Shelf life is a parameter of the lifetime distribution of a food product, usually the time until a specified proportion (1-50%) of the product has spoiled according to taste. The data used to estimate shelf life typically come from a planned experiment with sampled food items observed at specified times. The observation times are usually selected adaptively using ‘staggered sampling.’ Ad-hoc methods based on linear regression have been recommended to estimate shelf life. However, other methods based on maximizing a likelihood (MLE) have been proposed, studied, and used. Both methods assume the Weibull distribution. The observed lifetimes in shelf life studies are censored, a fact that the ad-hoc methods largely ignore. One purpose of this project is to compare the statistical properties of the ad-hoc estimators and the maximum likelihood estimator. The simulation study showed that the MLE methods have higher coverage than the regression methods, better asymptotic properties in regards to bias, and have lower median squared errors (mese) values, especially when shelf life is defined by smaller percentiles. Thus, they should be used in practice. A genetic algorithm (Hamada et al. 2001) was used to find near-optimal sampling designs. This was successfully programmed for general shelf life estimation. The genetic algorithm generally produced designs that had much smaller median squared errors than the staggered design that is used commonly in practice. These designs were radically different than the standard designs. Thus, the genetic algorithm may be used to plan studies in the future that have good estimation properties.

Cette thèse rassemble principalement des contributions en économie de la science à laquelle les deux premières parties sont consacrées. La première teste l'importance des choix méthodologiques dans la mesure de la production scientifique et étudie les canaux de diffusion de la connaissance. La deuxième s'intéresse aux déterminants individuels et locaux de la productivité des chercheurs et au différentiel de promotion entre hommes et femmes sur le marché du travail académique. Sont établis les résultats suivants : les choix méthodologiques dans la mesure de la production scientifique n'affectent que très peu les classements des institutions de recherche. Les citations et les poids associés à la qualité des journaux mesurent globalement la même productivité de la recherche. La localisation des chercheurs a un impact sur leur productivité dans la mesure où certaines universités génèrent davantage d'externalités que d'autres. Ces externalités sont plus importantes là où les chercheurs sont homogènes en terme de performances, où la diversité thématique est grande, et dans une moindre mesure dans les grands centres de recherche, lorsqu'il y a plus de femmes, de chercheurs âgés, de stars et là où les chercheurs sont connectés à des co-auteurs à l'étranger. Si les femmes sont moins souvent Professeur des Universités (par opposition à Maître de Conférences) que les hommes, ce n'est ni parce qu'elles sont discriminées dans le processus de promotion, ni que le coût de promotion (mobilité) est plus important pour elles, ni qu'elles ont des préférences différentes concernant le salaire et le prestige des institutions dans lesquelles elles travaillent. / The core of this thesis lies in the field of economics of science to which the two first parts are devoted. The first part questions the impact of methodological choices in the measurement of research productivity and studies the channels of knowledge diffusion. The second part studies the impact on individual publication records of both individual and departments' characteristics and analyse the gender gap in occupations on the academic labour market. The main results are the following: methodological choices in the measurement of research productivity do not impact the estimated hierarchy of research institutions. Citations and journal quality weights measure the same dimension of publication productivity. Location matters in the academic research activity: some departments generate more externalities than others. Externalities are higher where academics are homogeneous in terms of publication performance and have diverse research fields, and, to a lower extent, if the department is large, with more women, older academics, stars and co-authors connection to foreign departments. If women are less likely to be full Professor (with respect to Assistant Professor) than men, this is neither because they are discriminated against in the promotion process, neither because the promotion cost (mobility) is higher for them, nor because they have different preferences for salaries versus department prestige. A possible, but not tested, explanation is that women self-select themselves by participating less in or exerting lower effort during the promotion process.

Neste trabalho, apresentamos as equações de estimação generalizadas desenvolvidas por Liang e Zeger (1986), sob a ótica da teoria de funções de estimação apresentada por Godambe (1991). Essas equações de estimação são obtidas para os modelos lineares generalizados (MLGs) considerando medidas repetidas. Apresentamos também um processo iterativo para estimação dos parâmetros de regressão, assim como testes de hipóteses para esses parâmetros. Para a análise de resíduos, generalizamos para dados com medidas repetidas algumas técnicas de diagnóstico usuais em MLGs. O gráfico de probabilidade meio-normal com envelope simulado é uma proposta para avaliarmos a adequação do ajuste do modelo. Para a construção desse gráfico, simulamos respostas correlacionadas por meio de algoritmos que descrevemos neste trabalho. Por fim, realizamos aplicações a conjuntos de dados reais. / In this work, we consider the generalized estimation equations developed by Liang and Zeger (1986) focusing the theory of estimating functions presented by Godambe (1991). These estimation equations are an extension of generalized linear models (GLMs) to the analysis of repeated measurements. We present an iterative procedure to estimate the regression parameters as well as hypothesis testing of these parameters. For the residual analysis, we generalize to repeated measurements some diagnostic methods available for GLMs. The half-normal probability plot with a simulated envelope is useful for diagnosing model inadequacy and detecting outliers. To obtain this plot, we consider an algorithm for generating a set of nonnegatively correlated variables having a specified correlation structure. Finally, the theory is applied to real data sets.

Cette thèse est consacrée à l'inférence de modèles stochastiques d'évolution de l'ADN avec dépendance au contexte, l'étude portant spécifiquement sur la classe de modèles stochastiques RN95+YpR. Cette classe de modèles repose sur un renforcement des taux d'occurrence de certaines substitutions en fonction du contexte local, ce qui introduit des phénomènes de dépendance dans l'évolution des différents sites de la séquence d'ADN. Du fait de cette dépendance, le calcul direct de la vraisemblance des séquences observées met en jeu des matrices de dimensions importantes, et est en général impraticable. Au moyen d'encodages spécifiques à la classe RN95+YpR, nous mettons en évidence de nouvelles structures de dépendance spatiales pour ces modèles, qui sont associées à l'évolution des séquences d'ADN sur toute leur histoire évolutive. Ceci rend notamment possible l'utilisation de méthodes numériques particulaires, développées dans le cadre des modèles de Markov cachés, afin d'obtenir des approximations consistantes de la vraisemblance recherchée. Un autre type d'approximation de la vraisemblance, basé sur des vraisemblances composites, est également introduit. Ces méthodes d'approximation de la vraisemblance sont implémentées au moyen d'un code en C++. Elles sont mises en œuvre sur des données simulées afin d'étudier empiriquement certaines de leurs propriétés, et sur des données génomiques, notamment à des fins de comparaison de modèles d'évolution / This thesis is devoted to the inference of context-dependent evolutionary models of DNA sequences, and is specifically focused on the RN95+YPR class of stochastic models. This class of models is based on the reinforcement of some substitution rates depending on the local context, which introduces dependence phenomena between sites in the evolution of the DNA sequence. Because of these dependencies, the direct computation of the likelihood of the observed sequences involves high-dimensional matrices, and is usually infeasible. Through encodings specific to the RN95+YpR class, we highlight new spatial dependence structures for these models, which are related to the evolution of DNA sequences throughout their evolutionary history. This enables the use of particle filter algorithms, developed in the context of hidden Markov models, in order to obtain consistent approximations of the likelihood. Another type of approximation of the likelihood, based on composite likelihoods, is also introduced. These approximation methods for the likelihood are implemented in a C++ program. They are applied on simulated data to empirically investigate some of their properties, and on genomic data, especially for comparison of evolutionary models

Neste trabalho, apresentamos as equações de estimação generalizadas desenvolvidas por Liang e Zeger (1986), sob a ótica da teoria de funções de estimação apresentada por Godambe (1991). Essas equações de estimação são obtidas para os modelos lineares generalizados (MLGs) considerando medidas repetidas. Apresentamos também um processo iterativo para estimação dos parâmetros de regressão, assim como testes de hipóteses para esses parâmetros. Para a análise de resíduos, generalizamos para dados com medidas repetidas algumas técnicas de diagnóstico usuais em MLGs. O gráfico de probabilidade meio-normal com envelope simulado é uma proposta para avaliarmos a adequação do ajuste do modelo. Para a construção desse gráfico, simulamos respostas correlacionadas por meio de algoritmos que descrevemos neste trabalho. Por fim, realizamos aplicações a conjuntos de dados reais. / In this work, we consider the generalized estimation equations developed by Liang and Zeger (1986) focusing the theory of estimating functions presented by Godambe (1991). These estimation equations are an extension of generalized linear models (GLMs) to the analysis of repeated measurements. We present an iterative procedure to estimate the regression parameters as well as hypothesis testing of these parameters. For the residual analysis, we generalize to repeated measurements some diagnostic methods available for GLMs. The half-normal probability plot with a simulated envelope is useful for diagnosing model inadequacy and detecting outliers. To obtain this plot, we consider an algorithm for generating a set of nonnegatively correlated variables having a specified correlation structure. Finally, the theory is applied to real data sets.