Antedependence (AD) of order p, also known as the Markov property of order p, is a property of index-ordered random variables in which each variable, given at least p immediately preceding variables, is independent of all further preceding variables. Zimmerman and Nunez-Anton (2010) present statistical methodology for fitting and performing inference for AD models for continuous (primarily normal) longitudinal data. But analogous AD-model methodology for categorical longitudinal data has not yet been well developed. In this thesis, we derive maximum likelihood estimators of transition probabilities under antedependence of any order, and we use these estimators to develop likelihood-based methods for determining the order of antedependence of categorical longitudinal data. Specifically, we develop a penalized likelihood method for determining variable-order antedependence structure, and we derive the likelihood ratio test, score test, Wald test and an adaptation of Fisher's exact test for pth-order antedependence against the unstructured (saturated) multinomial model. Simulation studies show that the score (Pearson's Chi-square) test performs better than all the other methods for complete and monotone missing data, while the likelihood ratio test is applicable for data with arbitrary missing pattern. But since the likelihood ratio test is oversensitive under the null hypothesis, we modify it by equating the expectation of the test statistic to its degrees of freedom so that it has actual size closer to nominal size. Additionally, we modify the likelihood ratio tests for use in testing for pth-order antedependence against qth-order antedependence, where q > p, and for testing nested variable-order antedependence models. We extend the methods to deal with data having a monotone or arbitrary missing pattern. For antedependence models of constant order p, we develop methods for testing transition probability stationarity and strict stationarity and for maximum likelihood estimation of parametric generalized linear models that are transition probability stationary AD(p) models. The methods are illustrated using three data sets.

In many agricultural and biological contexts, the response variable is a nonnegative integer value which we wish to explain or analyze in terms of a set of covariates. Unlike the Gaussian linear model, the response variable is discrete with a distribution that places probability mass at natural numbers only. The Poisson regression is the standard model for count data. However, assumptions of this model forces the equality between mean and variance, which may be implausible in many applications. Motivated by experimental data sets, this work intended to develop more realistic methods for the analysis of count data. We proposed a novel parametrization of the COM-Poisson distribution and explored the regression models based on it. We extended the model to allow the dispersion, as well as the mean, depending on covariates. A set of count statistical models, namely COM-Poisson, Gamma-count, discrete Weibull, generalized Poisson, double Poisson and Poisson-Tweedie, was reviewed and compared, considering the dispersion, zero-inflation, and heavy tail indexes, together with the results of data analyzes. The computational routines developed in this dissertation were organized in two R packages available on GitHub. / Em diversos estudos agrícolas e biológicos, a variável resposta é um número inteiro não negativo que desejamos explicar ou analisar em termos de um conjunto de covariáveis. Diferentemente do modelo linear Gaussiano, a variável resposta é discreta com distribuição de probabilidade definida apenas em valores do conjunto dos naturais. O modelo Poisson é o modelo padrão para dados em forma de contagens. No entanto, as suposições desse modelo forçam que a média seja igual a variância, o que pode ser implausível em muitas aplicações. Motivado por conjuntos de dados experimentais, este trabalho teve como objetivo desenvolver métodos mais realistas para a análise de contagens. Foi proposta uma nova reparametrização da distribuição COM-Poisson e explorados modelos de regressão baseados nessa distribuição. Uma extensão desse modelo para permitir que a dispersão, assim como a média, dependa de covariáveis, foi proposta. Um conjunto de modelos para contagens, nomeadamente COM-Poisson, Gamma-count, Weibull discreto, Poisson generalizado, duplo Poisson e Poisson-Tweedie, foi revisado e comparado, considerando os índices de dispersão, inflação de zero e cauda pesada, juntamente com os resultados de análises de dados. As rotinas computacionais desenvolvidas nesta dissertação foram organizadas em dois pacotes R disponíveis no GitHub.

Les copulas archimédiennes hiérarchiques ont récemment gagné en intérêt puisqu’elles généralisent la famille de copules archimédiennes, car elles introduisent une asymétrie partielle. Des algorithmes d’échantillonnages et des méthodes ont largement été développés pour de telles copules. Néanmoins, concernant l’estimation par maximum de vraisemblance et les tests d’adéquations, il est important d’avoir à disposition la densité de ces variables aléatoires. Ce travail remplie ce manque. Après une courte introduction aux copules et aux copules archimédiennes hiérarchiques, une équation générale sur les dérivées des noeuds et générateurs internes apparaissant dans la densité des copules archimédiennes hiérarchique. sera dérivée. Il en suit une formule tractable pour la densité des copules archimédiennes hiérarchiques. Des exemples incluant les familles archimédiennes usuelles ainsi que leur transformations sont présentés. De plus, une méthode numérique efficiente pour évaluer le logarithme des densités est présentée. / Nested Archimedean copulas recently gained interest since they generalize the well-known class of Archimedean copulas to allow for partial asymmetry. Sampling algorithms and strategies have been well investigated for nested Archimedean copulas. However, for likelihood based inference such as estimation or goodness-of-fit testing it is important to have the density. The present work fills this gap. After a short introduction on copula and nested Archimedean copulas, a general formula for the derivatives of the nodes and inner generators appearing in nested Archimedean copulas is developed. This leads to a tractable formula for the density of nested Archimedean copulas. Various examples including famous Archimedean families and transformations of such are given. Furthermore, a numerically efficient way to evaluate the log-density is presented.

Les copulas archimédiennes hiérarchiques ont récemment gagné en intérêt puisqu’elles généralisent la famille de copules archimédiennes, car elles introduisent une asymétrie partielle. Des algorithmes d’échantillonnages et des méthodes ont largement été développés pour de telles copules. Néanmoins, concernant l’estimation par maximum de vraisemblance et les tests d’adéquations, il est important d’avoir à disposition la densité de ces variables aléatoires. Ce travail remplie ce manque. Après une courte introduction aux copules et aux copules archimédiennes hiérarchiques, une équation générale sur les dérivées des noeuds et générateurs internes apparaissant dans la densité des copules archimédiennes hiérarchique. sera dérivée. Il en suit une formule tractable pour la densité des copules archimédiennes hiérarchiques. Des exemples incluant les familles archimédiennes usuelles ainsi que leur transformations sont présentés. De plus, une méthode numérique efficiente pour évaluer le logarithme des densités est présentée. / Nested Archimedean copulas recently gained interest since they generalize the well-known class of Archimedean copulas to allow for partial asymmetry. Sampling algorithms and strategies have been well investigated for nested Archimedean copulas. However, for likelihood based inference such as estimation or goodness-of-fit testing it is important to have the density. The present work fills this gap. After a short introduction on copula and nested Archimedean copulas, a general formula for the derivatives of the nodes and inner generators appearing in nested Archimedean copulas is developed. This leads to a tractable formula for the density of nested Archimedean copulas. Various examples including famous Archimedean families and transformations of such are given. Furthermore, a numerically efficient way to evaluate the log-density is presented.

L’adaptation côtière est un impératif pour faire face à l’élévation du niveau marin,conséquence directe du réchauffement climatique. Cependant, la mise en place d’actions et de stratégies est souvent entravée par la présence de diverses et importantes incertitudes lors de l’estimation des aléas et risques futurs. Ces incertitudes peuvent être dues à une connaissance limitée (de l’élévation du niveau marin futur par exemple) ou à la variabilité naturelle de certaines variables (les conditions de mer extrêmes). La prise en compte des incertitudes dans la chaîne d’évaluation des risques est essentielle pour une adaptation efficace.L’objectif de ce travail est de proposer une méthodologie pour la quantification des incertitudes basée sur les fonctions de croyance – un formalisme de l’incertain plus flexible que les probabilités. Les fonctions de croyance nous permettent de décrire plus fidèlement l’information incomplète fournie par des experts (quantiles,intervalles, etc.), et de combiner différentes sources d’information. L’information statistique peut quand à elle être décrite par de fonctions des croyance définies à partir de la fonction de vraisemblance. Pour la propagation d’incertitudes, nous exploitons l’équivalence mathématique entre fonctions de croyance et intervalles aléatoires, et procédons par échantillonnage Monte Carlo. La méthodologie est appliquée dans l’estimation des projections de la remontée du niveau marin global à la fin du siècle issues de la modélisation physique, d’élicitation d’avis d’experts, et de modèle semi-empirique. Ensuite, dans une étude de cas, nous évaluons l’impact du changement climatique sur les conditions de mers extrêmes et évaluons le renforcement nécessaire d’une structure afin de maintenir son niveau de performance fonctionnelle. / Coastal adaptation is an imperative to deal with the elevation of the global sealevel caused by the ongoing global warming. However, when defining adaptationactions, coastal engineers encounter substantial uncertainties in the assessment of future hazards and risks. These uncertainties may stem from a limited knowledge (e.g., about the magnitude of the future sea-level rise) or from the natural variabilityof some quantities (e.g., extreme sea conditions). A proper consideration of these uncertainties is of principal concern for efficient design and adaptation.The objective of this work is to propose a methodology for uncertainty analysis based on the theory of belief functions – an uncertainty formalism that offers greater features to handle both aleatory and epistemic uncertainties than probabilities.In particular, it allows to represent more faithfully experts’ incomplete knowledge (quantiles, intervals, etc.) and to combine multi-sources evidence taking into account their dependences and reliabilities. Statistical evidence can be modeledby like lihood-based belief functions, which are simply the translation of some inference principles in evidential terms. By exploiting the mathematical equivalence between belief functions and random intervals, uncertainty can be propagated through models by Monte Carlo simulations. We use this method to quantify uncertainty in future projections of the elevation of the global sea level by 2100 and evaluate its impact on some coastal risk indicators used in coastal design. Sea-level rise projections are derived from physical modelling, expert elicitation, and historical sea-level measurements. Then, within a methodologically-oriented case study,we assess the impact of climate change on extreme sea conditions and evaluate there inforcement of a typical coastal defence asset so that its functional performance is maintained.