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Semiparametric Analysis of an Expanded Cox Proportional Hazards Model with Time-varying Covariates

Semiparametric Analysis of an Expanded Cox Proportional Hazards Model with Time-varying Covariates
Author: Wenying Zheng
Publisher:
Total Pages: 126
Release: 2016
Genre:
ISBN:

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Time-varying covariates are often encountered in survival analysis. The Cox proportional hazards model can incorporate time-varying covariates, while the interpretation of regression parameters is less straightforward. We instead propose a complementary log-log survival model. When covariates are time-independent, the proposed model reduces to the Cox proportional hazards model; however, when they are time-varying, the proposed model provides a direct interpretation of regression parameters in the survival function. We develop semiparametric estimation procedures based on estimating equations, and establish the asymptotic properties of the estimators for the regression parameters and survival functions. In addition, we include weight functions to the estimating equations to improve efficiency. We demonstrate the proposed methods by simulation studies and application to the Mayo Clinic Primary Biliary Cirrhosis data and data from a landmark HIV randomized prevention trial.


Competing Risks and Multistate Models with R

Competing Risks and Multistate Models with R
Author: Jan Beyersmann
Publisher: Springer Science & Business Media
Total Pages: 249
Release: 2011-11-18
Genre: Mathematics
ISBN: 1461420350

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This book covers competing risks and multistate models, sometimes summarized as event history analysis. These models generalize the analysis of time to a single event (survival analysis) to analysing the timing of distinct terminal events (competing risks) and possible intermediate events (multistate models). Both R and multistate methods are promoted with a focus on nonparametric methods.


Likelihood Methods in Survival Analysis

Likelihood Methods in Survival Analysis
Author: Jun Ma
Publisher: CRC Press
Total Pages: 401
Release: 2024-10-01
Genre: Mathematics
ISBN: 1351109707

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Many conventional survival analysis methods, such as the Kaplan-Meier method for survival function estimation and the partial likelihood method for Cox model regression coefficients estimation, were developed under the assumption that survival times are subject to right censoring only. However, in practice, survival time observations may include interval-censored data, especially when the exact time of the event of interest cannot be observed. When interval-censored observations are present in a survival dataset, one generally needs to consider likelihood-based methods for inference. If the survival model under consideration is fully parametric, then likelihood-based methods impose neither theoretical nor computational challenges. However, if the model is semi-parametric, there will be difficulties in both theoretical and computational aspects. Likelihood Methods in Survival Analysis: With R Examples explores these challenges and provides practical solutions. It not only covers conventional Cox models where survival times are subject to interval censoring, but also extends to more complicated models, such as stratified Cox models, extended Cox models where time-varying covariates are present, mixture cure Cox models, and Cox models with dependent right censoring. The book also discusses non-Cox models, particularly the additive hazards model and parametric log-linear models for bivariate survival times where there is dependence among competing outcomes. Features Provides a broad and accessible overview of likelihood methods in survival analysis Covers a wide range of data types and models, from the semi-parametric Cox model with interval censoring through to parametric survival models for competing risks Includes many examples using real data to illustrate the methods Includes integrated R code for implementation of the methods Supplemented by a GitHub repository with datasets and R code The book will make an ideal reference for researchers and graduate students of biostatistics, statistics, and data science, whose interest in survival analysis extend beyond applications. It offers useful and solid training to those who wish to enhance their knowledge in the methodology and computational aspects of biostatistics.


Survival Analysis and Causal Inference

Survival Analysis and Causal Inference
Author: Denise Rava
Publisher:
Total Pages: 329
Release: 2021
Genre:
ISBN:

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In chapter 1 we study explained variation under the additive hazards regression model for right-censored data. We consider different approaches for developing such a measure, and focus on one that estimates the proportion of variation in the failure time explained by the covariates. We study the properties of the measure both analytically, and through extensive simulations. We apply the measure to a well-known survival dataset as well as the linked surveillance, epidemiology, and end results-Medicare database for prediction of mortality in early stage prostate cancer patients using high-dimensional claims codes. In chapter 2 we propose a new flexible method for survival prediction: DeepHazard, a neural network for time-varying risks. Prognostic models in survival analysis are aimed at understanding the relationship between patients' covariates and the distribution of survival time. Traditionally, semiparametric models, such as the Cox model, have been assumed. These often rely on strong proportionality assumptions of the hazard that might be violated in practice. Moreover, they do not often include covariates' information updated over time. Our approach is tailored for a wide range of continuous hazards forms, with the only restriction of being additive in time. A flexible implementation, allowing different optimization methods, along with any norm penalty, is developed. Numerical examples illustrate that our approach outperforms existing state-of-the-art methodology in terms of predictive capability evaluated through the C-index metric. The same is revealed on the popular real datasets as METABRIC, GBSG, ACTG and PBC. In chapter 3 we consider the conditional treatment effect for competing risks data in observational studies. While it is described as a constant difference between the hazard functions given the covariates, we do not assume the additive hazards model in order to adjust for the covariates. We derive the efficient score for the treatment effect using modern semiparametric theory, as well as two doubly robust scores with respect to both the assumed propensity score for treatment and the censoring model, and the outcome models for the competing risks. We provide the asymptotic distributions of the estimators when the two sets of working models are both correct, or when only one of them is correct. We study the inference based on these estimators using simulation. The estimators are applied to the data from a cohort of Japanese men in Hawaii followed since 1960s in order to study the effect of midlife drinking behavior on late life cognitive outcomes. In chapter 4 we consider doubly robust estimation of the causal hazard ratio in observational studies. The treatment effect of interest, described as the constant ratio between the hazard functions of thetwo potential outcomes, is parametrized by the Marginal Structural Cox Model. Under the assumption of no unmeasured confounders, causal methods, as Cox-IPW, have been developed for estimation of the treatment effect of interest. However no doubly robust methods have been proposed under the Marginal Structural Cox model. We develop an AIPW estimator for this popular model that is both model and rate-doubly robust with respect to the treatment assignment model and the conditional outcome model. The proposed estimator is applied to the data from a cohort of Japanese men in Hawaii followed since 1960s in order to study the effect of mid-life alcohol exposure on overall death.


The Frailty Model

The Frailty Model
Author: Luc Duchateau
Publisher: Springer Science & Business Media
Total Pages: 329
Release: 2007-10-23
Genre: Mathematics
ISBN: 038772835X

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Readers will find in the pages of this book a treatment of the statistical analysis of clustered survival data. Such data are encountered in many scientific disciplines including human and veterinary medicine, biology, epidemiology, public health and demography. A typical example is the time to death in cancer patients, with patients clustered in hospitals. Frailty models provide a powerful tool to analyze clustered survival data. In this book different methods based on the frailty model are described and it is demonstrated how they can be used to analyze clustered survival data. All programs used for these examples are available on the Springer website.


The Statistical Analysis of Failure Time Data

The Statistical Analysis of Failure Time Data
Author: John D. Kalbfleisch
Publisher: John Wiley & Sons
Total Pages: 462
Release: 2011-01-25
Genre: Mathematics
ISBN: 1118031237

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Contains additional discussion and examples on left truncationas well as material on more general censoring and truncationpatterns. Introduces the martingale and counting process formulation swillbe in a new chapter. Develops multivariate failure time data in a separate chapterand extends the material on Markov and semi Markovformulations. Presents new examples and applications of data analysis.


Modeling Survival Data: Extending the Cox Model

Modeling Survival Data: Extending the Cox Model
Author: Terry M. Therneau
Publisher: Springer Science & Business Media
Total Pages: 356
Release: 2013-11-11
Genre: Mathematics
ISBN: 1475732945

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This book is for statistical practitioners, particularly those who design and analyze studies for survival and event history data. Building on recent developments motivated by counting process and martingale theory, it shows the reader how to extend the Cox model to analyze multiple/correlated event data using marginal and random effects. The focus is on actual data examples, the analysis and interpretation of results, and computation. The book shows how these new methods can be implemented in SAS and S-Plus, including computer code, worked examples, and data sets.


Absolute Risk

Absolute Risk
Author: Ruth M. Pfeiffer
Publisher: CRC Press
Total Pages: 201
Release: 2017-08-10
Genre: Mathematics
ISBN: 1466561688

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Absolute Risk: Methods and Applications in Clinical Management and Public Health provides theory and examples to demonstrate the importance of absolute risk in counseling patients, devising public health strategies, and clinical management. The book provides sufficient technical detail to allow statisticians, epidemiologists, and clinicians to build, test, and apply models of absolute risk. Features: Provides theoretical basis for modeling absolute risk, including competing risks and cause-specific and cumulative incidence regression Discusses various sampling designs for estimating absolute risk and criteria to evaluate models Provides details on statistical inference for the various sampling designs Discusses criteria for evaluating risk models and comparing risk models, including both general criteria and problem-specific expected losses in well-defined clinical and public health applications Describes many applications encompassing both disease prevention and prognosis, and ranging from counseling individual patients, to clinical decision making, to assessing the impact of risk-based public health strategies Discusses model updating, family-based designs, dynamic projections, and other topics Ruth M. Pfeiffer is a mathematical statistician and Fellow of the American Statistical Association, with interests in risk modeling, dimension reduction, and applications in epidemiology. She developed absolute risk models for breast cancer, colon cancer, melanoma, and second primary thyroid cancer following a childhood cancer diagnosis. Mitchell H. Gail developed the widely used "Gail model" for projecting the absolute risk of invasive breast cancer. He is a medical statistician with interests in statistical methods and applications in epidemiology and molecular medicine. He is a member of the National Academy of Medicine and former President of the American Statistical Association. Both are Senior Investigators in the Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health.


Essays on Semiparametric Cox Proportional Hazard Models

Essays on Semiparametric Cox Proportional Hazard Models
Author: Huiyin Zhang
Publisher:
Total Pages: 111
Release: 2009
Genre: Estimation theory
ISBN:

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In this dissertation I study different versions of the semiparametric proportional hazard duration model and their practical applications under both frequentist and Bayesian econometrics frameworks. I use the unemployment spell data set that is created from the Panel Study of Income Dynamics (PSID). In Chapter 1 I study the effects of unemployment compensation and other important sociodemographic factors on unemployment duration. Whether duration dependence follows a particular function form is also examined. Discrete, semiparametric, proportional hazard models are used and compared among different specifications. I allow for nonparametric estimation of the effect of time on the unemployment exit rate. Because unobserved individual heterogeneity has the potential to bias the estimation results, we also consider gamma heterogeneity as an additional source of error in the hazard model (i.e., the so called mixed proportional hazard model, MPH). I find that the nonparametric baseline hazard estimations capture very well the shape of the empirical duration, which often does not belong to a specific parametric family; and unemployment insurance and socio-demographic aspects have significant impacts on the unemployment spell. In the second chapter I test whether different ways to resume work, such as new job and recall, have different duration behaviors. Hence a semiparametric dependent competing risks proportional hazard model is specified. Identifiability of such model is also discussed. By assuming linearity on the baseline hazard at each time interval, I allow for unrestricted correlation between the competing risks. My model guarantees that the unobserved failure occurs later than the observed failure at any possible time point, and censored observations are accommodated explicitly in the model specification. The estimated correlation coefficient suggests that recall duration and new job duration have a positive relationship that may not be negligible. We also find that there is significant difference in the hazard structure of returning to the same employer and a different employer. Different from the first two chapters, in the third chapter I investigate the ordered probit duration model semiparametrically using the Bayesian Markov Chain Monte Carlo (MCMC) methods. I develop and estimate the model without considering unobserved heterogeneity, and noninformative priors are assumed for both the baseline hazard and regressor parameters. Hybrid Metropolis-Hastings/Gibbs sampler is employed to speed up chain mixture. Convergence of the chains is assessed by the Gelman-Rubin scale reduction factor. Applications on the PSID unemployment duration data demonstrate that the proposed model and estimation method perform well.