In this thesis, ties and time-varying covariates in survival analysis are investigated. There are two types of ties: ties between event times (Type 1 ties) and ties between event times and the time that discrete time-varying covariates change or "jump"(Type 2 ties). The Cox proportional hazards model is one of the most important regression models for survival analysis. Methods for including Type 1 ties and time-varying covariates in the Cox proportional hazards model are well established in previous studies, but Type 2 ties have been ignored in the literature. This thesis discusses the effect of Type 2 ties on Cox's partial likelihood, the current default method to treat Type 2 ties in statistical packages SAS and R (called Fail before Jump in this thesis), and proposes alternative methods (Random and Equally Weighted) for Type 2 ties. A simulation study as well as an analysis of data sets from real research both suggest that both Random and Equally Weighted methods perform better than the other two methods. Also the effect of the percentages of Type 1 and Type 2 ties on these methods for handling both types of ties is discussed. / NSERC

Os modelos de fragilidade são utilizados para modelar as possíveis associações entre os tempos de sobrevivência. Uma outra alternativa desenvolvida para modelar a dependência entre dados multivariados é o uso dos modelos baseados em funções cópulas. Neste trabalho propusemos dois modelos de sobrevivência derivados das cópulas de Ali- Mikhail-Haq (AMH) e de Frank para modelar a dependência de dados bivariados na presença de covariáveis e observações censuradas. Para fins inferenciais, realizamos uma abordagem bayesiana usando métodos Monte Carlo em Cadeias de Markov (MCMC). Algumas discussões sobre os critérios de seleção de modelos são apresentadas. Com o objetivo de detectar observações influentes utilizamos o método bayesiano de análise de influência de deleção de casos baseado na divergência ψ. Por fim, mostramos a aplicabilidade dos modelos propostos a conjuntos de dados simulados e reais. Apresentamos, também, um novo modelo de sobrevivência bivariado com fração de cura, que leva em consideração três configurações para o mecanismo de ativação latente: ativação aleatória, primeira ativação é última ativação. Aplicamos este modelo a um conjunto de dados de empréstimo de Crédito Direto ao modo do Consumidor (DCC) e comparamos os ajustes por meio dos critérios bayesianos de seleção de modelos para verificar qual dos três modelos melhor se ajustou. Por fim, mostramos nossa proposta futura para a continuação da pesquisa. / The frailty models are used to model the possible associations between survival times. Another alternative developed for modeling the dependence between multivariate data is the use of models based on copulas functions. In this paper we propose two derived survival models of copula of the Ali-Mikhail-Haq (AMH) and of the Frank to model the dependence of bivariate data in the presence of covariates and censored observations. For inferential purposes, we conducted a Bayesian approach using Monte Carlo methods in Markov Chain (MCMC). Some discussions on the model selection criteria were presented. In order to detect influential observations we use the Bayesian method of cases of deletion of influence analysis based on the difference ψ. Finally, we show the applicability of the proposed models to sets of simulated and real data. We present, too, a new survival model with bivariate fraction of healing, which takes into account three settings for the latent activation mechanism: random activation, first activation and final activation. We apply this model to a set of Direct Credit loan data to the Consumer mode (DCC) and compare the settings, through Bayesian criteria for selection of models, which of the three models best fit. Finally, we show our future proposal for further research.

In HIV/AIDS studies, viral load (the number of copies of HIV-1 RNA) and CD4 cell counts are important biomarkers of the severity of viral infection, disease progression, and treatment evaluation. Recently, joint models, which have the capability on the bias reduction and estimates' efficiency improvement, have been developed to assess the longitudinal process, survival process, and the relationship between them simultaneously. However, the majority of the joint models are based on mean regression, which concentrates only on the mean effect of outcome variable conditional on certain covariates. In fact, in HIV/AIDS research, the mean effect may not always be of interest. Additionally, if obvious outliers or heavy tails exist, mean regression model may lead to non-robust results. Moreover, due to some data features, like left-censoring caused by the limit of detection (LOD), covariates with measurement errors and skewness, analysis of such complicated longitudinal and survival data still poses many challenges. Ignoring these data features may result in biased inference. Compared to the mean regression model, quantile regression (QR) model belongs to a robust model family, which can give a full scan of covariate effect at different quantiles of the response, and may be more robust to extreme values. Also, QR is more flexible, since the distribution of the outcome does not need to be strictly specified as certain parametric assumptions. These advantages make QR be receiving increasing attention in diverse areas. To the best of our knowledge, few study focuses on the QR-based joint models and applies to longitudinal-survival data with multiple features. Thus, in this dissertation research, we firstly developed three QR-based joint models via Bayesian inferential approach, including: (i) QR-based nonlinear mixed-effects joint models for longitudinal-survival data with multiple features; (ii) QR-based partially linear mixed-effects joint models for longitudinal data with multiple features; (iii) QR-based partially linear mixed-effects joint models for longitudinal-survival data with multiple features. The proposed joint models are applied to analyze the Multicenter AIDS Cohort Study (MACS) data. Simulation studies are also implemented to assess the performance of the proposed methods under different scenarios. Although this is a biostatistical methodology study, some interesting clinical findings are also discovered.

Submitted by Ronildo Prado (ronisp@ufscar.br) on 2017-08-17T14:39:42Z No. of bitstreams: 1 DissTRR.pdf: 2739559 bytes, checksum: 80c76b7b0d4fcf15e1c9962556cd8745 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-08-17T14:39:52Z (GMT) No. of bitstreams: 1 DissTRR.pdf: 2739559 bytes, checksum: 80c76b7b0d4fcf15e1c9962556cd8745 (MD5) / Approved for entry into archive by Ronildo Prado (ronisp@ufscar.br) on 2017-08-17T14:39:58Z (GMT) No. of bitstreams: 1 DissTRR.pdf: 2739559 bytes, checksum: 80c76b7b0d4fcf15e1c9962556cd8745 (MD5) / Made available in DSpace on 2017-08-17T14:40:04Z (GMT). No. of bitstreams: 1 DissTRR.pdf: 2739559 bytes, checksum: 80c76b7b0d4fcf15e1c9962556cd8745 (MD5) Previous issue date: 2017-03-31 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) / The frailty models are used to model the possible associations between survival times. Another alternative developed for modeling the dependence between multivariate data is the use of models based on copulas functions. In this paper we propose two derived survival models of copula of the Ali-Mikhail-Haq (AMH) and of the Frank to model the dependence of bivariate data in the presence of covariates and censored observations. For inferential purposes, we conducted a Bayesian approach using Monte Carlo methods in Markov Chain (MCMC). Some discussions on the model selection criteria were presented. In order to detect influential observations we use the Bayesian method of cases of deletion of influence analysis based on the difference ^. Finally, we show the applicability of the proposed models to sets of simulated and real data. We present, too, a new survival model with bivariate fraction of healing, which takes into account three settings for the latent activation mechanism: random activation, first activation and final activation. We apply this model to a set of Direct Credit loan data to the Consumer mode (DCC) and compare the settings, through Bayesian criteria for selection of models, which of the three models best fit. Finally, we show our future proposal for further research. / Os modelos de fragilidade são utilizados para modelar as possíveis associações entre os tempos de sobrevivência. Uma outra alternativa desenvolvida para modelar a dependência entre dados multivariados e o uso dos modelos baseados em funções cápulas. Neste trabalho propusemos dois modelos de sobrevivência derivados das copulas de Ali-Mikhail-Haq (AMH) e de Frank para modelar a dependência de dados bivariados na presença de covariáveis e observações censuradas. Para fins inferenciais, realizamos uma abordagem bayesiana usando métodos Monte Carlo em Cadeias de Markov (MCMC). Algumas discussões sobre os critérios de seleção de modelos são apresentadas. Com o objetivo de detectar observações influentes utilizamos o método bayesiano de analise de influencia de deleção de casos baseado na divergência. Por fim, mostramos a aplicabilidade dos modelos propostos a conjuntos de dados simulados e reais. Apresentamos, também, um novo modelo de sobrevivência bivariado com fração de cura, que leva em consideração três configurações para o mecanismo de ativação latente: ativação aleatória, primeira ativação e áltima ativação. Aplicamos este modelo a um conjunto de dados de empréstimo de Credito Direto ao modo do Consumidor (DCC) e comparamos os ajustes por meio dos critérios bayesianos de seleção de modelos para verificar qual dos três modelos melhor se ajustou. Por fim, mostramos nossa proposta futura para a continuaçaão da pesquisa.

Le design standard des essais randomisés de phase III suppose le recrutement d'un grand nombre de patients pour assurer un risque α de 0.025 unilatéral et une puissance d'au moins 80%. Ceci s'avérer difficile dans les maladies rares, ou encore si le traitement cible une population spécifique définie par un sous-type moléculaire rare. Nous avons évalué par simulation la performance d'une série d'essais randomisés. Au terme de chaque essai, s'il est associé à une amélioration significative, le traitement expérimental devient le contrôle de l'essai suivant. Les designs ont été évalués pour différents taux de recrutement, différentes sévérités de la maladie, et différentes distributions hypothétiques des effets d'un futur traitement. Nous avons montré, que sous des hypothèses raisonnables, une série d'essais de plus petite taille et avec un risque α relâché est associée à un plus grand bénéfice à long terme que deux essais de design standard. Nous avons enrichi cette approche avec des designs plus flexibles incluant des analyses intermédiaires d'efficacité et/ou futilité, et des designs adaptatifs à trois bras avec sélection de traitement. Nous avons montré qu'une analyse intermédiaire avec une règle d'arrêt pour futilité était associé à un gain supplémentaire et à une meilleure maitrise du risque, contrairement aux règles d'arrêt pour efficacité qui ne permettent pas d'améliorer la performance. Les séries d'essais à trois bras sont systématiquement plus performants que les séries d'essais à deux bras. Dans la troisième de la thèse, nous avons étudié les essais randomisés évaluant un algorithme de traitement plutôt que l'efficacité d'un seul traitement. Le traitement expérimental est déterminé selon la mutation. Nous avons comparé deux méthodes basées sur le modèles de Cox à effets aléatoires pour l'estimation de l'effet traitement dans chaque mutation : Maximum Integrated Partial Likellihood (MIPL) en utilisant le package coxme et Maximum H-Likelihood (MHL) en utilisant le package frailtyHL. La performance de la méthode MIPL est légèrement meilleure. En présence d'un effet traitement hétérogène, les deux méthodes sousestime l'effet dans les mutations avec un large effet, et le surestime dans les mutations avec un modeste effet. / Large sample sizes are required in randomized trials designed to meet typical one-sided α-level of 0.025 and at least 80% power. This may be unachievable in a reasonable time frame even with international collaborations. It is either because the medical condition is rare, or because the trial focuses on an uncommon subset of patients with a rare molecular subtype where the treatment tested is deemed relevant. We simulated a series of two-arm superiority trials over a long research horizon (15 years). Within the series of trials, the treatment selected after each trial becomes the control treatment of the next one. Different disease severities, accrual rates, and hypotheses of how treatments improve over time were considered. We showed that compared with two larger trials with the typical one-sided α-level of 0.025, performing a series of small trials with relaxed α-levels leads on average to larger survival benefits over a long research horizon, but also to higher risk of selecting a worse treatment at the end of the research period. We then extended this framework with more 'flexible' designs including interim analyses for futility and/or efficacy, and three-arm adaptive designs with treatment selection at interim. We showed that including an interim analysis with a futility rule is associated with an additional survival gain and a better risk control as compared to series with no interim analysis. Including an interim analysis for efficacy yields almost no additional gain. Series based on three-arm trials are associated with a systematic improvement of the survival gain and the risk control as compared to series of two-arm trials. In the third part of the thesis, we examined the issue of randomized trials evaluating a treatment algorithm instead of a single drugs' efficacy. The treatment in the experimental group depends on the mutation, unlike the control group. We evaluated two methods based on the Cox frailty model to estimate the treatment effect in each mutation: Maximum Integrated Partial Likellihood (MIPL) using package coxme and Maximum H-Likelihood (MHL) using package frailtyHL. MIPL method performs slightly better. In presence of a heterogeneous treatment effect, the two methods underestimate the treatment effect in mutations where the treatment effect is large, and overestimates the treatment effect in mutations where the treatment effect is small.

No description available.

如何藉由DNA微陣列資料跟存活資料的資訊來找出基因表現定型一直是個重要的議題。這些研究的主要目標是從大量的基因中找出那些真正跟存活時間或其它重要的臨床結果有顯著關係的小部分。Threshold Gradient Directed Regularization (TGDR)是ㄧ種已經被應用在高維度迴歸問題中能同時處理變數選取以及模型配適的演算法。然而，TGDR採用一種梯度投影型態的演算法使得收斂速率緩慢。在本篇論文中，我們建議新的包含Newton-Raphson求解演算法類型的改良版TGDR方法。我們建議的方法有類似TGDR的特性但卻有比較快的收斂速率。文中並利用一筆附有設限存活時間的真實微陣列癌症資料來做示範。 本篇論文的第二部份是關於適用於區間設限存活資料的重複抽樣Peto-Peto檢定。這個重複抽樣Peto-Peto檢定能夠評估存活函數估計方法的檢定力，例如Turnbull的估計方法以及Kaplan-Meier的估計方法。這個檢定方法顯示出在區間設限資料時Kaplan-Meier的估計方法的檢定力要比Turnbull的估計方法的檢定力來得低。這個檢定方法將以模擬的區間設限資料以及一筆真實關於乳癌研究的區間設限資料來說明。 / Analyzing censored survival data with high-dimensional covariates arising from the microarray data has been an important issue. The main goal is to find genes that have pivotal influence with patient's survival time or other important clinical outcomes. Threshold Gradient Directed Regularization (TGDR) method has been used for simultaneous variable selection and model building in high-dimensional regression problems. However, the TGDR method adopts a gradient-projection type of method and would have slow convergence rate. In this thesis, we proposed Modified TGDR algorithms which incorporate Newton-Raphson type of search algorithm. Our proposed approaches have the similar characteristics with TGDR but faster convergence rates. A real cancer microarray data with censored survival times is used for demonstration. The second part of this thesis is about a proposed resampling based Peto-Peto test for survival functions on interval censored data. The proposed resampling based Peto-Peto test can evaluate the power of survival function estimation methods, such as Turnbull’s Procedure and Kaplan-Meier estimate. The test shows that the power based on Kaplan-Meier estimate is lower than that based on Turnbull’s estimation on interval censored data. This proposed test is demonstrated on simulated data and a real interval censored data from a breast cancer study.

Made available in DSpace on 2015-03-03T15:28:31Z (GMT). No. of bitstreams: 1 JoaoBC_DISSERT_partes_autorizadas.pdf: 252147 bytes, checksum: e830f27faffa86c9087da28e43e699fd (MD5) Previous issue date: 2010-05-28 / Coordena??o de Aperfei?oamento de Pessoal de N?vel Superior / We considered prediction techniques based on models of accelerated failure time with random e ects for correlated survival data. Besides the bayesian approach through empirical Bayes estimator, we also discussed about the use of a classical predictor, the Empirical Best Linear Unbiased Predictor (EBLUP). In order to illustrate the use of these predictors, we considered applications on a real data set coming from the oil industry. More speci - cally, the data set involves the mean time between failure of petroleum-well equipments of the Bacia Potiguar. The goal of this study is to predict the risk/probability of failure in order to help a preventive maintenance program. The results show that both methods are suitable to predict future failures, providing good decisions in relation to employment and economy of resources for preventive maintenance. / Consideramos t?cnicas de predi??o baseadas em modelos de tempo de falha acelerado com efeito aleat?rio para dados de sobreviv?ncia correlacionados. Al?m do enfoque bayesiano atrav?s do Estimador de Bayes Emp?rico, tamb?m discutimos sobre o uso de um m?todo cl?ssico, o Melhor Preditor Linear N?o Viciado Emp?rico (EBLUP), nessa classe de modelos. Para ilustrar a utilidade desses m?todos, fazemos aplica??es a um conjunto de dados reais envolvendo tempos entre falhas de equipamentos de po?os de petr?leo da Bacia Potiguar. Neste contexto, o objetivo ? predizer os riscos/probabilidades de falha com a finalidade de subsidiar programas de manuten??o preventiva. Os resultados obtidos mostram que ambos os m?todos s?o adequados para prever falhas futuras, proporcionando boas decis?es em rela??o ao emprego e economia de recursos para manuten??o preventiva

Cette thèse a été conçu pour explorer les modèles dynamiques de régression, d’évaluer les inférences statistiques pour l’analyse des données de survie et de fiabilité. Ces modèles de régression dynamiques que nous avons considérés, y compris le modèle des hasards proportionnels paramétriques et celui de la vie accélérée avec les variables qui peut-être dépendent du temps. Nous avons discuté des problèmes suivants dans cette thèse.Nous avons présenté tout d’abord une statistique de test du chi-deux généraliséeY2nquiest adaptative pour les données de survie et fiabilité en présence de trois cas, complètes,censurées à droite et censurées à droite avec les covariables. Nous avons présenté en détailla forme pratique deY2nstatistique en analyse des données de survie. Ensuite, nous avons considéré deux modèles paramétriques très flexibles, d’évaluer les significations statistiques pour ces modèles proposées en utilisantY2nstatistique. Ces modèles incluent du modèle de vie accélérés (AFT) et celui de hasards proportionnels (PH) basés sur la distribution de Hypertabastic. Ces deux modèles sont proposés pour étudier la distribution de l’analyse de la duré de survie en comparaison avec d’autre modèles paramétriques. Nous avons validé ces modèles paramétriques en utilisantY2n. Les études de simulation ont été conçus.Dans le dernier chapitre, nous avons proposé les applications de ces modèles paramétriques à trois données de bio-médicale. Le premier a été fait les données étendues des temps de rémission des patients de leucémie aiguë qui ont été proposées par Freireich et al. sur la comparaison de deux groupes de traitement avec des informations supplémentaires sur les log du blanc du nombre de globules. Elle a montré que le modèle Hypertabastic AFT est un modèle précis pour ces données. Le second a été fait sur l’étude de tumeur cérébrale avec les patients de gliome malin, ont été proposées par Sauerbrei & Schumacher. Elle a montré que le meilleur modèle est Hypertabastic PH à l’ajout de cinq variables de signification. La troisième demande a été faite sur les données de Semenova & Bitukov, à concernant les patients de myélome multiple. Nous n’avons pas proposé un modèle exactement pour ces données. En raison de cela était les intersections de temps de survie.Par conséquent, nous vous conseillons d’utiliser un autre modèle dynamique que le modèle de la Simple Cross-Effect à installer ces données. / This thesis was designed to explore the dynamic regression models, assessing the sta-tistical inference for the survival and reliability data analysis. These dynamic regressionmodels that we have been considered including the parametric proportional hazards andaccelerated failure time models contain the possibly time-dependent covariates. We dis-cussed the following problems in this thesis.At first, we presented a generalized chi-squared test statisticsY2nthat is a convenient tofit the survival and reliability data analysis in presence of three cases: complete, censoredand censored with covariates. We described in detail the theory and the mechanism to usedofY2ntest statistic in the survival and reliability data analysis. Next, we considered theflexible parametric models, evaluating the statistical significance of them by usingY2nandlog-likelihood test statistics. These parametric models include the accelerated failure time(AFT) and a proportional hazards (PH) models based on the Hypertabastic distribution.These two models are proposed to investigate the distribution of the survival and reliabilitydata in comparison with some other parametric models. The simulation studies were de-signed, to demonstrate the asymptotically normally distributed of the maximum likelihood estimators of Hypertabastic’s parameter, to validate of the asymptotically property of Y2n test statistic for Hypertabastic distribution when the right censoring probability equal 0% and 20%.n the last chapter, we applied those two parametric models above to three scenes ofthe real-life data. The first one was done the data set given by Freireich et al. on thecomparison of two treatment groups with additional information about log white blood cellcount, to test the ability of a therapy to prolong the remission times of the acute leukemiapatients. It showed that Hypertabastic AFT model is an accurate model for this dataset.The second one was done on the brain tumour study with malignant glioma patients, givenby Sauerbrei & Schumacher. It showed that the best model is Hypertabastic PH onadding five significance covariates. The third application was done on the data set given by Semenova & Bitukov on the survival times of the multiple myeloma patients. We did not propose an exactly model for this dataset. Because of that was an existing oneintersection of survival times. We, therefore, suggest fitting other dynamic model as SimpleCross-Effect model for this dataset.

Indiana University-Purdue University Indianapolis (IUPUI) / Epidemiologic and clinical studies routinely collect longitudinal measures of multiple outcomes. These longitudinal outcomes can be used to establish the temporal order of relevant biological processes and their association with the onset of clinical symptoms. In the first part of this thesis, we proposed to use bivariate change point models for two longitudinal outcomes with a focus on estimating the correlation between the two change points. We adopted a Bayesian approach for parameter estimation and inference. In the second part, we considered the situation when time-to-event outcome is also collected along with multiple longitudinal biomarkers measured until the occurrence of the event or censoring. Joint models for longitudinal and time-to-event data can be used to estimate the association between the characteristics of the longitudinal measures over time and survival time. We developed a maximum-likelihood method to joint model multiple longitudinal biomarkers and a time-to-event outcome. In addition, we focused on predicting conditional survival probabilities and evaluating the predictive accuracy of multiple longitudinal biomarkers in the joint modeling framework. We assessed the performance of the proposed methods in simulation studies and applied the new methods to data sets from two cohort studies. / National Institutes of Health (NIH) Grants R01 AG019181, R24 MH080827, P30 AG10133, R01 AG09956.