0000000000123730
AUTHOR
Joaquín Martínez-minaya
The Integrated Nested Laplace Approximation for fitting Dirichlet regression models
This paper introduces a Laplace approximation to Bayesian inference in Dirichlet regression models, which can be used to analyze a set of variables on a simplex exhibiting skewness and heteroscedasticity, without having to transform the data.These data, which mainly consist of proportions or percentages of disjoint categories, are widely known as compositional data and are common in areas such as ecology, geology, and psychology. We provide both the theoretical foundations and a description of how Laplace approximation can be implemented in the case of Dirichlet regression.The paper also introduces the package dirinla in the R-language that extends the RINLA package, which can not deal dire…
Spatial Bayesian Modeling Applied to the Surveys of Xylella fastidiosa in Alicante (Spain) and Apulia (Italy)
The plant-pathogenic bacterium Xylella fastidiosa was first reported in Europe in 2013, in the province of Lecce, Italy, where extensive areas were affected by the olive quick decline syndrome, caused by the subsp. pauca. In Alicante, Spain, almond leaf scorch, caused by X. fastidiosa subsp. multiplex, was detected in 2017. The effects of climatic and spatial factors on the geographic distribution of X. fastidiosa in these two infested regions in Europe were studied. The presence/absence data of X. fastidiosa in the official surveys were analyzed using Bayesian hierarchical models through the integrated nested Laplace approximation (INLA) methodology. Climatic covariates were obtained from …
Modelling Inoculum Availability ofPlurivorosphaerella nawaein Persimmon Leaf Litter with Bayesian Beta Regression
AbstractCircular leaf spot (CLS), caused byPlurivorosphaerella nawae, is a serious disease of persimmon (Diospyros kaki) inducing necrotic lesions on leaves, defoliation and fruit drop. Under Mediter-ranean conditions,P. nawaeforms pseudothecia in the leaf litter during winter and ascospores are released in spring infecting susceptible leaves. Persimmon growers are advised to apply fungicides for CLS control during the period of inoculum availability, which was defined based on ascospore counts under the microscope. A model of inoculum availability ofP. nawaewas developed and evaluated as an alternative to ascospore counts. Leaf litter samples were collected weekly in L’Alcúdia from 2010 to…
A hierarchical Bayesian Beta regression approach to study the effects of geographical genetic structure and spatial autocorrelation on species distribution range shifts
Global climate change (GCC) may be causing distribution range shifts in many organisms worldwide. Multiple efforts are currently focused on the development of models to better predict distribution range shifts due to GCC. We addressed this issue by including intraspecific genetic structure and spatial autocorrelation (SAC) of data in distribution range models. Both factors reflect the joint effect of ecoevolutionary processes on the geographical heterogeneity of populations. We used a collection of 301 georeferenced accessions of the annual plant Arabidopsis thaliana in its Iberian Peninsula range, where the species shows strong geographical genetic structure. We developed spatial and nonsp…
Incorporating Biotic Information in Species Distribution Models: A Coregionalized Approach
In this work, we discuss the use of a methodological approach for modelling spatial relationships among species by means of a Bayesian spatial coregionalized model. Inference and prediction is performed using the integrated nested Laplace approximation methodology to reduce the computational burden. We illustrate the performance of the coregionalized model in species interaction scenarios using both simulated and real data. The simulation demonstrates the better predictive performance of the coregionalized model with respect to the univariate models. The case study focus on the spatial distribution of a prey species, the European anchovy (Engraulis encrasicolus), and one of its predator spe…
Dealing with physical barriers in bottlenose dolphin (Tursiops truncatus) distribution
Abstract Worldwide, cetacean species have started to be protected, but they are still very vulnerable to accidental damage from an expanding range of human activities at sea. To properly manage these potential threats we need a detailed understanding of the seasonal distributions of these highly mobile populations. To achieve this goal, a growing effort has been underway to develop species distribution models (SDMs) that correctly describe and predict preferred species areas. However, accuracy is not always easy to achieve when physical barriers, such as islands, are present. Indeed, SDMs assume, if only implicitly, that the spatial effect is stationary, and that correlation is only depende…