From Empirical Bayes to Full Bayes: Methods for Analyzubg Traffic Safey Data, October 25, 2004

Traffic safety engineers are among the early adopters of Bayesian statistical tools for analyzing crash data. As in many other areas of application, empirical Bayes methods were their first choice, perhaps because they represent an intuitively appealing, yet relatively easy to implement alternative to purely classical approaches. With the enormous progress in numerical methods made in recent years and with the availability of free, easy to use software that permits implementing a fully Bayesian approach, however, there is now ample justification to progress towards fully Bayesian analyses of crash data. The fully Bayesian approach, in particular as implemented via multi-level hierarchical models, has many advantages over the empirical Bayes approach. In a full Bayesian analysis, prior information and all available data are seamlessly integrated into posterior distributions on which practitioners can base their inferences. All uncertainties are thus accounted for in the analyses and there is no need to pre-process data to obtain Safety Performance Functions and other such prior estimates of the effect of covariates on the outcome of interest. In this light, fully Bayesian methods may well be less costly to implement and may result in safety estimates with more realistic standard errors. In this manuscript, we present the full Bayesian approach to analyzing traffic safety data and focus on highlighting the differences between the empirical Bayes and the full Bayes approaches. We use an illustrative example to discuss a step-by-step Bayesian analysis of the data and to show some of the types of inferences that are possible within the full Bayesian framework.

DnaSP, DNA polymorphism analyses by the coalescent and other methods

DnaSP is a software package for the analysis of DNA polymorphism data. Present version introduces several new modules and features which, among other options allow: (1) handling big data sets (~5 Mb per sequence); (2) conducting a large number of coalescent-based tests by Monte Carlo computer simulations; (3) extensive analyses of the genetic differentiation and gene flow among populations; (4) analysing the evolutionary pattern of preferred and unpreferred codons; (5) generating graphical outputs for an easy visualization of results. Availability: The software package, including complete documentation and examples, is freely available to academic users from: http://www.ub.es/dnasp

Rapid radiation in spiny lobsters (Palinurus spp) as revealed by classic and ABC methods using mtDNA and microsatellite data

Background: Molecular tools may help to uncover closely related and still diverging species from a wide variety of taxa and provide insight into the mechanisms, pace and geography of marine speciation. There is a certain controversy on the phylogeography and speciation modes of species-groups with an Eastern Atlantic-Western Indian Ocean distribution, with previous studies suggesting that older events (Miocene) and/or more recent (Pleistocene) oceanographic processes could have influenced the phylogeny of marine taxa. The spiny lobster genus Palinurus allows for testing among speciation hypotheses, since it has a particular distribution with two groups of three species each in the Northeastern Atlantic (P. elephas, P. mauritanicus and P. charlestoni) and Southeastern Atlantic and Southwestern Indian Oceans (P. gilchristi, P. delagoae and P. barbarae). In the present study, we obtain a more complete understanding of the phylogenetic relationships among these species through a combined dataset with both nuclear and mitochondrial markers, by testing alternative hypotheses on both the mutation rate and tree topology under the recently developed approximate Bayesian computation (ABC) methods. Results Our analyses support a North-to-South speciation pattern in Palinurus with all the South-African species forming a monophyletic clade nested within the Northern Hemisphere species. Coalescent-based ABC methods allowed us to reject the previously proposed hypothesis of a Middle Miocene speciation event related with the closure of the Tethyan Seaway. Instead, divergence times obtained for Palinurus species using the combined mtDNA-microsatellite dataset and standard mutation rates for mtDNA agree with known glaciation-related processes occurring during the last 2 my. Conclusion The Palinurus speciation pattern is a typical example of a series of rapid speciation events occurring within a group, with very short branches separating different species. Our results support the hypothesis that recent climate change-related oceanographic processes have influenced the phylogeny of marine taxa, with most Palinurus species originating during the last two million years. The present study highlights the value of new coalescent-based statistical methods such as ABC for testing different speciation hypotheses using molecular data.

Les méthodes d'études de cas en psychothérapie: perspectives actuelles [Methods of psychotherapy case studies: current perspectives].

There is a renewal of interest among psychotherapy researchers and psychotherapists towards psychotherapy case studies. This article presents two paradigms that have greatly influenced this increasing interest in psychotherapy case studies : the pragmatic case study and the theory-building case study paradigm. The origins, developments and key-concepts of both paradigms are presented, as well as their methodological and ethical specificities. Examples of case studies, along with models developed, are cited. The differential influence of the post-modern schools on both paradigms are presented, as well as their contribution to the field of methods of psychotherapy case studies discussed and assessed in terms of relevance for the researcher and the psychotherapist.

Optimization of analytical methods for the assessment of the quality of fats and oils used in continuous deep fat frying

La aplicabilidad, repetibilidad y capacidad de diferentes métodos de análisis para discriminar muestras de aceites con diferentes grados de oxidación fueron evaluadas mediante aceites recogidos en procesos de fritura en continuo en varias empresas españolas. El objetivo de este trabajo fue encontrar métodos complementarios a la determinación del índice de acidez para el control de calidad rutinario de los aceites de fritura empleados en estas empresas. La optimización de la determinación de la constante dieléctrica conllevó una clara mejora de la variabilidad. No obstante, excepto en el caso del índice del ATB, el resto de métodos ensayados mostraron una menor variabilidad. La determinación del índice del ATB fue descartada ya que su sensibilidad fue insuficiente para discriminar entre aceites con diferente grado de oxidación. Los diferentes parámetros de alteración determinados en los aceites de fritura mostraron correlaciones significativas entre el índice de acidez y varios parámetros de oxidación diferentes, como la constante dieléctrica, el índice de p-anisidina, la absorción al ultravioleta y el contenido en polímeros de los triacilgliceroles. El índice de acidez solo evalúa la alteración hidrolítica, por lo que estos parámetros aportan información complementaria al evaluar la alteración termooxidativa.

Inferring landscape effects on dispersal from genetic distances: how far can we go?

Functional connectivity affects demography and gene dynamics in fragmented populations. Besides species-specific dispersal ability, the connectivity between local populations is affected by the landscape elements encountered during dispersal. Documenting these effects is thus a central issue for the conservation and management of fragmented populations. In this study, we compare the power and accuracy of three methods (partial correlations, regressions and Approximate Bayesian Computations) that use genetic distances to infer the effect of landscape upon dispersal. We use stochastic individual-based simulations of fragmented populations surrounded by landscape elements that differ in their permeability to dispersal. The power and accuracy of all three methods are good when there is a strong contrast between the permeability of different landscape elements. The power and accuracy can be further improved by restricting analyses to adjacent pairs of populations. Landscape elements that strongly impede dispersal are the easiest to identify. However, power and accuracy decrease drastically when landscape complexity increases and the contrast between the permeability of landscape elements decreases. We provide guidelines for future studies and underline the needs to evaluate or develop approaches that are more powerful.

Stochastic generation of homogeneous isotropic turbulence with well-defined-spectra

A precise and simple computational model to generate well-behaved two-dimensional turbulent flows is presented. The whole approach rests on the use of stochastic differential equations and is general enough to reproduce a variety of energy spectra and spatiotemporal correlation functions. Analytical expressions for both the continuous and the discrete versions, together with simulation algorithms, are derived. Results for two relevant spectra, covering distinct ranges of wave numbers, are given.

A probabilistic approach to niche-based community models for spatial forecasts of assemblage properties and their uncertainties

Aim Conservation strategies are in need of predictions that capture spatial community composition and structure. Currently, the methods used to generate these predictions generally focus on deterministic processes and omit important stochastic processes and other unexplained variation in model outputs. Here we test a novel approach of community models that accounts for this variation and determine how well it reproduces observed properties of alpine butterfly communities. Location The western Swiss Alps. Methods We propose a new approach to process probabilistic predictions derived from stacked species distribution models (S-SDMs) in order to predict and assess the uncertainty in the predictions of community properties. We test the utility of our novel approach against a traditional threshold-based approach. We used mountain butterfly communities spanning a large elevation gradient as a case study and evaluated the ability of our approach to model species richness and phylogenetic diversity of communities. Results S-SDMs reproduced the observed decrease in phylogenetic diversity and species richness with elevation, syndromes of environmental filtering. The prediction accuracy of community properties vary along environmental gradient: variability in predictions of species richness was higher at low elevation, while it was lower for phylogenetic diversity. Our approach allowed mapping the variability in species richness and phylogenetic diversity projections. Main conclusion Using our probabilistic approach to process species distribution models outputs to reconstruct communities furnishes an improved picture of the range of possible assemblage realisations under similar environmental conditions given stochastic processes and help inform manager of the uncertainty in the modelling results

Reaction-diffusion fronts under stochastic advection

We study front propagation in stirred media using a simplified modelization of the turbulent flow. Computer simulations reveal the existence of the two limiting propagation modes observed in recent experiments with liquid phase isothermal reactions. These two modes respectively correspond to a wrinkled although sharp propagating interface and to a broadened one. Specific laws relative to the enhancement of the front velocity in each regime are confirmed by our simulations.

Diffusion of passive scalars under stochastic convection

The diffusion of passive scalars convected by turbulent flows is addressed here. A practical procedure to obtain stochastic velocity fields with well¿defined energy spectrum functions is also presented. Analytical results are derived, based on the use of stochastic differential equations, where the basic hypothesis involved refers to a rapidly decaying turbulence. These predictions are favorable compared with direct computer simulations of stochastic differential equations containing multiplicative space¿time correlated noise.

Mixed mating in androdioecious Mercurialis annua inferred using progeny arrays and diploid-acting microsatellite loci in a hexaploid background.

Background and Aims The frequency at which males can be maintained with hermaphrodites in androdioecious populations is predicted to depend on the selfing rate, because self-fertilization by hermaphrodites reduces prospective siring opportunities for males. In particular, high selfing rates by hermaphrodites are expected to exclude males from a population. Here, the first estimates are provided of the mating system from two wild hexaploid populations of the androdioecious European wind-pollinated plant M. annua with contrasting male frequencies.Methods Four diploid microsatellite loci were used to genotype 19-20 progeny arrays from two populations of M. annua, one with males and one without. Mating-system parameters were estimated using the program MLTR.Key Results Both populations had similar, intermediate outcrossing rates (t(m) = 0.64 and 0.52 for the population with and without males, respectively). The population without males showed a lower level of correlated paternity and biparental inbreeding and higher allelic richness and gene diversity than the population with males.Conclusions The results demonstrate the utility of new diploid microsatellite loci for mating system analysis in a hexaploid plant. It would appear that androdioecious M. annua has a mixed-mating system in the wild, an uncommon finding for wind-pollinated species. This study sets a foundation for future research to assess the relative importance of the sexual system, plant-density variation and stochastic processes for the regulation of male frequencies in M. annua over space and time.

Counterfactuals and causal inference: Methods and principles for social research

"Most quantitative empirical analyses are motivated by the desire to estimate the causal effect of an independent variable on a dependent variable. Although the randomized experiment is the most powerful design for this task, in most social science research done outside of psychology, experimental designs are infeasible. (Winship & Morgan, 1999, p. 659)." This quote from earlier work by Winship and Morgan, which was instrumental in setting the groundwork for their book, captures the essence of our review of Morgan and Winship's book: It is about causality in nonexperimental settings.

Chiroptical measurement of chiral aggregates at liquid-liquid interface in centrifugal liquid membrane cell by Mueller matrix and conventional circular dichroism methods

The centrifugal liquid membrane (CLM) cell has been utilized for chiroptical studies of liquid-liquid interfaces with a conventional circular dichroism (CD) spectropolarimeter. These studies required the characterization of optical properties of the rotating cylindrical CLM glass cell, which was used under the high speed rotation. In the present study, we have measured the circular and linear dichroism (CD and LD) spectra and the circular and linear birefringence (CB and LB) spectra of the CLM cell itself as well as those of porphyrine aggregates formed at the liquid-liquid interface in the CLM cell, applying Mueller matrix measurement method. From the results, it was confirmed that the CLM-CD spectra of the interfacial porphyrin aggregates observed by a conventional CD spectropolarimeter should be correct irrespective of LD and LB signals in the CLM cell.