Journal of Agricultural Biological and Environmental Statistics最新文献

We present a novel method for estimating species abundance using presence–absence maps. Our approach takes the spatial context into consideration, distinguishing it from conventional methods. The proposed method is built upon a well-known kernel estimation for point pattern intensity, with the addition of a new parameter representing the mean abundance in each occupied cell. The parameter estimate is obtained through maximum likelihood estimation. The expected abundance corresponds to the integral of the intensity over the study area, which can be estimated by taking the Riemann sum of the intensity. The implementation of our method is straightforward, using existing packages in the R software. We compared various bandwidth selection methods within our approach and assessed the estimation performance against some approaches based on the random placement model or negative binomial model through the simulation study and an empirical forestry data in Barro Colorado Island (BCI), Panama. The results of the simulation and the application demonstrate that our method, with a carefully chosen bandwidth, outperforms the alternatives for highly aggregated data and improves the issue of underestimation. Supplementary materials accompanying this paper appear online.

Many datasets have heavy-tailed behavior, and classical penalized models are not appropriate for them. To treat this problem, we propose a penalized regression that handles model selection and outliers issues simultaneously. We provide a LASSO regression for models with Cauchy distributed noises using the negative log-likelihood loss function. To select the regularization parameter, we define AIC and BIC type criteria. We study the distribution of the regression coefficients estimator in the simulation experiments. In addition, simulation study and real datasets analysis confirm the superiority of the proposed method.

In this research, we propose a novel technique for visualizing nonstationarity in geostatistics, particularly when confronted with a single realization of data at irregularly spaced locations. Our method hinges on formulating a statistic that tracks a stable microergodic parameter of the exponential covariance function, allowing us to address the intricate challenges of nonstationary processes that lack repeated measurements. We implement the fused lasso technique to elucidate nonstationary patterns at various resolutions. For prediction purposes, we segment the spatial domain into stationary sub-regions via Voronoi tessellations. Additionally, we devise a robust test for stationarity based on contrasting the sample means of our proposed statistics between two selected Voronoi subregions. The effectiveness of our method is demonstrated through simulation studies and its application to a precipitation dataset in Colorado. Supplementary materials accompanying this paper appear online.

Regression models for spatially varying data use spatial random effects to reflect spatial correlation structure. Such random effects, however, may interfere with the covariate effect estimates and make them unreliable. This problem, known as spatial confounding, is complex and has only been studied for models with linear covariate effects. However, as illustrated by a forestry example in which we assess the effect of soil, climate, and topography variables on tree health, the covariate effects of interest are in practice often unknown and nonlinear. We consider, for the first time, spatial confounding in spatial models with nonlinear effects implemented in the generalised additive models (GAMs) framework. We show that spatial+, a recently developed method for alleviating confounding in the linear case, can be adapted to this setting. In practice, spatial+ can then be used both as a diagnostic tool for investigating whether covariate effect estimates are affected by spatial confounding and for correcting the estimates for the resulting bias when it is present. Supplementary materials accompanying this paper appear online.

The management of forest pests relies on an accurate understanding of the species’ phenology. Thermal performance curves (TPCs) have traditionally been used to model insect phenology. Many such models have been proposed and fitted to data from both wild and laboratory-reared populations. Using Hamiltonian Monte Carlo for estimation, we implement and fit an individual-level, Bayesian hierarchical model of insect development to the observed larval stage durations of a population reared in a laboratory at constant temperatures. This hierarchical model handles interval censoring and temperature transfers between two constant temperatures during rearing. It also incorporates individual variation, quadratic variation in development rates across insects’ larval stages, and “flexibility” parameters that allow for deviations from a parametric TPC. Using a Bayesian method ensures a proper propagation of parameter uncertainty into predictions and provides insights into the model at hand. The model is applied to a population of eastern spruce budworm (Choristoneura fumiferana) reared at 7 constant temperatures. Resulting posterior distributions can be incorporated into a workflow that provides prediction intervals for the timing of life stages under different temperature regimes. We provide a basic example for the spruce budworm using a year of hourly temperature data from Timmins, Ontario, Canada. Supplementary materials accompanying this paper appear on-line.

In this paper, we propose a novel model to analyze serially correlated two-dimensional functional data observed sparsely and irregularly on a domain which may not be a rectangle. Our approach employs a mixed effects model that specifies the principal component functions as bivariate splines on triangles and the principal component scores as random effects which follow an auto-regressive model. We apply the thin-plate penalty for regularizing the bivariate function estimation and develop an effective EM algorithm along with Kalman filter and smoother for calculating the penalized likelihood estimates of the parameters. Our approach was applied on simulated datasets and on Texas monthly average temperature data from January year 1915 to December year 2014. Supplementary materials accompanying this paper appear online.

In this paper, we present a statistical approach to evaluate the relationship between variables observed in a two-factors experiment. We consider a three-level model with covariance structure ({varvec{Sigma }} otimes {varvec{Psi }}_1 otimes {varvec{Psi }}_2), where ({varvec{Sigma }}) is an arbitrary positive definite covariance matrix, and ({varvec{Psi }}_1) and ({varvec{Psi }}_2) are both correlation matrices with a compound symmetric structure corresponding to two different factors. The Rao’s score test is used to test the hypotheses that observations grouped by one or two factors are uncorrelated. We analyze a fermentation process to illustrate the results. Supplementary materials accompanying this paper appear online.

Rapid anthropogenic climate change has elevated the interest in studying the biotic responses of species during the Last Glacial Maximum. During this period, species retreated to highly spatially restricted geographic regions where survival was possible, known as glacial micro-refugia, from which they migrated and expanded when conditions became more suitable. Several distinct sources of evidence have contributed to developing a new understanding of how these regions might have impacted the sustainability of the natural populations of many species. Pollen records in Eastern Beringia have been used to explore the possibility that the region harbored glacial refugia for several plants from the arctic tundra and/or the boreal forest biomes common to the region. Our study focuses on Alnus viridis and Picea glauca, two predominant species of arcto-boreal vegetation. We propose to integrate genomic, SDM, and existing fossil data in a hierarchical Bayesian modeling (HBM) framework to determine whether multiple refugia existed in isolated geographic areas. This study demonstrates how the flexibility of HBMs makes the formal synthesis of such disparate data sources feasible. Our results highlight the regions of plausible refugia that can guide future investigations into studying the role of glacial refugia during climate change. Supplementary materials accompanying this paper appear online.