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Linear mixed models and generalized linear mixed models are random-effects models widely applied to analyze clustered or hierarchical data. Generally, random effects are often assumed to be normally distributed in the context of mixed models. However, in the mixed-effects logistic model, the violation of the assumption of normally distributed random effects may result in inconsistency for estimates of some fixed effects and the variance component of random effects when the variance of the random-effects distribution is large. On the other hand, summary statistics used for assessing goodness of fit in the ordinary logistic regression models may not be directly applicable to the mixed-effects logistic models. In this dissertation, we present our investigations of two independent studies related to goodness-of-fit tests in generalized linear mixed models. First, we consider a semi-nonparametric density representation for the random effects distribution and provide a formal statistical test for testing normality of the random-effects distribution in the mixed-effects logistic models. We obtain estimates of parameters by using a non-likelihood-based estimation procedure. Additionally, we not only evaluate the type I error rate of the proposed test statistic through asymptotic results, but also carry out a bootstrap hypothesis testing procedure to control the inflation of the type I error rate and to study the power performance of the proposed test statistic. Further, the methodology is illustrated by revisiting a case study in mental health. Second, to improve assessment of the model fit in the mixed-effects logistic models, we apply the nonparametric local polynomial smoothed residuals over within-cluster continuous covariates to the unweighted sum of squares statistic for assessing the goodness-of-fit of the logistic multilevel models. We perform a simulation study to evaluate the type I error rate and the power performance for detecting a missing quadratic or interaction term of fixed effects using the kernel smoothed unweighted sum of squares statistic based on the local polynomial smoothed residuals over x-space. We also use a real data set in clinical trials to illustrate this application.

Made available in DSpace on 2014-06-11T19:31:37Z (GMT). No. of bitstreams: 0 Previous issue date: 2010-11-16Bitstream added on 2014-06-13T21:02:57Z : No. of bitstreams: 1 barbosa_l_dr_botfca.pdf: 2587351 bytes, checksum: 76e343f1e0edbbbee5cb996188d8efd2 (MD5) / É bastante comum na área agrícola, experimentos cujas variáveis respostas são contagens ou proporções. Para esse tipo de dados, utiliza-se a metodologia de modelos lineares generalizados quando as respostas são independentes. Por outro lado, quando as respostas são dependentes, há uma correlação entre as observações e isso tem que ser levado em consideração na análise, para evitar inferências incorretas sobre os coeficientes de regressão. Na literatura há técnicas disponíveis para a modelagem e análise desses dados, sendo os modelos disponíveis extensões dos modelos lineares generalizados. No presente trabalho, utiliza-se a metodologia de equação de estimação generalizada, que inclui no modelo uma matriz de correlação para a obtenção de um melhor ajuste. Outra alternativa, também abordada neste trabalho, é a utilização de um modelo linear generalizado misto, no qual o uso de efeitos aleatórios também introduz uma correlação entre observações que tenham algum efeito em comum. Essas duas metodologias são aplicadas a um conjunto de dados obtidos de um experimento para avaliar certas condições na germinação de sementes de mamona da cultivar AL Guarany 2002, com o objetivo de se verificar qual o melhor modelo de estimação para esses dados / Experiments whose response variables are counts or proportions are very common in agriculture. For this type of data, if the observational units are independent, the methodology of generalized linear models can be appropriate. On the other hand, when responses are dependent or clustered, there is a correlation between the observations and that has to be taken into consideration in the analysis to avoid incorrect inferences about the regression coefficients. In the literature there are techniques available for modeling and analyzing such type data, the models being extensions of generalized linear models. The present study explores the use of: 1) generalized estimation equations, that includes a correlation matrix to obtain a better fit; 2) generalized linear mixed models, that introduce a correlation between clustered observations though the addition of random effects in the model. These two methodologies are applied to a data set obtained from an experiment to evaluate certain conditions on the germination of seeds of castor bean cultivar AL Guarany 2002 with the objective of determining the best estimation model for such data

abstract: Though the likelihood is a useful tool for obtaining estimates of regression parameters, it is not readily available in the fit of hierarchical binary data models. The correlated observations negate the opportunity to have a joint likelihood when fitting hierarchical logistic regression models. Through conditional likelihood, inferences for the regression and covariance parameters as well as the intraclass correlation coefficients are usually obtained. In those cases, I have resorted to use of Laplace approximation and large sample theory approach for point and interval estimates such as Wald-type confidence intervals and profile likelihood confidence intervals. These methods rely on distributional assumptions and large sample theory. However, when dealing with small hierarchical datasets they often result in severe bias or non-convergence. I present a generalized quasi-likelihood approach and a generalized method of moments approach; both do not rely on any distributional assumptions but only moments of response. As an alternative to the typical large sample theory approach, I present bootstrapping hierarchical logistic regression models which provides more accurate interval estimates for small binary hierarchical data. These models substitute computations as an alternative to the traditional Wald-type and profile likelihood confidence intervals. I use a latent variable approach with a new split bootstrap method for estimating intraclass correlation coefficients when analyzing binary data obtained from a three-level hierarchical structure. It is especially useful with small sample size and easily expanded to multilevel. Comparisons are made to existing approaches through both theoretical justification and simulation studies. Further, I demonstrate my findings through an analysis of three numerical examples, one based on cancer in remission data, one related to the China’s antibiotic abuse study, and a third related to teacher effectiveness in schools from a state of southwest US. / Dissertation/Thesis / Doctoral Dissertation Statistics 2017

Orientador: Luiza Aparecida Trinca / Banca: Liciana Vaz da Arruda / Banca: Osmar Delmanto Junior / Banca: Célia Regina Lopes Zimback / Banca: Marli Teixeira de A. Minhoni / Resumo: É bastante comum na área agrícola, experimentos cujas variáveis respostas são contagens ou proporções. Para esse tipo de dados, utiliza-se a metodologia de modelos lineares generalizados quando as respostas são independentes. Por outro lado, quando as respostas são dependentes, há uma correlação entre as observações e isso tem que ser levado em consideração na análise, para evitar inferências incorretas sobre os coeficientes de regressão. Na literatura há técnicas disponíveis para a modelagem e análise desses dados, sendo os modelos disponíveis extensões dos modelos lineares generalizados. No presente trabalho, utiliza-se a metodologia de equação de estimação generalizada, que inclui no modelo uma matriz de correlação para a obtenção de um melhor ajuste. Outra alternativa, também abordada neste trabalho, é a utilização de um modelo linear generalizado misto, no qual o uso de efeitos aleatórios também introduz uma correlação entre observações que tenham algum efeito em comum. Essas duas metodologias são aplicadas a um conjunto de dados obtidos de um experimento para avaliar certas condições na germinação de sementes de mamona da cultivar AL Guarany 2002, com o objetivo de se verificar qual o melhor modelo de estimação para esses dados / Abstract: Experiments whose response variables are counts or proportions are very common in agriculture. For this type of data, if the observational units are independent, the methodology of generalized linear models can be appropriate. On the other hand, when responses are dependent or clustered, there is a correlation between the observations and that has to be taken into consideration in the analysis to avoid incorrect inferences about the regression coefficients. In the literature there are techniques available for modeling and analyzing such type data, the models being extensions of generalized linear models. The present study explores the use of: 1) generalized estimation equations, that includes a correlation matrix to obtain a better fit; 2) generalized linear mixed models, that introduce a correlation between clustered observations though the addition of random effects in the model. These two methodologies are applied to a data set obtained from an experiment to evaluate certain conditions on the germination of seeds of castor bean cultivar AL Guarany 2002 with the objective of determining the best estimation model for such data / Doutor

abstract: Spatial regression is one of the central topics in spatial statistics. Based on the goals, interpretation or prediction, spatial regression models can be classified into two categories, linear mixed regression models and nonlinear regression models. This dissertation explored these models and their real world applications. New methods and models were proposed to overcome the challenges in practice. There are three major parts in the dissertation. In the first part, nonlinear regression models were embedded into a multistage workflow to predict the spatial abundance of reef fish species in the Gulf of Mexico. There were two challenges, zero-inflated data and out of sample prediction. The methods and models in the workflow could effectively handle the zero-inflated sampling data without strong assumptions. Three strategies were proposed to solve the out of sample prediction problem. The results and discussions showed that the nonlinear prediction had the advantages of high accuracy, low bias and well-performed in multi-resolution. In the second part, a two-stage spatial regression model was proposed for analyzing soil carbon stock (SOC) data. In the first stage, there was a spatial linear mixed model that captured the linear and stationary effects. In the second stage, a generalized additive model was used to explain the nonlinear and nonstationary effects. The results illustrated that the two-stage model had good interpretability in understanding the effect of covariates, meanwhile, it kept high prediction accuracy which is competitive to the popular machine learning models, like, random forest, xgboost and support vector machine. A new nonlinear regression model, Gaussian process BART (Bayesian additive regression tree), was proposed in the third part. Combining advantages in both BART and Gaussian process, the model could capture the nonlinear effects of both observed and latent covariates. To develop the model, first, the traditional BART was generalized to accommodate correlated errors. Then, the failure of likelihood based Markov chain Monte Carlo (MCMC) in parameter estimating was discussed. Based on the idea of analysis of variation, back comparing and tuning range, were proposed to tackle this failure. Finally, effectiveness of the new model was examined by experiments on both simulation and real data. / Dissertation/Thesis / Doctoral Dissertation Statistics 2020

Arbuscular mycorrhizal (AM) fungi are key soil symbiotic microorganisms, intensively studied for their roles in improving plant fitness and their ubiquity in terrestrial ecosystems. Research on AM fungi is difficult because their obligate biotrophic nature makes it impossible to culture them in the absence of a host. Over the last three decades, Ri T-DNA transformed roots have been the gold standard to study AM fungi under in vitro conditions. However, only two host plant species (Daucus carota and Cichorium intybus) have been routinely used to in vitro propagate less than 5% of the known AM fungal species. There is much evidence that host identity can significantly affect AM symbioses, therefore, we investigated any potential host-specific effects of two novel Ri T-DNA transformed root species, Medicago truncatula and Nicotiana benthamiana, by associating them with seven AM fungal species selected based on their contrasting behaviors when grown with Ri T-DNA transformed D. carota roots. To evaluate the performance of new Ri T-DNA transformed roots to host and propagate AM fungal species, a factorial set-up was used to generate nine unique pairs of hosts (M. truncatula, N. benthamiana, D. carota) and AM fungi (Rhizophagus irregularis, R. clarus, Glomus sp.). Using statistical modeling, all pairs of hosts and AM fungi were compared by their symbiosis development (SD) and sporulation patterns in the hyphal compartments (HCs) of two-compartment Petri dishes. Our results show that 1) most of the variation between host and AM fungus pairs relating to SD or HC sporulation was explained by an interaction between host and AM fungal identity, i.e., host identity alone was not sufficient to explain AM fungal behaviour, 2) AM symbioses involving different combinations of symbiont identities trigger heterogenous fungal behaviours. This work provides a robust framework to develop and evaluate new Ri T-DNA roots for the in vitro propagation of AM fungi, an important asset for germplasm collections and biodiversity preservation.

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