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"spatial statistics"
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Mapping local and global variability in plant trait distributions
Our ability to understand and predict the response of ecosystems to a changing environment depends on quantifying vegetation functional diversity. However, representing this diversity at the global scale is challenging. Typically, in Earth system models, characterization of plant diversity has been limited to grouping related species into plant functional types (PFTs), with all trait variation in a PFT collapsed into a single mean value that is applied globally. Using the largest global plant trait database and state of the art Bayesian modeling, we created fine-grained global maps of plant trait distributions that can be applied to Earth system models. Focusing on a set of plant traits closely coupled to photosynthesis and foliar respiration-specific leaf area (SLA) and dry mass-based concentrations of leaf nitrogen (N-m) and phosphorus (P-m), we characterize how traits vary within and among over 50,000 similar to 50 x 50-km cells across the entire vegetated land surface. We do this in several ways-without defining the PFT of each grid cell and using 4 or 14 PFTs; each model's predictions are evaluated against out-of-sample data. This endeavor advances prior trait mapping by generating global maps that preserve variability across scales by using modern Bayesian spatial statistical modeling in combination with a database over three times larger than that in previous analyses. Our maps reveal that the most diverse grid cells possess trait variability close to the range of global PFT means.
Journal Article
Mapping age- and sex-specific HIV prevalence in adults in sub-Saharan Africa, 2000–2018
Background
Human immunodeficiency virus and acquired immune deficiency syndrome (HIV/AIDS) is still among the leading causes of disease burden and mortality in sub-Saharan Africa (SSA), and the world is not on track to meet targets set for ending the epidemic by the Joint United Nations Programme on HIV/AIDS (UNAIDS) and the United Nations Sustainable Development Goals (SDGs). Precise HIV burden information is critical for effective geographic and epidemiological targeting of prevention and treatment interventions. Age- and sex-specific HIV prevalence estimates are widely available at the national level, and region-wide local estimates were recently published for adults overall. We add further dimensionality to previous analyses by estimating HIV prevalence at local scales, stratified into sex-specific 5-year age groups for adults ages 15–59 years across SSA.
Methods
We analyzed data from 91 seroprevalence surveys and sentinel surveillance among antenatal care clinic (ANC) attendees using model-based geostatistical methods to produce estimates of HIV prevalence across 43 countries in SSA, from years 2000 to 2018, at a 5 × 5-km resolution and presented among second administrative level (typically districts or counties) units.
Results
We found substantial variation in HIV prevalence across localities, ages, and sexes that have been masked in earlier analyses. Within-country variation in prevalence in 2018 was a median 3.5 times greater across ages and sexes, compared to for all adults combined. We note large within-district prevalence differences between age groups: for men, 50% of districts displayed at least a 14-fold difference between age groups with the highest and lowest prevalence, and at least a 9-fold difference for women. Prevalence trends also varied over time; between 2000 and 2018, 70% of all districts saw a reduction in prevalence greater than five percentage points in at least one sex and age group. Meanwhile, over 30% of all districts saw at least a five percentage point prevalence increase in one or more sex and age group.
Conclusions
As the HIV epidemic persists and evolves in SSA, geographic and demographic shifts in prevention and treatment efforts are necessary. These estimates offer epidemiologically informative detail to better guide more targeted interventions, vital for combating HIV in SSA.
Journal Article
dynamicSDM: An R package for species geographical distribution and abundance modelling at high spatiotemporal resolution
Species distribution models (SDM) are widely applied to understand changing species geographical distribution and abundance patterns. However, existing SDM tools are inherently static and inadequate for modelling species distributions that are driven by dynamic environmental conditions. dynamicSDM provides novel tools that explicitly consider the temporal dimension at key SDM stages, including functions for: (a) Cleaning and filtering species occurrence records by spatial and temporal qualities; (b) Generating pseudo‐absence records through space and time; (c) Extracting spatiotemporally buffered explanatory variables; (d) Fitting SDMs whilst accounting for temporal biases and autocorrelation and (e) Projecting intra‐ and inter‐ annual geographical distributions and abundances at high spatiotemporal resolution. Package functions have been designed to be: flexible for targeting specific study species; compatible with other SDM tools; and, by utilising Google Earth Engine and Google Drive, to have low computing power and storage needs. We illustrate dynamicSDM functions with an example of a nomadic bird in southern Africa, the red‐billed quelea Quelea quelea. As dynamicSDM functions are flexible and easily applied, we suggest that these tools could be readily applied to other taxa and systems globally.
Journal Article
Spatial and spatio-temporal bayesian models with R-INLA
Spatial and Spatio-Temporal Bayesian Models with R-INLA provides a much needed, practically oriented & innovative presentation of the combination of Bayesian methodology and spatial statistics. The authors combine an introduction to Bayesian theory and methodology with a focus on the spatial and spatio-temporal models used within the Bayesian framework and a series of practical examples which allow the reader to link the statistical theory presented to real data problems. The numerous examples from the fields of epidemiology, biostatistics and social science all are coded in the R package R-INLA, which has proven to be a valid alternative to the commonly used Markov Chain Monte Carlo simulations
eBook
Spatial analysis for the social sciences
\"Many theories in the social sciences predict spatial dependence or the similarity of behaviors at neighboring locations. Spatial Analysis for the Social Sciences demonstrates how researchers can diagnose and model this spatial dependence and draw more valid inferences as a result. The book is structured around the well-known Galton's problem and presents a step-by-step guide to the application of spatial analysis. The book examines a variety of spatial diagnostics and models through a series of applied examples drawn from the social sciences. These include spatial lag models that capture behavioral diffusion between actors, spatial error models that account for spatial dependence in errors, and models that incorporate spatial heterogeneity in the effects of covariates. Spatial Analysis for the Social Sciences also examines advanced spatial models for time-series cross-sectional data, categorical and limited dependent variables, count data, and survival data\"-- Provided by publisher.
Book
Handbook of Spatial Statistics
Based on the work of prominent researchers, this handbook provides broad, thorough coverage of this vibrant area, from historical to contemporary topics. It explores the modeling advances, computational approaches, and methodology that have emerged in recent years. The book focuses on continuous and discrete spatial variation, spatial point patterns, and spatio-temporal processes. It also covers multivariate spatial process models, spatial aggregation, spatial misalignment, and spatial gradients in depth. The theory and applications are illustrated with many real-world data examples.
eBook