Carlos Daniel Paulino

Binomial Regression with Misclassification

Motivated by a study of human papillomavirus infection in women, we present a Bayesian binomial regression analysis in which the response is subject to an unconstrained misclassification process. Our iterative approach provides inferences for the parameters that describe the relationships of the covariates with the response and for the misclassification probabilities. Furthermore, our approach applies to any meaningful generalized linear model, making model selection possible. Finally, it is straightforward to extend it to multinomial settings.

Bayesian analysis of correlated misclassified binary data

A Bayesian analysis for a random effect binary logistic regression model in the presence of misclassified data is considered. The introduction of a random effect captures the possible correlation among the binary data in each covariate pattern and hence may provide a good alternative to standard models in terms of overall fit. Markov Chain Monte Carlo methods are applied to perform the computations needed to draw inferences and make model assessment, through an illustrative example involving a real medical data set.

ON IDENTIFIABILITY OF PARAMETRIC STATISTICAL MODELS

This is a review article on statistical identifiability. Besides the definition of the main concepts, we deal with several questions relevant to the statistician: parallelism between parametric identifiability and sample sufficiency; relationship of identifiability with measures of sample information and with the inferential concept of estimability; several strategies of making inferences in unidentifiable models with emphasis on the distinct behaviour of the classical and Bayesian approaches. The concepts, ideas and methods discussed are illustrated with simple examples of statistical models.

Non-homogeneous Poisson models with a change-point: an application to ozone peaks in Mexico city

In this paper, we use some non-homogeneous Poisson models in order to study the behavior of ozone measurements in Mexico City. We assume that the number of ozone peaks follows a non-homogeneous Poisson process. We consider four types of rate function for the Poisson process: power law, Musa–Okumoto, Goel–Okumoto, and a generalized Goel–Okumoto rate function. We also assume that a change-point may or may not be present. The analysis of the problem is performed by using a Bayesian approach via Markov chain Monte Carlo methods. The best model is chosen using the DIC criterion as well as graphical approach.

A statistical model investigating the prevalence of tuberculosis in New York City using counting processes with two change-points

We considered a Bayesian analysis for the prevalence of tuberculosis cases in New York City from 1970 to 2000. This counting dataset presented two change-points during this period. We modelled this counting dataset considering non-homogeneous Poisson processes in the presence of the two-change points. A Bayesian analysis for the data is considered using Markov chain Monte Carlo methods. Simulated Gibbs samples for the parameters of interest were obtained using WinBugs software.

Allelic penetrance approach as a tool to model two-locus interaction in complex binary traits.

Many binary phenotypes do not follow a classical Mendelian inheritance pattern. Interaction between genetic and environmental factors is thought to contribute to the incomplete penetrance phenomena often observed in these complex binary traits. Several two-locus models for penetrance have been proposed to aid the genetic dissection of binary traits. Such models assume linear genetic effects of both loci in different mathematical scales of penetrance, resembling the analytical framework of quantitative traits. However, changes in phenotypic scale are difficult to envisage in binary traits and limited genetic interpretation is extractable from current modeling of penetrance. To overcome this limitation, we derived an allelic penetrance approach that attributes incomplete penetrance to the stochastic expression of the alleles controlling the phenotype, the genetic background and environmental factors. We applied this approach to formulate dominance and recessiveness in a single diallelic locus and to model different genetic mechanisms for the joint action of two diallelic loci. We fit the models to data on the genetic susceptibility of mice following infections with Listeria monocytogenes and Plasmodium berghei. These models gain in genetic interpretation, because they specify the alleles that are responsible for the genetic (inter)action and their genetic nature (dominant or recessive), and predict genotypic combinations determining the phenotype. Further, we show via computer simulations that the proposed models produce penetrance patterns not captured by traditional two-locus models. This approach provides a new analysis framework for dissecting mechanisms of interlocus joint action in binary traits using genetic crosses.

Incomplete categorical data analysis: a bayesian perspective

In this paper the Bayesian analysis of incomplete categorical data under informative general censoring proposed by Paulino and Pereira (1995) is revisited. That analysis is based on Dirichlet priors and can be applied to any missing data pattern. However, the known properties of the posterior distributions are scarce and therefore severe limitations to the posterior computations remain. Here is shown how a Monte Carlo simulation approach based on an alternative parameterisation can be used to overcome the former computational difficulties. The proposed simulation approach makes available the approximate estimation of general parametric functions and can be implemented in a very straightforward way.

Bayesian analysis of categorical data informatively censored

This article presents a general Bayesian analysis of incomplete categorical data considered as generated by a statistical model involving the categorical sampling process and the observable censoring process. The novelty is that we allow dependence of the censoring process paramenters on the sampling categories; i.e., an informative censoring process. In this way, we relax the assumptions under which both classical and Bayesian solutions have been de-veloped. The proposed solution is outlined for the relevant case of the censoring pattern based on partitions. It is completely developed for a simple but typical examples. Several possible extensions of our procedure are discussed in the final remarks.

Missing data mechanisms and their implications on the analysis of categorical data

We review some issues related to the implications of different missing data mechanisms on statistical inference for contingency tables and consider simulation studies to compare the results obtained under such models to those where the units with missing data are disregarded. We confirm that although, in general, analyses under the correct missing at random and missing completely at random models are more efficient even for small sample sizes, there are exceptions where they may not improve the results obtained by ignoring the partially classified data. We show that under the missing not at random (MNAR) model, estimates on the boundary of the parameter space as well as lack of identifiability of the parameters of saturated models may be associated with undesirable asymptotic properties of maximum likelihood estimators and likelihood ratio tests; even in standard cases the bias of the estimators may be low only for very large samples. We also show that the probability of a boundary solution obtained under the correct MNAR model may be large even for large samples and that, consequently, we may not always conclude that a MNAR model is misspecified because the estimate is on the boundary of the parameter space.

Sample size and power calculations for detecting changes in malaria transmission using antibody seroconversion rate.

BackgroundSeveral studies have highlighted the use of serological data in detecting a reduction in malaria transmission intensity. These studies have typically used serology as an adjunct measure and no formal examination of sample size calculations for this approach has been conducted.MethodsA sample size calculator is proposed for cross-sectional surveys using data simulation from a reverse catalytic model assuming a reduction in seroconversion rate (SCR) at a given change point before sampling. This calculator is based on logistic approximations for the underlying power curves to detect a reduction in SCR in relation to the hypothesis of a stable SCR for the same data. Sample sizes are illustrated for a hypothetical cross-sectional survey from an African population assuming a known or unknown change point.ResultsOverall, data simulation demonstrates that power is strongly affected by assuming a known or unknown change point. Small sample sizes are sufficient to detect strong reductions in SCR, but invariantly lead to poor precision of estimates for current SCR. In this situation, sample size is better determined by controlling the precision of SCR estimates. Conversely larger sample sizes are required for detecting more subtle reductions in malaria transmission but those invariantly increase precision whilst reducing putative estimation bias.ConclusionsThe proposed sample size calculator, although based on data simulation, shows promise of being easily applicable to a range of populations and survey types. Since the change point is a major source of uncertainty, obtaining or assuming prior information about this parameter might reduce both the sample size and the chance of generating biased SCR estimates.