A quasi-score statistic for homogeneity testing against covariate-varying heterogeneity

Testing latent class of subjects with structural zeros in negative binomial models with applications to gut microbiome data

Human microbiome research has become a hot-spot in health and medical research in the past decade due to the rapid development of modern high-throughput. Typical data in a microbiome study consisting of the operational taxonomic unit counts may have over-dispersion and/or structural zero issues. In such cases, negative binomial models can be applied to address the over-dispersion issue, while zero-inflated negative binomial models can be applied to address both issues. In practice, it is essential to know if there is zero-inflation in the data before applying negative binomial or zero-inflated negative binomial models because zero-inflated negative binomial models may be unnecessarily complex and difficult to interpret, or may even suffer from convergence issues if there is no zero-inflation in the data. On the other hand, negative binomial models may yield invalid inferences if the data does exhibit excessive zeros. In this paper, we develop a new test for detecting zero-inflation resulting from a latent class of subjects with structural zeros in a negative binomial regression model by directly comparing the amount of observed zeros with what would be expected under the negative binomial regression model. A closed form of the test statistic as well as its asymptotic properties are derived based on estimating equations. Intensive simulation studies are conducted to investigate the performance of the new test and compare it with the classical Wald, likelihood ratio, and score tests. The tests are also applied to human gut microbiome data to test latent class in microbial genera.

Generalized fiducial inference on the mean of zero-inflated Poisson and Poisson hurdle models

Zero-inflated and hurdle models are widely applied to count data possessing excess zeros, where they can simultaneously model the process from how the zeros were generated and potentially help mitigate the effects of overdispersion relative to the assumed count distribution. Which model to use depends on how the zeros are generated: zero-inflated models add an additional probability mass on zero, while hurdle models are two-part models comprised of a degenerate distribution for the zeros and a zero-truncated distribution. Developing confidence intervals for such models is challenging since no closed-form function is available to calculate the mean. In this study, generalized fiducial inference is used to construct confidence intervals for the means of zero-inflated Poisson and Poisson hurdle models. The proposed methods are assessed by an intensive simulation study. An illustrative example demonstrates the inference methods.

Testing inflated zeros in binomial regression models

Binomial regression models are commonly applied to proportion data such as those relating to the mortality and infection rates of diseases. However, it is often the case that the responses may exhibit excessive zeros; in such cases a zero-inflated binomial (ZIB) regression model can be applied instead. In practice, it is essential to test if there are excessive zeros in the outcome to help choose an appropriate model. The binomial models can yield biased inference if there are excessive zeros, while ZIB models may be unnecessarily complex and hard to interpret, and even face convergence issues, if there are no excessive zeros. In this paper, we develop a new test for testing zero inflation in binomial regression models by directly comparing the amount of observed zeros with what would be expected under the binomial regression model. A closed form of the test statistic, as well as the asymptotic properties of the test, is derived based on estimating equations. Our systematic simulation studies show that the new test performs very well in most cases, and outperforms the classical Wald, likelihood ratio, and score tests, especially in controlling type I errors. Two real data examples are also included for illustrative purpose.