arXiv subjects

Andrew O. Finley

Publications and source records attributed to Andrew O. Finley.

At least 37 records · Page 2Linked to original sources

arXiv2023

Quantifying and correcting geolocation error in spaceborne LiDAR forest canopy observations using high spatial accuracy ALS: A Bayesian model approach

Geolocation error in spaceborne sampling light detection and ranging (LiDAR) measurements of forest structure can compromise forest attribute estimates and degrade integration with georeferenced field measurements or other remotely sensed data. Data integration is especially problematic when geolocation error is not well quantified. We propose a general model that uses airborne laser scanning (ALS) data to quantify and correct geolocation error in spaceborne sampling LiDAR. To illustrate the model, LiDAR data from NASA Goddard's LiDAR Hyperspectral & Thermal Imager (G-LiHT) was used with a subset of LiDAR data from NASA's Global Ecosystem Dynamics Investigation (GEDI). The model accommodates multiple canopy height metrics derived from a simulated GEDI footprint kernel using spatially coincident G-LiHT, and incorporates both additive and multiplicative mapping between the canopy height metrics generated from both datasets. A Bayesian implementation provides probabilistic uncertainty quantification in both parameter and geolocation error estimates. Results show a systematic geolocation error of 9.62 m in the southwest direction. In addition, estimated geolocation errors within GEDI footprints were highly variable, with results showing a ~0.45 probability the true footprint center is within 20 m. Estimating and correcting geolocation error via the model outlined here can help inform subsequent efforts to integrate spaceborne LiDAR data, like GEDI, with other georeferenced data.

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arXiv2023

Modeling complex species-environment relationships through spatially-varying coefficient occupancy models

Occupancy models are frequently used by ecologists to quantify spatial variation in species distributions while accounting for observational biases in the collection of detection-nondetection data. However, the common assumption that a single set of regression coefficients can adequately explain species-environment relationships is often unrealistic, especially across large spatial domains. Here we develop single-species (i.e., univariate) and multi-species (i.e., multivariate) spatially-varying coefficient (SVC) occupancy models to account for spatially-varying species-environment relationships. We employ Nearest Neighbor Gaussian Processes and Polya-Gamma data augmentation in a hierarchical Bayesian framework to yield computationally efficient Gibbs samplers, which we implement in the spOccupancy R package. For multi-species models, we use spatial factor dimension reduction to efficiently model datasets with large numbers of species (e.g., > 10). The hierarchical Bayesian framework readily enables generation of posterior predictive maps of the SVCs, with fully propagated uncertainty. We apply our SVC models to quantify spatial variability in the relationships between maximum breeding season temperature and occurrence probability of 21 grassland bird species across the U.S. Jointly modeling species generally outperformed single-species models, which all revealed substantial spatial variability in species occurrence relationships with maximum temperatures. Our models are particularly relevant for quantifying species-environment relationships using detection-nondetection data from large-scale monitoring programs, which are becoming increasingly prevalent for answering macroscale ecological questions regarding wildlife responses to global change.

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arXiv2023

Guidelines for the use of spatially-varying coefficients in species distribution models

Species distribution models (SDMs) are increasingly applied across macroscales. Such models typically assume that a single set of regression coefficients can adequately describe species-environment relationships and/or population trends. However, such relationships often show nonlinear and/or spatially-varying patterns that arise from complex interactions with abiotic and biotic processes that operate at different scales. Spatially-varying coefficient (SVC) models can readily account for variability in the effects of environmental covariates. Yet, their use in ecology is relatively scarce due to gaps in understanding the inferential benefits that SVC models can provide compared to simpler frameworks. Here we demonstrate the inferential benefits of SVC SDMs, with a particular focus on how this approach can be used to generate and test ecological hypotheses regarding the drivers of spatial variability in population trends and species-environment relationships. We illustrate the inferential benefits of SVC SDMs with simulations and two case studies: one that assesses spatially-varying trends of 51 forest bird species in the eastern US over two decades and a second that evaluates spatial variability in the effects of five decades of land cover change on Grasshopper Sparrow occurrence across the continental US. We found strong support for SVC SDMs compared to simpler alternatives in both empirical case studies. These applications display the utility of SVC SDMs to help reveal the environmental factors that drive species distributions across both local and broad scales. We conclude by discussing the potential applications of SVC SDMs in ecology and conservation.

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arXiv2022

Joint species distribution models with imperfect detection for high-dimensional spatial data

Determining spatial distributions of species and communities are key objectives of ecology and conservation. Joint species distribution models use multi-species detection-nondetection data to estimate species and community distributions. The analysis of such data is complicated by residual correlations between species, imperfect detection, and spatial autocorrelation. While methods exist to accommodate each of these complexities, there are few examples in the literature that address and explore all three complexities simultaneously. Here we developed a spatial factor multi-species occupancy model to explicitly account for species correlations, imperfect detection, and spatial autocorrelation. The proposed model uses a spatial factor dimension reduction approach and Nearest Neighbor Gaussian Processes to ensure computational efficiency for data sets with both a large number of species (e.g., > 100) and spatial locations (e.g., 100,000). We compare the proposed model performance to five candidate models, each addressing a subset of the three complexities. We implemented the proposed and competing models in the spOccupancy software, designed to facilitate application via an accessible, well-documented, and open-source R package. Using simulations, we found ignoring the three complexities when present leads to inferior model predictive performance. Using a case study on 98 bird species across the continental US, the spatial factor multi-species occupancy model had the highest predictive performance among the candidate models. Our proposed framework, together with its implementation in spOccupancy, serves as a user-friendly tool to understand spatial variation in species distributions and biodiversity metrics while addressing common complexities in multi-species detection-nondetection data.

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arXiv2022

spOccupancy: An R package for single-species, multi-species, and integrated spatial occupancy models

Occupancy modeling is a common approach to assess spatial and temporal species distribution patterns, while explicitly accounting for measurement errors common in detection-nondetection data. Numerous extensions of the basic single species occupancy model exist to address dynamics, multiple species or states, interactions, false positive errors, autocorrelation, and to integrate multiple data sources. However, development of specialized and computationally efficient software to fit spatial models to large data sets is scarce or absent. We introduce the spOccupancy R package designed to fit single-species, multi-species, and integrated spatially-explicit occupancy models. Using a Bayesian framework, we leverage Pólya-Gamma data augmentation and Nearest Neighbor Gaussian Processes to ensure models are computationally efficient for potentially massive data sets. spOccupancy provides 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, in which we estimate occurrence of the Black-throated Green Warbler (Setophaga virens) across the eastern USA and species richness of a foliage-gleaning bird community in the Hubbard Brook Experimental Forest in New Hampshire, USA. The spOccupancy package provides a user-friendly approach 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 data sets.

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arXiv2022

Simplifying small area estimation with rFIA: a demonstration of tools and techniques

The United States (US) Forest Service Forest Inventory and Analysis (FIA) program operates the national forest inventory of the US. Traditionally, the FIA program has relied on sample-based approaches -- permanent plot networks and associated design-based estimators -- to estimate forest variables across large geographic areas and long periods of time. These approaches generally offer unbiased inference on large domains but fail to provide reliable estimates for small domains due to low sample sizes. Rising demand for small domain estimates will thus require the FIA program to adopt non-traditional estimation approaches that are capable of delivering defensible estimates of forest variables at increased spatial and temporal resolution, without the expense of collecting additional field data. In light of this challenge, the development of small area estimation (SAE) methods for FIA data has become an active and highly productive area of research. Yet, SAE methods remain difficult to apply to FIA data, due in part to the complex data structures and inventory design used by the FIA program. Thus, we argue that a new suite of estimation tools (i.e., software) will be required to accommodate shifts in demand for inference on large geographic areas and long time periods to inference on small spatial and/or temporal domains. Herein, we present rFIA, an open-source R package designed to increase the accessibility of FIA data, as one such tool. Specifically, we present two case studies chosen to demonstrate rFIA's potential to simplify the application of a broad suite of SAE methods to FIA data: (1) estimation of contemporary county-level forest carbon stocks across the conterminous US using a spatial Fay-Herriot model; and (2) temporally-explicit estimation of multi-decadal trends in merchantable wood volume in Washington County, Maine using a Bayesian mixed-effects model.

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arXiv2021

Estimating timber volume loss due to storm damage in Carinthia, Austria, using ALS/TLS and spatial regression models

A spatial regression model framework is presented to predict growing stock volume loss due to storm Adrian which caused heavy forest damage in the upper Gail valley in Carinthia, Austria, in October 2018. Model parameters were estimated using growing stock volume measured with a terrestrial laser scanner on 62 sample plots distributed across five sub-regions. Predictor variables were derived from high resolution vegetation height measurements collected during an airborne laser scanning campaign. Non-spatial and spatial candidate models were proposed and assessed based on fit to observed data and out-of-sample prediction. Spatial Gaussian processes associated model intercepts and regression coefficients were used to capture spatial dependence. Results show a spatially-varying coefficient model, which allowed the intercept and regression coefficients to vary spatially, yielded the best fit and prediction. Two approaches were considered for prediction over blowdown areas: 1) an areal approach that viewed each blowdown as a single prediction unit indexed by its centroid; and 2) a block approach where each blowdown was partitioned into smaller prediction units to better align with sample plots' spatial support. Joint prediction was used to acknowledge spatial dependence among block units. Results demonstrated the block approach is preferable as it mitigated change-of-support issues encountered in the areal approach. Despite the small sample size, predictions for 55% of the total 564 blowdown areas, accounting for 93% of the total loss, had a coefficient of variation less than 25%. Key advantages of the proposed regression framework are the ability to quantify uncertainty in spatial covariance parameters, propagate parameter uncertainty through to prediction, and provide statistically valid prediction point and interval estimates for individual blowdowns and collections of blowdowns.

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arXiv2021

Trends in bird abundance differ among protected forests but not bird guilds

Improved monitoring and associated inferential tools to efficiently identify declining bird populations, particularly of rare or sparsely distributed species, is key to informed conservation and management across large spatio-temporal regions. We assess abundance trends for 106 bird species in a network of eight national park forests located within the northeast USA from 2006-2019 using a novel hierarchical model. We develop a multi-species, multi-region removal sampling model that shares information across species and parks to enable inference on rare species and sparsely sampled parks and to evaluate the effects of local forest structure. Trends in bird abundance over time varied widely across parks, but species showed similar trends within parks. Three parks (Acadia, Marsh-Billings-Rockefeller, and Morristown) decreased in bird abundance across all species, while three parks (Saratoga, Roosevelt-Vanderbilt, and Weir-Farm) increased in abundance. Bird abundance peaked at medium levels of basal area and high levels of percent forest and forest regeneration, with percent forest having the largest effect. Variation in these effects across parks could be a result of differences in forest structural stage and diversity. Our novel hierarchical model enables estimates of abundance at the network, park, guild, and species levels. We found large variation in abundance trends across parks but not across bird guilds, suggesting that local forest condition may have a broad and consistent effect on the entire bird community within a given park. Management should target the three parks with overall decreasing trends in bird abundance to further identify what specific factors are driving observed declines across the bird community. Understanding how bird communities respond to local forest structure and other stressors is crucial for informed and lasting management.

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arXiv2021

Integrating automated acoustic vocalization data and point count surveys for estimation of bird abundance

Monitoring wildlife abundance across space and time is an essential task to study their population dynamics and inform effective management. Acoustic recording units are a promising technology for efficiently monitoring bird populations and communities. We present an integrated modeling framework that combines high-quality but temporally sparse bird point count survey data with acoustic recordings. Using simulations, we compare the accuracy and precision of abundance estimates using differing amounts of acoustic vocalizations obtained from a clustering algorithm, point count data, and a subset of manually validated acoustic vocalizations. We also use our modeling framework in a case study to estimate abundance of the Eastern Wood-Pewee (Contopus virens) in Vermont, U.S.A. The simulation study reveals that combining acoustic and point count data via an integrated model improves accuracy and precision of abundance estimates compared with models informed by either acoustic or point count data alone. Combining acoustic data with only a small number of point count surveys yields estimates of abundance without the need for validating any of the identified vocalizations from the acoustic data. Within our case study, the integrated models provided moderate support for a decline of the Eastern Wood-Pewee in this region. Our integrated modeling approach combines dense acoustic data with few point count surveys to deliver reliable estimates of species abundance without the need for manual identification of acoustic vocalizations or a prohibitively expensive large number of repeated point count surveys. Our proposed approach offers an efficient monitoring alternative for large spatio-temporal regions when point count data are difficult to obtain or when monitoring is focused on rare species with low detection probability.

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arXiv2021

spNNGP R package for Nearest Neighbor Gaussian Process models

This paper describes and illustrates functionality of the spNNGP R package. The package provides a suite of spatial regression models for Gaussian and non-Gaussian point-referenced outcomes that are spatially indexed. The package implements several Markov chain Monte Carlo (MCMC) and MCMC-free Nearest Neighbor Gaussian Process (NNGP) models for inference about large spatial data. Non-Gaussian outcomes are modeled using a NNGP Polya-Gamma latent variable. OpenMP parallelization options are provided to take advantage of multiprocessor systems. Package features are illustrated using simulated and real data sets.

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arXiv2020

High-dimensional Multivariate Geostatistics: A Bayesian Matrix-Normal Approach

Joint modeling of spatially-oriented dependent variables is commonplace in the environmental sciences, where scientists seek to estimate the relationships among a set of environmental outcomes accounting for dependence among these outcomes and the spatial dependence for each outcome. Such modeling is now sought for massive data sets with variables measured at a very large number of locations. Bayesian inference, while attractive for accommodating uncertainties through hierarchical structures, can become computationally onerous for modeling massive spatial data sets because of its reliance on iterative estimation algorithms. This manuscript develops a conjugate Bayesian framework for analyzing multivariate spatial data using analytically tractable posterior distributions that obviate iterative algorithms. We discuss differences between modeling the multivariate response itself as a spatial process and that of modeling a latent process in a hierarchical model. We illustrate the computational and inferential benefits of these models using simulation studies and analysis of a Vegetation Index data set with spatially dependent observations numbering in the millions.

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arXiv2020

Highly Scalable Bayesian Geostatistical Modeling via Meshed Gaussian Processes on Partitioned Domains

We introduce a class of scalable Bayesian hierarchical models for the analysis of massive geostatistical datasets. The underlying idea combines ideas on high-dimensional geostatistics by partitioning the spatial domain and modeling the regions in the partition using a sparsity-inducing directed acyclic graph (DAG). We extend the model over the DAG to a well-defined spatial process, which we call the Meshed Gaussian Process (MGP). A major contribution is the development of a MGPs on tessellated domains, accompanied by a Gibbs sampler for the efficient recovery of spatial random effects. In particular, the cubic MGP (Q-MGP) can harness high-performance computing resources by executing all large-scale operations in parallel within the Gibbs sampler, improving mixing and computing time compared to sequential updating schemes. Unlike some existing models for large spatial data, a Q-MGP facilitates massive caching of expensive matrix operations, making it particularly apt in dealing with spatiotemporal remote-sensing data. We compare Q-MGPs with large synthetic and real world data against state-of-the-art methods. We also illustrate using Normalized Difference Vegetation Index (NDVI) data from the Serengeti park region to recover latent multivariate spatiotemporal random effects at millions of locations. The source code is available at https://github.com/mkln/meshgp.

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arXiv2020

A Bayesian hierarchical model to estimate land surface phenology parameters with harmonized Landsat 8 and Sentinel-2 images

We develop a Bayesian Land Surface Phenology (LSP) model and examine its performance using Enhanced Vegetation Index (EVI) observations derived from the Harmonized Landsat Sentinel-2 (HLS) dataset. Building on previous work, we propose a double logistic function that, once couched within a Bayesian model, yields posterior distributions for all LSP parameters. We assess the efficacy of the Normal, Truncated Normal, and Beta likelihoods to deliver robust LSP parameter estimates. Two case studies are presented and used to explore aspects of the proposed model. The first, conducted over forested pixels within a HLS tile, explores choice of likelihood and space-time varying HLS data availability for long-term average LSP parameter point and uncertainty estimation. The second, conducted on a small area of interest within the HLS tile on an annual time-step, further examines the impact of sample size and choice of likelihood on LSP parameter estimates. Results indicate that while the Truncated Normal and Beta likelihoods are theoretically preferable when the vegetation index is bounded, all three likelihoods performed similarly when the number of index observations is sufficiently large and values are not near the index bounds. Both case studies demonstrate how pixel-level LSP parameter posterior distributions can be used to propagate uncertainty through subsequent analysis. As a companion to this article, we provide an open-source \R package \pkg{rsBayes} and supplementary data and code used to reproduce the analysis results. The proposed model specification and software implementation delivers computationally efficient, statistically robust, and inferentially rich LSP parameter posterior distributions at the pixel-level across massive raster time series datasets.

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arXiv2020

rFIA: An R package for estimation of forest attributes with the Forest Inventory and Analysis Database

Forest Inventory and Analysis (FIA) is a US Department of Agriculture Forest Service program that aims to monitor changes in forests across the US. FIA hosts one of the largest ecological datasets in the world, though its complexity limits access for many potential users. rFIA is an R package designed to simplify the estimation of forest attributes using data collected by the FIA Program. Specifically, rFIA improves access to the spatio-temporal estimation capacity of the FIA Database via space-time indexed summaries of forest variables within user-defined population boundaries (e.g., geographic, temporal, biophysical). The package implements multiple design-based estimators, and has been validated against official estimates and sampling errors produced by the FIA Program. We demonstrate the utility of rFIA by assessing changes in abundance and mortality rates of ash (Fraxinus spp.) populations in the Lower Peninsula of Michigan following the establishment of emerald ash borer (Agrilus planipennis).

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arXiv2020

Characterizing functional relationships between anthropogenic and biological sounds: A western New York state soundscape case study

Roads are a widespread feature of landscapes worldwide, and road traffic sound potentially makes nearby habitat unsuitable for acoustically communicating organisms. It is important to understand the influence of roads at the soundscape level to mitigate negative impacts of road sound on individual species as well as subsequent effects on the surrounding landscape. We seek to characterize the relationship between anthropogenic and biological sounds in western New York and assess the extent to which available traffic data explains variability in anthropogenic noise. Recordings were obtained in the spring of 2016 at 18 sites throughout western New York. We used the Welch Power Spectral Density (PSD) at low frequencies (0.5-2 kHz) to represent anthropogenic noise and PSD values at higher frequencies (2-11 kHz) to represent biological sound. Relationships were modeled using a novel two-stage hierarchical Bayesian model utilizing beta regression and basis splines. Model results and map predictions illustrate that anthropogenic noise and biological sound have an inverse relationship, and anthropogenic noise is greatest in close proximity to high traffic volume roads. The predictions have large uncertainty, resulting from the temporal coarseness of public road data used as a proxy for traffic sound. Results suggest that finer temporal resolution traffic sound data, such as crowd-sourced time-indexed traffic data from geographic positioning systems, might better account for observed temporal changes in the soundscape. The use of such data, in combination with the proposed modeling framework, could have important implications for the development of sound management policies.

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arXiv2019

Bayesian spatially varying coefficient models in the spBayes R package

This paper describes and illustrates new functionality for fitting spatially varying coefficients models in the spBayes (version 0.4-2) R package. The new spSVC function uses a computationally efficient Markov chain Monte Carlo algorithm and extends current spBayes functions, that fit only space-varying intercept regression models, to fit independent or multivariate Gaussian process random effects for any set of columns in the regression design matrix. Newly added OpenMP parallelization options for spSVC are discussed and illustrated, as well as helper functions for joint and point-wise prediction and model fit diagnostics. The utility of the proposed models is illustrated using a PM10 analysis over central Europe.

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arXiv2019

ForestFit : An R package for modeling tree diameter distributions

Modeling the diameter distribution of trees in forest stands is a common forestry task that supports key biologically and economically relevant management decisions. The choice of model used to represent the diameter distribution and how to estimate its parameters has received much attention in the forestry literature; however, accessible software that facilitates comprehensive comparison of the myriad modeling approaches is not available. To this end, we developed an R package called ForestFit that simplifies estimation of common probability distributions used to model tree diameter distributions, including the two- and three-parameter Weibull distributions, Johnson's SB distribution, Birnbaum-Saunders distribution, and finite mixture distributions. Frequentist and Bayesian techniques are provided for individual tree diameter data, as well as grouped data. Additional functionality facilitates fitting growth curves to height-diameter data. The package also provides a set of functions for computing probability distributions and simulating random realizations from common finite mixture models.

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arXiv2019

Assessing soundscape disturbance through hierarchical models and acoustic indices: a case study on a shelterwood logged northern Michigan forest

Assessing the effects of anthropogenic disturbances on wildlife is a necessary conservation task. The soundscape is a critical habitat component for acoustically communicating organisms, but the use of the soundscape as a tool for assessing disturbance impacts has been relatively unexplored until recently. Here we present a broad modeling framework for assessing disturbance impacts on soundscapes, which we apply to quantify the influence of a shelterwood logging on soundscapes in northern Michigan. Our modeling approach can be broadly applied to assess anthropogenic disturbance impacts on soundscapes. The approach accommodates inherent differences in control and treatment sites to improve inference about treatment effects, while also accounting for extraneous variables (e.g., rain) that influence acoustic indices. Recordings were obtained at 13 sites before and after a shelterwood logging. Four sites were in the logging region and nine sites served as control recordings outside the logging region. We quantify the soundscapes using common acoustic indices (Normalized Difference Soundscape Index (NDSI), Acoustic Entropy (H), Acoustic Complexity Index (ACI), Acoustic Evenness Index (AEI), Welch Power Spectral Density (PSD)) and build two hierarchical Bayesian models to quantify the changes in the soundscape over the study period. Our analysis reveals no long-lasting effects of the shelterwood logging on the soundscape diversity as measured by the NDSI, but analysis of H, AEI, and PSD suggest changes in the evenness of sounds across the frequency spectrum, indicating a potential shift in the avian species communicating in the soundscapes as a result of the logging. Acoustic recordings, in conjunction with this modeling framework, can deliver cost efficient assessment of disturbance impacts on the landscape and underlying biodiversity as represented through the soundscape.

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