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Quantifying the interactions between functional diversity and environmental change is important for understanding the effects of biodiversity on ecosystem processes. This study aims to evaluate zooplankton secondary production and biomass in an experiment with different levels of functional diversity and environmental stress in the form of increased salinity. It is expected that communities that are more functionally diverse will present higher secondary production and biomass, even under conditions of environmental stress. To test this hypothesis, a mesocosm experiment with two factors was performed: low and high diversity and with and without salt totaling four possible combinations of treatments over the duration of 4 weeks. The high functional diversity treatments showed higher zooplankton secondary production and biomass than those of the low diversity treatments, even under salt addition. The salinity decreased zooplankton production and functional diversity, but its effects were more pronounced in the low than in the high diversity communities. However, in the low diversity treatments the zooplankton biomass and production were maintained due to the dominance of species with certain traits. In summary, our study contributed to understanding the role of zooplankton functional diversity on ecosystem processes in the face of environmental changes promoted by increased salinity.

Source at https://doi.org/10.1214/17-sts576rej. INTRODUCTION: The point of departure for our paper is that most modern statistical models are built to be flexible enough to model diverse data generating mechanisms. Good statistical practice requires us to limit this flexibility, which is typically controlled by a small number of parameters, to the amount “needed” to model the data at hand. The Bayesian framework provides a natural method for doing this although, as DD points out, this trend for penalising model complexity casts a broad shadow over all of modern statistics and data science.The PC prior framework argues for setting priors on these flexibility parameters that are specifically built to penalise a certain type of complexity and avoid overfitting. The discussants raised various points about this core idea. First, DD pointed out that while over-fitting a model is a bad thing, under-fitting is not better: we do not want Occam’s razor to slit our throat. We saw this behaviour when using a half-Normal prior on the distance, while the exponential prior does not lead to obvious attenuation of the estimates. This is confirmed experimentally by Klein and Kneib (2016).

This work extends the integrated nested Laplace approximation (INLA) method to latent models outside the scope of latent Gaussian models, where independent components of the latent field can have a near-Gaussian distribution. The proposed methodology is an essential component of a bigger project that aims to extend the R package INLA in order to allow the user to add flexibility and challenge the Gaussian assumptions of some of the model components in a straightforward and intuitive way. Our approach is applied to two examples, and the results are compared with that obtained by Markov chain Monte Carlo, showing similar accuracy with only a small fraction of computational time. Implementation of the proposed extension is available in the R-INLA package.

In this work we propose a model for the intensity of a space-time point process, specified by a sequence of spatial surfaces that evolve dynamically in time. This specification allows flexible structures for the components of the model, in order to handle temporal and spatial variations both separately and jointly. These structures make use of state-space and Gaussian process tools. They are combined to create a richer class of models for the intensity process. This structural approach allows for a decomposition of the intensity into purely temporal, purely spatial and spatio-temporal terms. Inference is performed under a fully Bayesian approach, with the description of simulation-based and analytic methods for approximating the posterior distributions. The proposed methodology is applied to model the incidence of impulses in the small intestine, illustrated by a data-set obtained through an experiment conducted in cats, in order to understand the interaction between the nervous and digestive systems. This application illustrates the usefulness of the proposed methodology and shows it compares favorably against existing alternatives. The paper is concluded with a few directions for further investigation.

In this paper, we introduce a new concept for constructing prior distributions. We exploit the natural nested structure inherent to many model components, which defines the model component to be a flexible extension of a base model. Proper priors are defined to penalise the complexity induced by deviating from the simpler base model and are formulated after the input of a user-defined scaling parameter for that model component, both in the univariate and the multivariate case. These priors are invariant to reparameterisations, have a natural connection to Jeffreys' priors, are designed to support Occam's razor and seem to have excellent robustness properties, all which are highly desirable and allow us to use this approach to define default prior distributions. Through examples and theoretical results, we demonstrate the appropriateness of this approach and how it can be applied in various situations., Major revision of previous version. Includes a beefed up literature review and new desiderata for hierarchical priors. Removes (for space) the Cox proportional hazard model and the section on hyperparameters for Gaussian random fields

Prior sensitivity examination plays an important role in applied Bayesian analyses. This is especially true for Bayesian hierarchical models, where interpretability of the parameters within deeper layers in the hierarchy becomes challenging. In addition, lack of information together with identifiability issues may imply that the prior distributions for such models have an undesired influence on the posterior inference. Despite its relevance, informal approaches to prior sensitivity analysis are currently used. They require repetitive re-runs of the model with ad-hoc modified base prior parameter values. Other formal approaches to prior sensitivity analysis suffer from a lack of popularity in practice, mainly due to their high computational cost and absence of software implementation. We propose a novel formal approach to prior sensitivity analysis which is fast and accurate. It quantifies sensitivity without the need for a model re-run. We develop a ready-to-use priorSens package in R for routine prior sensitivity investigation by R-INLA. Throughout a series of examples we show how our approach can be used to detect high prior sensitivities of some parameters as well as identifiability issues in possibly over-parametrized Bayesian hierarchical models., Comment: 25 pages, 3 figures

The INLA approach for approximate Bayesian inference for latent Gaussian models has been shown to give fast and accurate estimates of posterior marginals and also to be a valuable tool in practice via the R-package R-INLA. In this paper we formalize new developments in the R-INLA package and show how these features greatly extend the scope of models that can be analyzed by this interface. We also discuss the current default method in R-INLA to approximate posterior marginals of the hyperparameters using only a modest number of evaluations of the joint posterior distribution of the hyperparameters, without any need for numerical integration.