Misspecification tests for binomial and beta-binomial models

Beta distribution misspecification tests with application to Covid-19 mortality rates in the United States

The beta distribution is routinely used to model variables that assume values in the standard unit interval, (0, 1). Several alternative laws have, nonetheless, been proposed in the literature, such as the Kumaraswamy and simplex distributions. A natural and empirically motivated question is: does the beta law provide an adequate representation for a given dataset? We test the null hypothesis that the beta model is correctly specified against the alternative hypothesis that it does not provide an adequate data fit. Our tests are based on the information matrix equality, which only holds when the model is correctly specified. They are thus sensitive to model misspecification. Simulation evidence shows that the tests perform well, especially when coupled with bootstrap resampling. We model state and county Covid-19 mortality rates in the United States. The misspecification tests indicate that the beta law successfully represents Covid-19 death rates when they are computed using either data from prior to the start of the vaccination campaign or data collected when such a campaign was under way. In the latter case, the beta law is only accepted when the negative impact of vaccination reach on death rates is moderate. The beta model is rejected under data heterogeneity, i.e., when mortality rates are computed using information gathered during both time periods.

Comparing performance between log-binomial and robust Poisson regression models for estimating risk ratios under model misspecification

BACKGROUND

Log-binomial and robust (modified) Poisson regression models are popular approaches to estimate risk ratios for binary response variables. Previous studies have shown that comparatively they produce similar point estimates and standard errors. However, their performance under model misspecification is poorly understood.

METHODS

In this simulation study, the statistical performance of the two models was compared when the log link function was misspecified or the response depended on predictors through a non-linear relationship (i.e. truncated response).

RESULTS

Point estimates from log-binomial models were biased when the link function was misspecified or when the probability distribution of the response variable was truncated at the right tail. The percentage of truncated observations was positively associated with the presence of bias, and the bias was larger if the observations came from a population with a lower response rate given that the other parameters being examined were fixed. In contrast, point estimates from the robust Poisson models were unbiased.

CONCLUSION

Under model misspecification, the robust Poisson model was generally preferable because it provided unbiased estimates of risk ratios.

Comprehensive approach to analyzing rare genetic variants

Recent findings suggest that rare variants play an important role in both monogenic and common diseases. Due to their rarity, however, it remains unclear how to appropriately analyze the association between such variants and disease. A common approach entails combining rare variants together based on a priori information and analyzing them as a single group. Here one must make some assumptions about what to aggregate. Instead, we propose two approaches to empirically determine the most efficient grouping of rare variants. The first considers multiple possible groupings using existing information. The second is an agnostic "step-up" approach that determines an optimal grouping of rare variants analytically and does not rely on prior information. To evaluate these approaches, we undertook a simulation study using sequence data from genes in the one-carbon folate metabolic pathway. Our results show that using prior information to group rare variants is advantageous only when information is quite accurate, but the step-up approach works well across a broad range of plausible scenarios. This agnostic approach allows one to efficiently analyze the association between rare variants and disease while avoiding assumptions required by other approaches for grouping such variants.

Global goodness-of-fit tests for group testing regression models

In a variety of biomedical applications, particularly those involving screening for infectious diseases, testing individuals (e.g. blood/urine samples, etc.) in pools has become a standard method of data collection. This experimental design, known as group testing (or pooled testing), can provide a large reduction in testing costs and can offer nearly the same precision as individual testing. To account for covariate information on individual subjects, regression models for group testing data have been proposed recently. However, there are currently no tools available to check the adequacy of these models. In this paper, we present various global goodness-of-fit tests for regression models with group testing data. We use simulation to examine the small-sample size and power properties of the tests for different pool composition strategies. We illustrate our methods using two infectious disease data sets, one from an HIV study in Kenya and one from the Infertility Prevention Project.