Hidden Markov models for zero‐inflated Poisson counts with an application to substance use

The Poisson regression model is widely used for count data. This model assumes equidispersion. In practice, equidispersion is seldom reflected in data. However, in real-life data, the variance usually exceeds the mean. This situation is known as overdispersion. Negative binomial distribution and other Poisson mix models are often used to model overdispersion count data. Another extension of the negative binomial distribution in another model for count data is the univariate generalized Waring. In addition, the model developed by Famoye can be used in the analysis of count data. When the count data contains a large number of zeros, it is necessary to use zero-inflated models. In this study, different generalized regression models are emphasized for the analysis of excessive zeros count data. For this purpose, a real data set was analysed with the generalized Poisson model, generalized negative binomial model, generalized negative binomial Famoye, generalized Waring model, and the foregoing zero-inflated models. Log-likelihood, Akaike information criterion, Bayes information criterion, Vuong statistics were used for model comparisons.

Asthma is an important chronic disease of childhood. An intervention programme for managing asthma was designed on principles of self-regulation and was evaluated by a randomized longitudinal study.The study focused on several outcomes, and, typically, missing data remained a pervasive problem. We develop a pattern-mixture model to evaluate the outcome of intervention on the number of hospitalizations with non-ignorable dropouts. Pattern-mixture models are not generally identifiable as no data may be available to estimate a number of model parameters. Sensitivity analyses are performed by imposing structures on the unidentified parameters.We propose a parameterization which permits sensitivity analyses on clustered longitudinal count data that have missing values due to non-ignorable missing data mechanisms. This parameterization is expressed as ratios between event rates across missing data patterns and the observed data pattern and thus measures departures from an ignorable missing data mechanism. Sensitivity analyses are performed within a Bayesian framework by averaging over different prior distributions on the event ratios. This model has the advantage of providing an intuitive and flexible framework for incorporating the uncertainty of the missing data mechanism in the final analysis.

The methodological advancements made in the field of joint models are numerous. None the less, the case of competing risks joint models has largely been neglected, especially from a practitioner's point of view. In the relevant works on competing risks joint models, the assumptions of a Gaussian linear longitudinal series and proportional cause-specific hazard functions, amongst others, have remained unchallenged. In this article, we provide a framework based on R-INLA to apply competing risks joint models in a unifying way such that non-Gaussian longitudinal data, spatial structures, times-dependent splines and various latent association structures, to mention a few, are all embraced in our approach. Our motivation stems from the SANAD trial which exhibits non-linear longitudinal trajectories and competing risks for failure of treatment. We also present a discrete competing risks joint model for longitudinal count data as well as a spatial competing risks joint model as specific examples.

Longitudinal count data analysis has been widely used in various social science and nature science. In this paper, we proposed a semi-parametric negative multinomia model for longitudinal count data. Using local likelihood technique and marginal distribution, we proposed an estimation procedure for our new model. The finite-sample properties are studied with a simulation study.

Models of Count with Endogenous Choices

Models of count with endogenous choices

S ome P oints of D iscussion • What are counts? What are count data? • What is a linear statistical model? • What is the relationship between a probability distribution function (PDF) and a statistical model? • What are the parameters of a statistical model? Where do they come from, and can we ever truly know them? • How does a count model differ from other regression models? • What are the basic count models, and how do they relate with one another? • What is over dispersion, and why is it considered to be the fundamental problem when modeling count data? W hat A re C ounts ? When discussing the modeling of count data, it's important to clarify exactly what is meant by a count, as well as “count data” and “count variable.” The word “count” is typically used as a verb meaning to enumerate units, items, or events. We might count the number of road kills observed on a stretch of highway, how many patients died at a particular hospital within 48 hours of having a myocardial infarction, or how many separate sunspots were observed in March 2013. “Count data,” on the other hand, is a plural noun referring to observations made about events or items that are enumerated. In statistics, count data refer to observations that have only nonnegative integer values ranging from zero to some greater undetermined value. Theoretically, counts can range from zero to infinity, but they are always limited to some lesser distinct value – generally the maximum value of the count data being modeled.

Microorganisms play critical roles in human health and disease. They live in diverse communities in which they interact synergistically or antagonistically. Thus for estimating microbial associations with clinical covariates, such as treatment effects, joint (multivariate) statistical models are preferred. Multivariate models allow one to estimate and exploit complex interdependencies among multiple taxa, yielding more powerful tests of exposure or treatment effects than application of taxon-specific univariate analyses. Analysis of microbial count data also requires special attention because data commonly exhibit zero inflation, i.e., more zeros than expected from a standard count distribution. To meet these needs, we developed a Bayesian variable selection model for multivariate count data with excess zeros that incorporates information on the covariance structure of the outcomes (counts for multiple taxa), while estimating associations with the mean levels of these outcomes. Though there has been much work on zero-inflated models for longitudinal data, little attention has been given to high-dimensional multivariate zero-inflated data modeled via a general correlation structure. Through simulation, we compared performance of the proposed method to that of existing univariate approaches, for both the binary ("excess zero") and count parts of the model. When outcomes were correlated the proposed variable selection method maintained type I error while boosting the ability to identify true associations in the binary component of the model. For the count part of the model, in some scenarios the univariate method had higher power than the multivariate approach. This higher power was at a cost of a highly inflated false discovery rate not observed with the proposed multivariate method. We applied the approach to oral microbiome data from the Pediatric HIV/AIDS Cohort Oral Health Study and identified five (of 44) species associated with HIV infection.

The purpose of this chapter is to present recent advances in models for genomic-enabled prediction developed for ordinal categorical and count data. For both models we provide details of their corresponding derivation and then apply them to a real data set. The proposed models were derived using a Bayesian framework. Bayesian logistic ordinal regression (BLOR) and Bayesian negative binomial regression (BNBR) make use of the Polya-Gamma distribution to produce an analytic Gibbs, a sampler with similar full conditional distributions of a model with Gaussian response and can be used for complex data sets as those that arise in the context of genomic selection where the sample size usually is smaller than the number of covariates (markers). We illustrate the proposed models using simulation and a real data set. Results indicate that our models for ordinal categorical and count data are a good alternative for analyzing ordinal and count data in the context of genomic-enabled prediction.

This paper discusses the problem of variance specification in models for event count data. Event counts are dependent variables that can take on only nonnegative integer values, such as the number of wars or coups d'etat in a year. I discuss several generalizations of the Poisson regression model, presented in King (1988), to allow for substantively interesting stochastic processes that do not fit into the Poisson framework. Individual models that cope with, and help analyze, heterogeneity, contagion. and negative contagion are each shown to lead to specific statistical models for event count data. In addition. I derive a new generalized event count (GEC) model that enables researchers to extract significant amounts of new information from existing data by estimating features of these unobserved substantive processes. Applications of this model to congressional challenges of presidential vetoes and superpower conflict demonstrate the dramatic advantages of this approach.

Overdispersion is common in models of count data in ecology and evolutionary biology, and can occur due to missing covariates, non-independent (aggregated) data, or an excess frequency of zeroes (zero-inflation). Accounting for overdispersion in such models is vital, as failing to do so can lead to biased parameter estimates, and false conclusions regarding hypotheses of interest. Observation-level random effects (OLRE), where each data point receives a unique level of a random effect that models the extra-Poisson variation present in the data, are commonly employed to cope with overdispersion in count data. However studies investigating the efficacy of observation-level random effects as a means to deal with overdispersion are scarce. Here I use simulations to show that in cases where overdispersion is caused by random extra-Poisson noise, or aggregation in the count data, observation-level random effects yield more accurate parameter estimates compared to when overdispersion is simply ignored. Conversely, OLRE fail to reduce bias in zero-inflated data, and in some cases increase bias at high levels of overdispersion. There was a positive relationship between the magnitude of overdispersion and the degree of bias in parameter estimates. Critically, the simulations reveal that failing to account for overdispersion in mixed models can erroneously inflate measures of explained variance (r2), which may lead to researchers overestimating the predictive power of variables of interest. This work suggests use of observation-level random effects provides a simple and robust means to account for overdispersion in count data, but also that their ability to minimise bias is not uniform across all types of overdispersion and must be applied judiciously.

Panel count data occur in many fields including clinical, demographical and industrial studies and an extensive literature has been established for their regression analysis. However, most of the existing methods apply only to the situations where both covariates and their effects are constant or one of them may be time-dependent. In the first part of this dissertation, we consider a situation where both covariates and their effects may be time-dependent and an estimating equation-based approach is developed for estimating those time-varying effects. In the method, B-spline functions are employed to approximate time-dependent coefficients and the asymptotic properties of the proposed estimators are established. To assess the performance of the proposed approach, an extensive simulation study is conducted and suggests that it works well in practical situations. An application to the China Health and Nutrition Survey (CHNS) study is provided. In practice, there could exist more than one type of event of interest, such as two types of tumor recurrence, leading to multivariate panel count data. The second part of this dissertation considers marginal mean model for multivariate panel count data with time-dependent coefficient and covariate effects, which has limited previous research. Based on the conditional estimating equation method developed for time-dependent covariates, we approximate the coefficients by B-splines, hence allow both coefficients and covariates to be time-dependent. Simulation studies show that the proposed estimation procedures work well for practical situations. The methodology is again applied to the China Health and Nutrition Survey (CHNS) study. When we consider time-varying covariates and coefficients effects, most of the previous study focused on the proportional mean model because the likelihood function under the rate model involves intractable integration. However, the rate model is more realistic and efficient. Hence, in the third part of this dissertation, we propose a semi-parametric MLE method under the rate model for panel count data with time-dependent covariates and time-varying effects. B-spline functions are employed again to approximate time-dependent coefficients and an efficient Expectation-Maximization-type algorithm is developed to overcome the computational difficulty. The resulting estimators are shown to be consistent and asymptotically efficient. Monte Carlo simulation studies demonstrate that the proposed method enjoys desirable finite-sample properties. An application to The Young Women's Project (YWP) is provided.

This article applies growth curve models to longitudinal count data characterized by an excess of zero counts. We discuss a zero-inflated Poisson regression model for longitudinal data in which the impact of covariates on the initial counts and the rate of change in counts over time is the focus of inference. Basic growth curve models using a single outcome are described, as well as a model in which two linked outcomes constitute a dual-trajectory growth process. This model is applied to assess the impact of changes in financial stress on longitudinal change in smoking.

The Poisson regression model is an important analytic tool that should be used in count data modeling. When the value of excess dispersion of variables, then the model is not appropriate to apply in case the value of the mean is not equal to the value of the variance of the Poisson distribution. The results are compatible with data when there is the use of Bell regression model. The number of zeros in the count data that is seen is very high. In this case, the Zero-Inflated Bell regression model is an alternative to the Bell regression model. Parameters of the Zero-Inflated Bell regression model are estimated mostly through the approach of maximum likelihood. In an extended linear model, in which the response variable is modeled by two or more explanatory variables, as in the Zero-Inflated Bell regression model, linear dependence is a threat in a real-life analysis. It reduced the maximum likelihood estimator in its effectiveness. In a bid to solve this issue, this paper explores the performance of the generalized shrinkage estimator in the zero-inflated Bell regression model. The superiority of the proposed approaches over the traditional maximum likelihood estimator is validated by results of the simulations and implementations.

This study presents several extensions of the most familiar models for count data, the Poisson and negative binomial models. We develop an encompassing model for two well-known variants of the negative binomial model (the NB1 and NB2 forms). We then analyze some alternative approaches to the standard log gamma model for introducing heterogeneity into the loglinear conditional means for these models. The lognormal model provides a versatile alternative specification that is more flexible (and more natural) than the log gamma form, and provides a platform for several “two part” extensions, including zero inflation, hurdle, and sample selection models. (We briefly present some alternative approaches to modeling heterogeneity.) We also resolve some features in Hausman, Hall and Griliches (1984, Economic models for count data with an application to the patents-R&D relationship, Econometrica52, 909–938) widely used panel data treatments for the Poisson and negative binomial models that appear to conflict with more familiar models of fixed and random effects. Finally, we consider a bivariate Poisson model that is also based on the lognormal heterogeneity model. Two recent applications have used this model. We suggest that the correlation estimated in their model frameworks is an ambiguous measure of the correlation of the variables of interest, and may substantially overstate it. We conclude with a detailed application of the proposed methods using the data employed in one of the two aforementioned bivariate Poisson studies.