Multi-scale processes in metapopulations : Contributions of stage structure, rescue effect, and correlated extinctions

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Spatial targeting of infectious disease control: identifying multiple, unknown sources

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Use and Communication of Probabilistic Forecasts

Probabilistic forecasts are becoming more and more available. How should they be used and communicated? What are the obstacles to their use in practice? I review experience with five problems where probabilistic forecasting played an important role. This leads me to identify five types of potential users: Low Stakes Users, who don't need probabilistic forecasts; General Assessors, who need an overall idea of the uncertainty in the forecast; Change Assessors, who need to know if a change is out of line with expectatations; Risk Avoiders, who wish to limit the risk of an adverse outcome; and Decision Theorists, who quantify their loss function and perform the decision-theoretic calculations. This suggests that it is important to interact with users and to consider their goals. The cognitive research tells us that calibration is important for trust in probability forecasts, and that it is important to match the verbal expression with the task. The cognitive load should be minimized, reducing the probabilistic forecast to a single percentile if appropriate. Probabilities of adverse events and percentiles of the predictive distribution of quantities of interest seem often to be the best way to summarize probabilistic forecasts. Formal decision theory has an important role, but in a limited range of applications

Modeling large scale species abundance with latent spatial processes

Modeling species abundance patterns using local environmental features is an important, current problem in ecology. The Cape Floristic Region (CFR) in South Africa is a global hot spot of diversity and endemism, and provides a rich class of species abundance data for such modeling. Here, we propose a multi-stage Bayesian hierarchical model for explaining species abundance over this region. Our model is specified at areal level, where the CFR is divided into roughly $37{,}000$ one minute grid cells; species abundance is observed at some locations within some cells. The abundance values are ordinally categorized. Environmental and soil-type factors, likely to influence the abundance pattern, are included in the model. We formulate the empirical abundance pattern as a degraded version of the potential pattern, with the degradation effect accomplished in two stages. First, we adjust for land use transformation and then we adjust for measurement error, hence misclassification error, to yield the observed abundance classifications. An important point in this analysis is that only $28$ of the grid cells have been sampled and that, for sampled grid cells, the number of sampled locations ranges from one to more than one hundred. Still, we are able to develop potential and transformed abundance surfaces over the entire region. In the hierarchical framework, categorical abundance classifications are induced by continuous latent surfaces. The degradation model above is built on the latent scale. On this scale, an areal level spatial regression model was used for modeling the dependence of species abundance on the environmental factors.Comment: Published in at http://dx.doi.org/10.1214/10-AOAS335 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

A hierarchical Bayesian model for understanding the spatiotemporal dynamics of the intestinal epithelium

Our work addresses two key challenges, one biological and one methodological. First, we aim to understand how proliferation and cell migration rates in the intestinal epithelium are related under healthy, damaged (Ara-C treated) and recovering conditions, and how these relations can be used to identify mechanisms of repair and regeneration. We analyse new data, presented in more detail in a companion paper, in which BrdU/IdU cell-labelling experiments were performed under these respective conditions. Second, in considering how to more rigorously process these data and interpret them using mathematical models, we use a probabilistic, hierarchical approach. This provides a best-practice approach for systematically modelling and understanding the uncertainties that can otherwise undermine the generation of reliable conclusions-uncertainties in experimental measurement and treatment, difficult-to-compare mathematical models of underlying mechanisms, and unknown or unobserved parameters. Both spatially discrete and continuous mechanistic models are considered and related via hierarchical conditional probability assumptions. We perform model checks on both in-sample and out-of-sample datasets and use them to show how to test possible model improvements and assess the robustness of our conclusions. We conclude, for the present set of experiments, that a primarily proliferation-driven model suffices to predict labelled cell dynamics over most time-scales

Empiricism and stochastics in cellular automaton modeling of urban land use dynamics

An increasing number of models for predicting land use change in regions of rapidurbanization are being proposed and built using ideas from cellular automata (CA)theory. Calibrating such models to real situations is highly problematic and to date,serious attention has not been focused on the estimation problem. In this paper, wepropose a structure for simulating urban change based on estimating land usetransitions using elementary probabilistic methods which draw their inspiration fromBayes' theory and the related ?weights of evidence? approach. These land use changeprobabilities drive a CA model ? DINAMICA ? conceived at the Center for RemoteSensing of the Federal University of Minas Gerais (CSR-UFMG). This is based on aneight cell Moore neighborhood approach implemented through empirical land useallocation algorithms. The model framework has been applied to a medium-size townin the west of São Paulo State, Bauru. We show how various socio-economic andinfrastructural factors can be combined using the weights of evidence approach whichenables us to predict the probability of changes between land use types in differentcells of the system. Different predictions for the town during the period 1979-1988were generated, and statistical validation was then conducted using a multipleresolution fitting procedure. These modeling experiments support the essential logicof adopting Bayesian empirical methods which synthesize various information aboutspatial infrastructure as the driver of urban land use change. This indicates therelevance of the approach for generating forecasts of growth for Brazilian citiesparticularly and for world-wide cities in general