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Andrew O. Finley

Publications and source records attributed to Andrew O. Finley.

50 records · Page 3Linked to original sources

Conjugate Nearest Neighbor Gaussian Process Models for Efficient Statistical Interpolation of Large Spatial Data

A key challenge in spatial statistics is the analysis for massive spatially-referenced data sets. Such analyses often proceed from Gaussian process specifications that can produce rich and robust inference, but involve dense covariance matrices that lack computationally exploitable structures. The matrix computations required for fitting such models involve floating point operations in cubic order of the number of spatial locations and dynamic memory storage in quadratic order. Recent developments in spatial statistics offer a variety of massively scalable approaches. Bayesian inference and hierarchical models, in particular, have gained popularity due to their richness and flexibility in accommodating spatial processes. Our current contribution is to provide computationally efficient exact algorithms for spatial interpolation of massive data sets using scalable spatial processes. We combine low-rank Gaussian processes with efficient sparse approximations. Following recent work by [1], we model the low-rank process using a Gaussian predictive process (GPP) and the residual process as a sparsity-inducing nearest-neighbor Gaussian process (NNGP). A key contribution here is to implement these models using exact conjugate Bayesian modeling to avoid expensive iterative algorithms. Through the simulation studies, we evaluate performance of the proposed approach and the robustness of our models, especially for long range prediction. We implement our approaches for remotely sensed light detection and ranging (LiDAR) data collected over the US Forest Service Tanana Inventory Unit (TIU) in a remote portion of Interior Alaska.

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EcoMem: An R package for quantifying ecological memory

Ecological processes may exhibit memory to past disturbances affecting the resilience of ecosystems to future disturbance. Understanding the role of ecological memory in shaping ecosystem responses to disturbance under global change is a critical step toward developing effective adaptive management strategies to maintain ecosystem function and biodiversity. We developed EcoMem, an R package for quantifying ecological memory functions using common environmental time series data (continuous, count, proportional) applying a Bayesian hierarchical framework. The package estimates memory functions for continuous and binary (e.g., disturbance chronology) variables making no a priori assumption on the form of the functions. EcoMem allows users to quantify ecological memory for a wide range of ecosystem processes and responses. The utility of the package to advance understanding of the memory of ecosystems to environmental drivers is demonstrated using a simulated dataset and a case study assessing the memory of boreal tree growth to insect defoliation.

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Spatial Factor Models for High-Dimensional and Large Spatial Data: An Application in Forest Variable Mapping

Gathering information about forest variables is an expensive and arduous activity. As such, directly collecting the data required to produce high-resolution maps over large spatial domains is infeasible. Next generation collection initiatives of remotely sensed Light Detection and Ranging (LiDAR) data are specifically aimed at producing complete-coverage maps over large spatial domains. Given that LiDAR data and forest characteristics are often strongly correlated, it is possible to make use of the former to model, predict, and map forest variables over regions of interest. This entails dealing with the high-dimensional ($\sim$$10^2$) spatially dependent LiDAR outcomes over a large number of locations (~10^5-10^6). With this in mind, we develop the Spatial Factor Nearest Neighbor Gaussian Process (SF-NNGP) model, and embed it in a two-stage approach that connects the spatial structure found in LiDAR signals with forest variables. We provide a simulation experiment that demonstrates inferential and predictive performance of the SF-NNGP, and use the two-stage modeling strategy to generate complete-coverage maps of forest variables with associated uncertainty over a large region of boreal forests in interior Alaska.

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Remote sensing to reduce the effects of spatial autocorrelation on design-based inference for forest inventory using systematic samples

Systematic sampling is often used to select plot locations for forest inventory estimation. However, it is not possible to derive a design-unbiased variance estimator for a systematic sample using one random start. As a result, many forest inventory analysts resort to applying variance estimators that are design-unbiased following simple random sampling to their systematic samples even though this typically leads to conservative estimates of error. We explore the influence of spatial autocorrelation on variance estimation when systematic sampling is employed using repeated sampling. We generate a sequence of 1000 synthetic populations with increasing spatial autocorrelation and repeatedly sample from each to examine how the performance of estimators change as spatial autocorrelation changes. We also repeatedly sample from a tree census plot in Harvard Forest, Massachusetts and examine the performance of similar estimators. Results indicate that applying variance estimators that are unbiased following simple random sampling to systematic samples from populations exhibiting stronger spatial autocorrelation tend to be more conservative. We also find that incorporating ancillary wall-to-wall covariates, e.g., remote sensing data, using generalized regression estimators can reduce variance over-estimation by explaining some or all of the spatial structure in the population.

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Efficient algorithms for Bayesian Nearest Neighbor Gaussian Processes

We consider alternate formulations of recently proposed hierarchical Nearest Neighbor Gaussian Process (NNGP) models (Datta et al., 2016a) for improved convergence, faster computing time, and more robust and reproducible Bayesian inference. Algorithms are defined that improve CPU memory management and exploit existing high-performance numerical linear algebra libraries. Computational and inferential benefits are assessed for alternate NNGP specifications using simulated datasets and remotely sensed light detection and ranging (LiDAR) data collected over the US Forest Service Tanana Inventory Unit (TIU) in a remote portion of Interior Alaska. The resulting data product is the first statistically robust map of forest canopy for the TIU.

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Geostatistical estimation of forest biomass in interior Alaska combining Landsat-derived tree cover, sampled airborne lidar and field observations

The goal of this research was to develop and examine the performance of a geostatistical coregionalization modeling approach for combining field inventory measurements, strip samples of airborne lidar and Landsat-based remote sensing data products to predict aboveground biomass (AGB) in interior Alaska's Tanana Valley. The proposed modeling strategy facilitates pixel-level mapping of AGB density predictions across the entire spatial domain. Additionally, the coregionalization framework allows for statistically sound estimation of total AGB for arbitrary areal units within the study area---a key advance to support diverse management objectives in interior Alaska. This research focuses on appropriate characterization of prediction uncertainty in the form of posterior predictive coverage intervals and standard deviations. Using the framework detailed here, it is possible to quantify estimation uncertainty for any spatial extent, ranging from pixel-level predictions of AGB density to estimates of AGB stocks for the full domain. The lidar-informed coregionalization models consistently outperformed their counterpart lidar-free models in terms of point-level predictive performance and total AGB precision. Additionally, the inclusion of Landsat-derived forest cover as a covariate further improved estimation precision in regions with lower lidar sampling intensity. Our findings also demonstrate that model-based approaches that do not explicitly account for residual spatial dependence can grossly underestimate uncertainty, resulting in falsely precise estimates of AGB. On the other hand, in a geostatistical setting, residual spatial structure can be modeled within a Bayesian hierarchical framework to obtain statistically defensible assessments of uncertainty for AGB estimates.

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A Model-Based Approach to Wildland Fire Reconstruction Using Sediment Charcoal Records

Lake sediment charcoal records are used in paleoecological analyses to reconstruct fire history including the identification of past wildland fires. One challenge of applying sediment charcoal records to infer fire history is the separation of charcoal associated with local fire occurrence and charcoal originating from regional fire activity. Despite a variety of methods to identify local fires from sediment charcoal records, an integrated statistical framework for fire reconstruction is lacking. We develop a Bayesian point process model to estimate probability of fire associated with charcoal counts from individual-lake sediments and estimate mean fire return intervals. A multivariate extension of the model combines records from multiple lakes to reduce uncertainty in local fire identification and estimate a regional mean fire return interval. The univariate and multivariate models are applied to 13 lakes in the Yukon Flats region of Alaska. Both models resulted in similar mean fire return intervals (100-350 years) with reduced uncertainty under the multivariate model due to improved estimation of regional charcoal deposition. The point process model offers an integrated statistical framework for paleo-fire reconstruction and extends existing methods to infer regional fire history from multiple lake records with uncertainty following directly from posterior distributions.

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Joint hierarchical models for sparsely sampled high-dimensional LiDAR and forest variables

Recent advancements in remote sensing technology, specifically Light Detection and Ranging (LiDAR) sensors, provide the data needed to quantify forest characteristics at a fine spatial resolution over large geographic domains. From an inferential standpoint, there is interest in prediction and interpolation of the often sparsely sampled and spatially misaligned LiDAR signals and forest variables. We propose a fully process-based Bayesian hierarchical model for above ground biomass (AGB) and LiDAR signals. The process-based framework offers richness in inferential capabilities, e.g., inference on the entire underlying processes instead of estimates only at pre-specified points. Key challenges we obviate include misalignment between the AGB observations and LiDAR signals and the high-dimensionality in the model emerging from LiDAR signals in conjunction with the large number of spatial locations. We offer simulation experiments to evaluate our proposed models and also apply them to a challenging dataset comprising LiDAR and spatially coinciding forest inventory variables collected on the Penobscot Experimental Forest (PEF), Maine. Our key substantive contributions include AGB data products with associated measures of uncertainty for the PEF and, more broadly, a methodology that should find use in a variety of current and upcoming forest variable mapping efforts using sparsely sampled remotely sensed high-dimensional data.

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Variable Effects of Climate on Forest Growth in Relation to Climate Extremes, Disturbance, and Forest Stand Dynamics

Changes in the frequency, duration, and severity of climate extremes are forecast to occur under global climate change. The impacts of climate extremes on forest productivity and health are complicated by potential interactions with disturbance events and stand dynamics. The effects of stand dynamics on forest responses to climate and disturbance are particularly important given forest characteristics driven by stand dynamics can be modified through forest management with the goal of increasing forest resistance and resilience to climate change. We develop a hierarchical Bayesian state-space model allowing climate effects on tree growth to vary over time and in relation to climate extremes, disturbance events, and stand dynamics. We apply the model to a dendrochronology dataset comprising measurements from forest stands of varying composition, structure, and development stage in northeastern Minnesota. Results indicate average forest growth was most sensitive to variables describing climatic water deficit. Forest growth responses to water deficit were partitioned into responses driven by climatic threshold exceedances and interactions with forest tent caterpillar defoliation. Forest growth was both resistant and resilient to climate extremes with the majority of forest growth responses occurring after multiple climatic threshold exceedances or insect defoliation events. Forest growth was most sensitive to water deficit during periods of high stem density following major regeneration events when average inter-tree competition was high. Results suggest that forest growth resistance and resilience to interactions between climate extremes and insect defoliation can be increased through management steps such as thinning to reduce competition during early stages of stand development and small-group selection harvests to maintain forest structures characteristic of older, mature stands.

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Non-separable Dynamic Nearest-Neighbor Gaussian Process Models for Large spatio-temporal Data With an Application to Particulate Matter Analysis

Particulate matter (PM) is a class of malicious environmental pollutants known to be detrimental to human health. Regulatory efforts aimed at curbing PM levels in different countries often require high resolution space-time maps that can identify red-flag regions exceeding statutory concentration limits. Continuous spatio-temporal Gaussian Process (GP) models can deliver maps depicting predicted PM levels and quantify predictive uncertainty. However, GP based approaches are usually thwarted by computational challenges posed by large datasets. We construct a novel class of scalable Dynamic Nearest Neighbor Gaussian Process (DNNGP) models that can provide a sparse approximation to any spatio-temporal GP (e.g., with non-separable covariance structures). The DNNGP we develop here can be used as a sparsity-inducing prior for spatio-temporal random effects in any Bayesian hierarchical model to deliver full posterior inference. Storage and memory requirements for a DNNGP model are linear in the size of the dataset thereby delivering massive scalability without sacrificing inferential richness. Extensive numerical studies reveal that the DNNGP provides substantially superior approximations to the underlying process than low rank approximations. Finally, we use the DNNGP to analyze a massive air quality dataset to substantially improve predictions of PM levels across Europe in conjunction with the LOTOS-EUROS chemistry transport models (CTMs).

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Hierarchical Nearest-Neighbor Gaussian Process Models for Large Geostatistical Datasets

Spatial process models for analyzing geostatistical data entail computations that become prohibitive as the number of spatial locations become large. This manuscript develops a class of highly scalable Nearest Neighbor Gaussian Process (NNGP) models to provide fully model-based inference for large geostatistical datasets. We establish that the NNGP is a well-defined spatial process providing legitimate finite-dimensional Gaussian densities with sparse precision matrices. We embed the NNGP as a sparsity-inducing prior within a rich hierarchical modeling framework and outline how computationally efficient Markov chain Monte Carlo (MCMC) algorithms can be executed without storing or decomposing large matrices. The floating point operations (flops) per iteration of this algorithm is linear in the number of spatial locations, thereby rendering substantial scalability. We illustrate the computational and inferential benefits of the NNGP over competing methods using simulation studies and also analyze forest biomass from a massive United States Forest Inventory dataset at a scale that precludes alternative dimension-reducing methods.

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Dynamic spatial regression models for space-varying forest stand tables

Many forest management planning decisions are based on information about the number of trees by species and diameter per unit area. This information is commonly summarized in a stand table, where a stand is defined as a group of forest trees of sufficiently uniform species composition, age, condition, or productivity to be considered a homogeneous unit for planning purposes. Typically information used to construct stand tables is gleaned from observed subsets of the forest selected using a probability-based sampling design. Such sampling campaigns are expensive and hence only a small number of sample units are typically observed. This data paucity means that stand tables can only be estimated for relatively large areal units. Contemporary forest management planning and spatially explicit ecosystem models require stand table input at higher spatial resolution than can be affordably provided using traditional approaches. We propose a dynamic multivariate Poisson spatial regression model that accommodates both spatial correlation between observed diameter distributions and also correlation between tree counts across diameter classes within each location. To improve fit and prediction at unobserved locations, diameter specific intensities can be estimated using auxiliary data such as management history or remotely sensed information. The proposed model is used to analyze a diverse forest inventory dataset collected on the United States Forest Service Penobscot Experimental Forest in Bradley, Maine. Results demonstrate that explicitly modeling the residual spatial structure via a multivariate Gaussian process and incorporating information about forest structure from LiDAR covariates improve model fit and can provide high spatial resolution stand table maps with associated estimates of uncertainty.

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spBayes for large univariate and multivariate point-referenced spatio-temporal data models

In this paper we detail the reformulation and rewrite of core functions in the spBayes R package. These efforts have focused on improving computational efficiency, flexibility, and usability for point-referenced data models. Attention is given to algorithm and computing developments that result in improved sampler convergence rate and efficiency by reducing parameter space; decreased sampler run-time by avoiding expensive matrix computations, and; increased scalability to large datasets by implementing a class of predictive process models that attempt to overcome computational hurdles by representing spatial processes in terms of lower-dimensional realizations. Beyond these general computational improvements for existing model functions, we detail new functions for modeling data indexed in both space and time. These new functions implement a class of dynamic spatio-temporal models for settings where space is viewed as continuous and time is taken as discrete.

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Hierarchical spatial models for predicting tree species assemblages across large domains

Spatially explicit data layers of tree species assemblages, referred to as forest types or forest type groups, are a key component in large-scale assessments of forest sustainability, biodiversity, timber biomass, carbon sinks and forest health monitoring. This paper explores the utility of coupling georeferenced national forest inventory (NFI) data with readily available and spatially complete environmental predictor variables through spatially-varying multinomial logistic regression models to predict forest type groups across large forested landscapes. These models exploit underlying spatial associations within the NFI plot array and the spatially-varying impact of predictor variables to improve the accuracy of forest type group predictions. The richness of these models incurs onerous computational burdens and we discuss dimension reducing spatial processes that retain the richness in modeling. We illustrate using NFI data from Michigan, USA, where we provide a comprehensive analysis of this large study area and demonstrate improved prediction with associated measures of uncertainty.

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