Phylogenetics is the study of the evolutionary relationship between species. Inference of phylogeny relies heavily on statistical models that have been extended and refined tremendously over the past years into very complex hierarchical models. Paper I introduces probabilistic graphical models to statistical phylogenetics and elaborates on the potential advantages a unified graphical model representation could have for the community, e.g., by facilitating communication and improving reproducibility of statistical analyses of phylogeny and evolution. Once the phylogeny is reconstructed it is possible to infer the rates of diversification (speciation and extinction). In this thesis I extend the birth-death process model, so that it can be applied to incompletely sampled phylogenies, that is, phylogenies of only a subsample of the presently living species from one group. Previous work only considered the case when every species had the same probability to be included and here I examine two alternative sampling schemes: diversified taxon sampling and cluster sampling. Paper II introduces these sampling schemes under a constant rate birth-death process and gives the probability density for reconstructed phylogenies. These models are extended in Paper IV to time-dependent diversification rates, again, under different sampling schemes and applied to empirical phylogenies. Paper III focuses on fast and unbiased simulations of reconstructed phylogenies. The efficiency is achieved by deriving the analytical distribution and density function of the speciation times in the reconstructed phylogeny. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 1: Manuscript. Paper 4: Accepted.</p>

The aim of this thesis is to formulate and implement an algorithm that calculates the probability for two genes being orthologs, given a gene tree and a species tree. To do this, reconciliations between the gene tree and the species trees are used. A birth and death process is used to model the evolution, and used to calculate the orthology probability. The birth and death parameters are approximated with a Markov Chain Monte Carlo (MCMC). A MCMC framework for probability calculations of reconciliations written by Arvestad et al. (2003) is used. Rules for orthologous reconciliations are developed and implemented to calculate the probability for the reconciliations that have two genes as orthologs. The rules where integrated with the Arvestad et al. (2003) framework, and the algorithm was then validated and tested.

<p>The aim of this thesis is to formulate and implement an algorithm that calculates the probability for two genes being orthologs, given a gene tree and a species tree. To do this, reconciliations between the gene tree and the species trees are used. A birth and death process is used to model the evolution, and used to calculate the orthology probability. The birth and death parameters are approximated with a Markov Chain Monte Carlo (MCMC). A MCMC framework for probability calculations of reconciliations written by Arvestad et al. (2003) is used. Rules for orthologous reconciliations are developed and implemented to calculate the probability for the reconciliations that have two genes as orthologs. The rules where integrated with the Arvestad et al. (2003) framework, and the algorithm was then validated and tested.</p>

Use of progression-free survival in the evaluation of clinical interventions is hampered by a variety of issues, including censoring patterns not addressed in the usual methods for survival analysis. Progression can be right-censored before survival or interval-censored between inspection times. Current practice calls for imputing events to their time of detection. Such an approach is prone to bias, underestimates standard errors and makes inefficient use of the data at hand. Moreover a composite outcome prevents inference about the actual treatment effect on the risk of progression. This thesis develops semiparametric and sieve maximum likelihood estimators to more formally analyze progression-related endpoints. For the special case where death rarely precedes progression, a Cox-Aalen model is proposed for regression analysis of time-to-progression under intermittent inspection. The general setting considering both progression and survival is examined with a Markov Cox-type illness-death model under various censoring schemes. All of the resulting estimators globally converge to the truth slower than the parametric rate, but their finite-dimensional components are asymptotically efficient. Numerical studies suggest that the new methods perform better than their imputation-based alternatives under moderate to large samples having higher rates of censoring.

Conduzida na cidade de Porto Alegre, Brasil, a pesquisa etnográfica aqui apresentada descreve as dinâmicas no interior de um conjunto de mediações do complexo funerário, que não somente perpassa diferentes instâncias institucionais e econômicas, mas também modelam o processo de fabricação da morte e da pessoa morta através de intervenções físicas no corpo e da criação de uma memória a ela relacionada. Morte é, portanto, mais do que a destituição de uma vida: é a instituição de um novo estado, significa tornar-se algo. Um novo conjunto de documentos é requerido e há uma transposição de estatutos jurídicos. Assim, os circuitos funerários atuam na construção desse novo estado enquanto, simultaneamente, reconhecem a presença da pessoa morta nessa dinâmica por meio da imposição de uma presença moral e corpórea. A pessoa morta, não sendo um locus de passividade, mostra a sua vida ao impor padrões de comportamento nas negociações concernentes ao seu funeral, assim como ao influenciar escolhas e decisões. / Conducted in the city of Porto Alegre, Brazil, the ethnographic research presented by this work describes the dynamics within a set of mediations, which not only pervades different institutional and economic instances, but also shapes the construction process of death and of the dead person through a physical intervention on the body as well as through the creation of a specific memory. Death is thus more than the mere destitution of a life: it is the institution of a new state, it means becoming something else. A new set of papers are in order as much as the transposition of the legal status. The funeral circuits are hence acting upon the construction of this new state while simultaneously acknowledging the dead person’s presence through the imposition of a moral and corporeal presence. The dead person, not being a locus of passivity, displays his/hers life by setting behavioral guidelines in dealings concerning his/hers funeral arrangements, as well as by influencing choices and decisions through his/hers presence within the aforementioned dynamics.

Conduzida na cidade de Porto Alegre, Brasil, a pesquisa etnográfica aqui apresentada descreve as dinâmicas no interior de um conjunto de mediações do complexo funerário, que não somente perpassa diferentes instâncias institucionais e econômicas, mas também modelam o processo de fabricação da morte e da pessoa morta através de intervenções físicas no corpo e da criação de uma memória a ela relacionada. Morte é, portanto, mais do que a destituição de uma vida: é a instituição de um novo estado, significa tornar-se algo. Um novo conjunto de documentos é requerido e há uma transposição de estatutos jurídicos. Assim, os circuitos funerários atuam na construção desse novo estado enquanto, simultaneamente, reconhecem a presença da pessoa morta nessa dinâmica por meio da imposição de uma presença moral e corpórea. A pessoa morta, não sendo um locus de passividade, mostra a sua vida ao impor padrões de comportamento nas negociações concernentes ao seu funeral, assim como ao influenciar escolhas e decisões. / Conducted in the city of Porto Alegre, Brazil, the ethnographic research presented by this work describes the dynamics within a set of mediations, which not only pervades different institutional and economic instances, but also shapes the construction process of death and of the dead person through a physical intervention on the body as well as through the creation of a specific memory. Death is thus more than the mere destitution of a life: it is the institution of a new state, it means becoming something else. A new set of papers are in order as much as the transposition of the legal status. The funeral circuits are hence acting upon the construction of this new state while simultaneously acknowledging the dead person’s presence through the imposition of a moral and corporeal presence. The dead person, not being a locus of passivity, displays his/hers life by setting behavioral guidelines in dealings concerning his/hers funeral arrangements, as well as by influencing choices and decisions through his/hers presence within the aforementioned dynamics.

Conduzida na cidade de Porto Alegre, Brasil, a pesquisa etnográfica aqui apresentada descreve as dinâmicas no interior de um conjunto de mediações do complexo funerário, que não somente perpassa diferentes instâncias institucionais e econômicas, mas também modelam o processo de fabricação da morte e da pessoa morta através de intervenções físicas no corpo e da criação de uma memória a ela relacionada. Morte é, portanto, mais do que a destituição de uma vida: é a instituição de um novo estado, significa tornar-se algo. Um novo conjunto de documentos é requerido e há uma transposição de estatutos jurídicos. Assim, os circuitos funerários atuam na construção desse novo estado enquanto, simultaneamente, reconhecem a presença da pessoa morta nessa dinâmica por meio da imposição de uma presença moral e corpórea. A pessoa morta, não sendo um locus de passividade, mostra a sua vida ao impor padrões de comportamento nas negociações concernentes ao seu funeral, assim como ao influenciar escolhas e decisões. / Conducted in the city of Porto Alegre, Brazil, the ethnographic research presented by this work describes the dynamics within a set of mediations, which not only pervades different institutional and economic instances, but also shapes the construction process of death and of the dead person through a physical intervention on the body as well as through the creation of a specific memory. Death is thus more than the mere destitution of a life: it is the institution of a new state, it means becoming something else. A new set of papers are in order as much as the transposition of the legal status. The funeral circuits are hence acting upon the construction of this new state while simultaneously acknowledging the dead person’s presence through the imposition of a moral and corporeal presence. The dead person, not being a locus of passivity, displays his/hers life by setting behavioral guidelines in dealings concerning his/hers funeral arrangements, as well as by influencing choices and decisions through his/hers presence within the aforementioned dynamics.

This research investigates existing relationships between the three apparently unrelated subjects: Markov process, Semigroups and Partial difierential equations. Markov processes define semigroups through their transition functions. Conversely particular semigroups determine transition functions and can be regarded as Markov processes. We have exploited these relationships to study some Markov chains. The infnitesimal generator of a Feller semigroup on the closure of a bounded domain of Rn; (n ^ 2), is an integro-diferential operator in the interior of the domain and verifes a boundary condition. The existence of a Feller semigroup defined by a diferential operator and a boundary condition is due to the existence of solution of a bounded value problem. From this result other existence suficient conditions on the existence of Feller semigroups have been obtained and we have applied some of them to construct Feller semigroups on the unity disk of R2. / Decision Sciences / M. Sc. (Operations Research)

This research investigates existing relationships between the three apparently unrelated subjects: Markov process, Semigroups and Partial difierential equations. Markov processes define semigroups through their transition functions. Conversely particular semigroups determine transition functions and can be regarded as Markov processes. We have exploited these relationships to study some Markov chains. The infnitesimal generator of a Feller semigroup on the closure of a bounded domain of Rn; (n ^ 2), is an integro-diferential operator in the interior of the domain and verifes a boundary condition. The existence of a Feller semigroup defined by a diferential operator and a boundary condition is due to the existence of solution of a bounded value problem. From this result other existence suficient conditions on the existence of Feller semigroups have been obtained and we have applied some of them to construct Feller semigroups on the unity disk of R2. / Decision Sciences / M. Sc. (Operations Research)

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