly varying time series via a measure of pairwise extremal dependencies, the tail pairwise dependence function (TPDF). We state consistency requirements among the finite‐dimensional collections of the elements of a regularly varying time series and show that the TPDF's value does not depend on the dimension of the random vector being considered. So that our models take non‐negative values, we use transformed‐linear operations. We show existence and stationarity of these models, and develop their properties such as the model TPDFs. We fit models to hourly windspeed and daily fire weather index data, and we find that the fitted transformed‐linear models produce better estimates of upper tail quantities than a traditional ARMA model, classical linear regularly varying models, a max‐ARMA model, and a Markov model. 

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4. A Value‐Based Model Selection Approach for Environmental Random Variables

   https://doi.org/10.1029/2018WR023000  

   Müller, M. F.; Thompson, S. E. (January 2019, Water Resources Research)

   Abstract Environmental decisions with substantial social and environmental implications are regularly informed by model predictions, incurring inevitable uncertainty. The selection of a set of model predictions to inform a decision is usually based on model performance, measured by goodness‐of‐fit metrics. Yet goodness‐of‐fit metrics have a questionable relationship to a model's value to end users, particularly when validation data are themselves uncertain. For example, decisions based on flow frequency models are not necessarily improved by adopting models with the best overall goodness of fit. We propose an alternative model evaluation approach based on the conditional value of sample information, first defined in 1961, which has found extensive use in sampling design optimization but which has not previously been used for model evaluation. The metric uses observations from a validation set to estimate the expected monetary costs associated with model prediction uncertainties. A model is only considered superior to alternatives if (i) its predictions reduce these costs and (ii) sufficient validation data are available to distinguish its performance from alternative models. By describing prediction uncertainties in monetary terms, the metric facilitates the communication of prediction uncertainty by end users, supporting the inclusion of uncertainty analysis in decision making. 

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5. spOccupancy: An R package for single‐species, multi‐species, and integrated spatial occupancy models

   https://doi.org/10.1111/2041-210X.13897  

   Doser, Jeffrey W.; Finley, Andrew O.; Kéry, Marc; Zipkin, Elise F. (May 2022, Methods in Ecology and Evolution)

   Abstract Occupancy modelling is a common approach to assess species distribution patterns, while explicitly accounting for false absences in detection–nondetection data. Numerous extensions of the basic single‐species occupancy model exist to model multiple species, spatial autocorrelation and to integrate multiple data types. However, development of specialized and computationally efficient software to incorporate such extensions, especially for large datasets, is scarce or absent.We introduce thespOccupancy Rpackage designed to fit single‐species and multi‐species spatially explicit occupancy models. We fit all models within a Bayesian framework using Pólya‐Gamma data augmentation, which results in fast and efficient inference.spOccupancyprovides functionality for data integration of multiple single‐species detection–nondetection datasets via a joint likelihood framework. The package leverages Nearest Neighbour Gaussian Processes to account for spatial autocorrelation, which enables spatially explicit occupancy modelling for potentially massive datasets (e.g. 1,000s–100,000s of sites).spOccupancyprovides user‐friendly functions for data simulation, model fitting, model validation (by posterior predictive checks), model comparison (using information criteria and k‐fold cross‐validation) and out‐of‐sample prediction. We illustrate the package's functionality via a vignette, simulated data analysis and two bird case studies.ThespOccupancypackage provides a user‐friendly platform to fit a variety of single and multi‐species occupancy models, making it straightforward to address detection biases and spatial autocorrelation in species distribution models even for large datasets. 

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