Zero-inflated sum of Conway-Maxwell-Poissons (ZISCMP) regression

Randomized quantile residuals for diagnosing zero-inflated generalized linear mixed models with applications to microbiome count data

BACKGROUND

For differential abundance analysis, zero-inflated generalized linear models, typically zero-inflated NB models, have been increasingly used to model microbiome and other sequencing count data. A common assumption in estimating the false discovery rate is that the p values are uniformly distributed under the null hypothesis, which demands that the postulated model fit the count data adequately. Mis-specification of the distribution of the count data may lead to excess false discoveries. Therefore, model checking is critical to control the FDR at a nominal level in differential abundance analysis. Increasing studies show that the method of randomized quantile residual (RQR) performs well in diagnosing count regression models. However, the performance of RQR in diagnosing zero-inflated GLMMs for sequencing count data has not been extensively investigated in the literature.

RESULTS

We conduct large-scale simulation studies to investigate the performance of the RQRs for zero-inflated GLMMs. The simulation studies show that the type I error rates of the GOF tests with RQRs are very close to the nominal level; in addition, the scatter-plots and Q-Q plots of RQRs are useful in discerning the good and bad models. We also apply the RQRs to diagnose six GLMMs to a real microbiome dataset. The results show that the OTU counts at the genus level of this dataset (after a truncation treatment) can be modelled well by zero-inflated and zero-modified NB models.

CONCLUSION

RQR is an excellent tool for diagnosing GLMMs for zero-inflated count data, particularly the sequencing count data arising in microbiome studies. In the supplementary materials, we provided two generic R functions, called rqr.glmmtmb and rqr.hurdle.glmmtmb, for calculating the RQRs given fitting outputs of the R package glmmTMB.

A flexible univariate moving average time-series model for dispersed count data

Al-Osh and Alzaid (1988) consider a Poisson moving average (PMA) model to describe the relation among integer-valued time series data; this model, however, is constrained by the underlying equi-dispersion assumption for count data (i.e., that the variance and the mean equal). This work instead introduces a flexible integer-valued moving average model for count data that contain over- or under-dispersion via the Conway-Maxwell-Poisson (CMP) distribution and related distributions. This first-order sum-of-Conway-Maxwell-Poissons moving average (SCMPMA(1)) model offers a generalizable construct that includes the PMA (among others) as a special case. We highlight the SCMPMA model properties and illustrate its flexibility via simulated data examples.