Bringing game theory to hypothesis testing: Establishing finite sample bounds on inference

Small sample properties are of fundamental interest when only limited data is avail-able. Exact inference is limited by constraints imposed by speci.c nonrandomizedtests and of course also by lack of more data. These e¤ects can be separated as we propose to evaluate a test by comparing its type II error to the minimal type II error among all tests for the given sample. Game theory is used to establish this minimal type II error, the associated randomized test is characterized as part of a Nash equilibrium of a .ctitious game against nature.We use this method to investigate sequential tests for the di¤erence between twomeans when outcomes are constrained to belong to a given bounded set. Tests ofinequality and of noninferiority are included. We .nd that inference in terms oftype II error based on a balanced sample cannot be improved by sequential sampling or even by observing counter factual evidence providing there is a reasonable gap between the hypotheses.

The crew-scheduling module in the GIST system

The public transportation is gaining importance every year basically duethe population growth, environmental policies and, route and streetcongestion. Too able an efficient management of all the resources relatedto public transportation, several techniques from different areas are beingapplied and several projects in Transportation Planning Systems, indifferent countries, are being developed. In this work, we present theGIST Planning Transportation Systems, a Portuguese project involving twouniversities and six public transportation companies. We describe indetail one of the most relevant modules of this project, the crew-scheduling module. The crew-scheduling module is based on the application of meta-heuristics, in particular GRASP, tabu search and geneticalgorithm to solve the bus-driver-scheduling problem. The metaheuristicshave been successfully incorporated in the GIST Planning TransportationSystems and are actually used by several companies.

Effect of genetic convergence on phylogenetic inference.

Phylogenetic reconstructions are a major component of many studies in evolutionary biology, but their accuracy can be reduced under certain conditions. Recent studies showed that the convergent evolution of some phenotypes resulted from recurrent amino acid substitutions in genes belonging to distant lineages. It has been suggested that these convergent substitutions could bias phylogenetic reconstruction toward grouping convergent phenotypes together, but such an effect has never been appropriately tested. We used computer simulations to determine the effect of convergent substitutions on the accuracy of phylogenetic inference. We show that, in some realistic conditions, even a relatively small proportion of convergent codons can strongly bias phylogenetic reconstruction, especially when amino acid sequences are used as characters. The strength of this bias does not depend on the reconstruction method but varies as a function of how much divergence had occurred among the lineages prior to any episodes of convergent substitutions. While the occurrence of this bias is difficult to predict, the risk of spurious groupings is strongly decreased by considering only 3rd codon positions, which are less subject to selection, as long as saturation problems are not present. Therefore, we recommend that, whenever possible, topologies obtained with amino acid sequences and 3rd codon positions be compared to identify potential phylogenetic biases and avoid evolutionarily misleading conclusions.

Inference with the lognormal distribution

Several estimators of the expectation, median and mode of the lognormal distribution are derived. They aim to be approximately unbiased, efficient, or have a minimax property in the class of estimators we introduce. The small-sample properties of these estimators are assessed by simulations and, when possible, analytically. Some of these estimators of the expectation are far more efficient than the maximum likelihood or the minimum-variance unbiased estimator, even for substantial samplesizes.

Subsampling inference in threshold autoregressive models

This paper discusses inference in self exciting threshold autoregressive (SETAR)models. Of main interest is inference for the threshold parameter. It iswell-known that the asymptotics of the corresponding estimator depend uponwhether the SETAR model is continuous or not. In the continuous case, thelimiting distribution is normal and standard inference is possible. Inthe discontinuous case, the limiting distribution is non-normal and cannotbe estimated consistently. We show valid inference can be drawn by theuse of the subsampling method. Moreover, the method can even be extendedto situations where the (dis)continuity of the model is unknown. In thiscase, also the inference for the regression parameters of the modelbecomes difficult and subsampling can be used advantageously there aswell. In addition, we consider an hypothesis test for the continuity ofthe SETAR model. A simulation study examines small sample performance.

L'examen clinique du sein : vidéos d'enseignement des compétences cliniques en gynécologie destinés à un module en ligne

Cette thèse présente un travail audiovisuel « L'examen clinique du sein ». Avec l'unité « L'examen génital » elle forme le module « Gynécologie » du projet Virtual Skills Lab (VSL). Le but du projet VSL est d'établir un portail d'enseignement en ligne pour l'enseignement des compétences cliniques (ce terme étant utilisé ici comme équivalent de l'anglais « clinical skills »). Les compétences traitées sont celles exigées par le Catalogue suisse des objectifs d'apprentissage. L'unité « L'examen clinique du sein » est constituée d'une multitude de courtes séquences vidéo qui peuvent être regardées à la suite ou de manière individuelle. Elle est divisée en étapes logiques telles que l'inspection ou la palpation. Chacune de ces étapes appelées « skill » est présentée de deux façons : comme vue d'ensemble et par une approche pas à pas. La séquence « vue d'ensemble » présente le skill en temps réel et représente donc une visualisation du but à atteindre par l'apprenant. Le skill est décomposé en petites étapes (step), les procédures sont montrées au ralenti, munies d'une explication par une voix off. Le format de ces séquences est présenté en double largeur, la partie de gauche montre l'action, la partie de droite est utilisée pour des tableaux ou des graphiques explicatifs. Les différents gestes des compétences cliniques sont rarement standardisés. Pour VSL, un processus de validation sur la base d'un consensus suisse a été mis en place. Ceci ne veut néanmoins pas dire que les modules VSL validés ont été intégrés dans le curriculum de toutes les universités suisses. Vu la complexité des curriculums et la multitude de facteurs entrant enjeu, notamment sur l'intégration des moyens d'enseignement audiovisuels, leur implémentation est une phase critique de tout projet de ce genre. En Suisse, le multilinguisme y ajoute un degré de complexité. A Lausanne, « L'examen clinique du sein » a été introduit aussi bien dans la formation pré- que postgraduée.

Analyse des besoins du système de prise en charge des addictions en Suisse: Module 1 : revue de littérature

Le but de cette étude est d'explorer et de définir, par une analyse des besoins, si l'offre actuelle en services dans le domaine des addictions est encore adaptée à la situation épidémiologique actuelle des addictions, à l'évolution des types de comportements liés à la dépendance et aux besoins des clients. Il s'agit en particulier de répondre aux questions suivantes: Existe-t-il actuellement des besoins en traitement pour lesquels il n'existe aucune offre appropriée ? Quels groupes ne sont pas ou sont insuffisamment atteints par l'offre existante? A quels genres de problèmes liés à la dépendance et à quels nouveaux besoins des clients les structures oeuvrant dans le domaine de la dépendance sont-elles confrontées? Quels sont les besoins d'adaptation du système de prise en charge nécessaires concernant soit les groupes-cibles de services, soit les types d'offres - en particulier le besoin en nouveaux concepts/modèles de prise en charge pour répondre à l'évolution des besoins? Comment ces structures font-elles face à l'accroissement de l'usage de multiples substances (multi-consommation)?

Landscape structure affects dispersal in the greater white-toothed shrew: inference between genetic and simulated ecological distances

Animal dispersal in a fragmented landscape depends on the complex interaction between landscape structure and animal behavior. To better understand how individuals disperse, it is important to explicitly represent the properties of organisms and the landscape in which they move. A common approach to modelling dispersal includes representing the landscape as a grid of equal sized cells and then simulating individual movement as a correlated random walk. This approach uses a priori scale of resolution, which limits the representation of all landscape features and how different dispersal abilities are modelled. We develop a vector-based landscape model coupled with an object-oriented model for animal dispersal. In this spatially explicit dispersal model, landscape features are defined based on their geographic and thematic properties and dispersal is modelled through consideration of an organism's behavior, movement rules and searching strategies (such as visual cues). We present the model's underlying concepts, its ability to adequately represent landscape features and provide simulation of dispersal according to different dispersal abilities. We demonstrate the potential of the model by simulating two virtual species in a real Swiss landscape. This illustrates the model's ability to simulate complex dispersal processes and provides information about dispersal such as colonization probability and spatial distribution of the organism's path

Effects of communication training on real practice performance: a role-play module versus a standardized patient module.

This study investigated the effectiveness of modules involving standardized patients and role-plays on training communication skills. The first module involved standardized patients and an Objective Structured Clinical Examination (OSCE); the second module consisted of peer role-plays and a written examination. A randomized posttest-only control group design with first-year nursing students was used. The intervention group received one-to-one communication training with direct oral feedback from the standardized patient. The control group had training with peer role-playing and mutual feedback. The posttest involved students' rating their self-efficacy, and real patients and clinical supervisors evaluated their communication skills. No significant differences were found between self-efficacy and patient ratings. However, the clinical supervisors rated the intervention group's communication skills to be significantly (p < 0.0001) superior. Assessments by clinical supervisors indicate that communication training modules including standardized patients and an OSCE are superior to communication training modules with peer role-playing.

Inference of chromosomal inversion dynamics from Pool-Seq data in natural and laboratory populations of Drosophila melanogaster.

Sequencing of pools of individuals (Pool-Seq) represents a reliable and cost-effective approach for estimating genome-wide SNP and transposable element insertion frequencies. However, Pool-Seq does not provide direct information on haplotypes so that, for example, obtaining inversion frequencies has not been possible until now. Here, we have developed a new set of diagnostic marker SNPs for seven cosmopolitan inversions in Drosophila melanogaster that can be used to infer inversion frequencies from Pool-Seq data. We applied our novel marker set to Pool-Seq data from an experimental evolution study and from North American and Australian latitudinal clines. In the experimental evolution data, we find evidence that positive selection has driven the frequencies of In(3R)C and In(3R)Mo to increase over time. In the clinal data, we confirm the existence of frequency clines for In(2L)t, In(3L)P and In(3R)Payne in both North America and Australia and detect a previously unknown latitudinal cline for In(3R)Mo in North America. The inversion markers developed here provide a versatile and robust tool for characterizing inversion frequencies and their dynamics in Pool-Seq data from diverse D. melanogaster populations.

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.

What drives invasibility? A multi-model inference test and spatial modelling of alien plant species richness patterns in northern Portugal

Understanding and anticipating biological invasions can focus either on traits that favour species invasiveness or on features of the receiving communities, habitats or landscapes that promote their invasibility. Here, we address invasibility at the regional scale, testing whether some habitats and landscapes are more invasible than others by fitting models that relate alien plant species richness to various environmental predictors. We use a multi-model information-theoretic approach to assess invasibility by modelling spatial and ecological patterns of alien invasion in landscape mosaics and testing competing hypotheses of environmental factors that may control invasibility. Because invasibility may be mediated by particular characteristics of invasiveness, we classified alien species according to their C-S-R plant strategies. We illustrate this approach with a set of 86 alien species in Northern Portugal. We first focus on predictors influencing species richness and expressing invasibility and then evaluate whether distinct plant strategies respond to the same or different groups of environmental predictors. We confirmed climate as a primary determinant of alien invasions and as a primary environmental gradient determining landscape invasibility. The effects of secondary gradients were detected only when the area was sub-sampled according to predictions based on the primary gradient. Then, multiple predictor types influenced patterns of alien species richness, with some types (landscape composition, topography and fire regime) prevailing over others. Alien species richness responded most strongly to extreme land management regimes, suggesting that intermediate disturbance induces biotic resistance by favouring native species richness. Land-use intensification facilitated alien invasion, whereas conservation areas hosted few invaders, highlighting the importance of ecosystem stability in preventing invasions. Plants with different strategies exhibited different responses to environmental gradients, particularly when the variations of the primary gradient were narrowed by sub-sampling. Such differential responses of plant strategies suggest using distinct control and eradication approaches for different areas and alien plant groups.

Validation of the 34-item Supportive Care Needs Survey and 8-item Breast module French versions (SCNS-SF34-Fr and SCNS-BR8-Fr) in breast cancer patients.

This study aimed to assess the psychometric robustness of the French version of the Supportive Care Needs Survey and breast cancer (BC) module (SCNS-SF34-Fr and SCNS-BR8-Fr). Breast cancer patients were recruited in two hospitals (in Paris, France and Lausanne, Switzerland) either in ambulatory chemotherapy or radiotherapy, or surgery services. They were invited to complete the SCNS-SF34-Fr and SCNS-BR8-Fr as well as quality of life and patient satisfaction questionnaires. Three hundred and eighty-four (73% response rate) BC patients returned completed questionnaires. A five-factor model was confirmed for the SCNS-SF34-Fr with adequate goodness-of-fit indexes, although some items evidenced content redundancy, and a one-factor was identified for the SCNS-BR8-Fr. Internal consistency and test-retest estimates were satisfactory for most scales. The SCNS-SF34-Fr and SCNS-BR8-Fr scales demonstrated conceptual differences with the quality of life and satisfaction with care scales, highlighting the specific relevance of this assessment. Different levels of needs could be differentiated between groups of BC patients in terms of age and level of education (P < 0.001). The SCNS-SF34-Fr and SCNS-BR8-Fr present adequate psychometric properties despite some redundant items. These questionnaires allow for the crucial endeavour to design appropriate care services according to BC patients' characteristics.