Zero-inflated Generalized Poisson Research Articles

A GLM-based zero-inflated generalized Poisson factor model for analyzing microbiome data.

High-throughput sequencing technology facilitates the quantitative analysis of microbial communities, improving the capacity to investigate the associations between the human microbiome and diseases. Our primary motivating application is to explore the association between gut microbes and obesity. The complex characteristics of microbiome data, including high dimensionality, zero inflation, and over-dispersion, pose new statistical challenges for downstream analysis. We propose a GLM-based zero-inflated generalized Poisson factor analysis (GZIGPFA) model to analyze microbiome data with complex characteristics. The GZIGPFA model is based on a zero-inflated generalized Poisson (ZIGP) distribution for modeling microbiome count data. A link function between the generalized Poisson rate and the probability of excess zeros is established within the generalized linear model (GLM) framework. The latent parameters of the GZIGPFA model constitute a low-rank matrix comprising a low-dimensional score matrix and a loading matrix. An alternating maximum likelihood algorithm is employed to estimate the unknown parameters, and cross-validation is utilized to determine the rank of the model in this study. The proposed GZIGPFA model demonstrates superior performance and advantages through comprehensive simulation studies and real data applications.

Accuracy of Zero Inflated Generalized Poisson Exponentially Moving Average Control Chart

The Zero-Inflated Generalized Poisson (ZIGP) distribution is a case-based distribution where the discrete data has a large number of zeros and an overdispersion occurs, i.e. the variance is greater than the mean value. The purpose of this study is to determine the Exponential Weight Moving Average (EWMA) control chart with the assumption that the data has a Zero-Inflated Generalized Poisson (ZIP) distribution. The results show that the ARL value of the ARL ZIGP EWMA control chart has better accuracy when compared to when using the ZIP EWMA control chart on ZIGP distributed data. This is indicated by the smaller ARL value compared to the ZIP EWMA control chart, namely when φ = 1.4, and φ = 0.6. So that the ARL ZIGP EWMA control chart has a fairly good accuracy in detecting out of control conditions for ZIGP distributed data. In addition, the modified ARL shows the same values ​​before and after the modification for the underdispersion data and shows a larger or negative value for the overdispersion data. This can eliminate or reduce errors in analyzing the accuracy of the control chart.

Count Regression Models with an Application to Zoological Data Containing Structural Zeros

Recently, count regression models have been used to model over dispersed and zero-inflated count response variable that is affected by one or more covariates. Generalized Poisson (GP) and negative binomial (NB) regression models have been suggested to deal with over-dispersion. Zero inflated count regression models such as the zero-inflated Poisson (ZIP), zero-inflated negative binomial (ZINB) and zero-inflated generalized Pois son (ZIGP) regression models have been used to handle count data with many zeros. The aim of this study is to model the number of C. caretta hatchlings dying from exposure to the sun. We present an evaluation frame work to the suitability of applying the Poisson, NB, GP, ZIP and ZIGP to zoological data set where the count data may exhibit evidence of many zeros and over-dispersion. Estimation of the model parameters using the method of maximum likelihood (ML) is provided. Based on the score test and the goodness of fit measure for zoological data, the GP regression model performs better than other count regression models.

Zero-Inflated Generalized Poisson Regression Model with an Application to Domestic Violence Data

The generalized Poisson regression model has been used to model dispersed count data. It is a good competitor to the negative binomial regression model when the count data is over-dispersed. Zero-inflated Poisson and zero-inflated negative binomial regression models have been proposed for the situations where the data generating process results into too many zeros. In this paper, we propose a zero-inflated generalized Poisson (ZIGP) regression model to model domestic violence data with too many zeros. Estimation of the model parameters using the method of maximum likelihood is provided. A score test is presented to test whether the number of zeros is too large for the generalized Poisson model to adequately fit the domestic violence data

Bayesian regression models for ecological count data in PyMC3

Ecological inferences need structurally flexible statistical models to accommodate complex ecological phenomena. PyMC3 is a Probabilistic Programming Language (PPL) and allows for custom statistical distributions to build complex statistical models. This study used PyMC3 to implement Bayesian generalized Poisson (GP), zero-inflated GP, and hurdle GP regression models for over- and under-dispersed counts. The Bayesian GP regression models were fitted to simulated counts and real-world counts of over- and under-dispersion, respectively. Coefficient estimates of the Bayesian regression models were consistent with the known values used in the simulations and those of published work or models. Simulations demonstrated that Bayesian GP regression models with the NUTS sampler worked correctly for under-dispersed counts if the number of non-zero frequency classes was five or more. PyMC3 is not only flexible for building complex statistical models using custom likelihood functions, but also syntactically concise. The programming flexibility of PyMC3 can provide ecologists and environmental scientists with flexible, robust Bayesian computational platforms.

Estimation in zero-inflated Generalized Poisson distribution

Overdispersion is a common phenomenon in Poisson modelling. The generalized Poisson (GP) distribution accommodates both overdispersion and under dispersion in count data. In this paper, we briefly overview different overdispersed and zero-inflated regression models. To study the impact of fitting inaccurate model to data simulated from some other model, we simulate data from ZIGP distribution and fit Poisson, Generalized Poisson (GP), Zero-inflated Poisson (ZIP), Zero-inflated Generalized Poisson (ZIGP) and Zero-inflated Negative Binomial (ZINB) model. We compare the performance of the estimates of Poisson, GP, ZIP, ZIGP and ZINB through mean square error, bias and standard error when the samples are generated from ZIGP distribution. We propose estimators of parameters of ZIGP distribution based on the first two sample moments and proportion of zeros referred to as MOZE estimator and compare its performance with maximum likelihood estimate (MLE) through a simulation study. It is observed that MOZE are almost equal or even more efficient than that of MLE of the parameters of ZIGP distribution.

Bayesian interval mapping of count trait loci based on zero-inflated generalized Poisson regression model.

Count phenotypes with excessive zeros are often observed in the biological world. Researchers have studied many statistical methods for mapping the quantitative trait loci (QTLs) of zero-inflated count phenotypes. However, most of the existing methods consist of finding the approximate positions of the QTLs on the chromosome by genome-wide scanning. Additionally, most of the existing methods use the EM algorithm for parameter estimation. In this paper, we propose a Bayesian interval mapping scheme of QTLs for zero-inflated count data. The method takes advantage of a zero-inflated generalized Poisson (ZIGP) regression model to study the influence of QTLs on the zero-inflated count phenotype. The MCMC algorithm is used to estimate the effects and position parameters of QTLs. We use the Haldane map function to realize the conversion between recombination rate and map distance. Monte Carlo simulations are conducted to test the applicability and advantage of the proposed method. The effects of QTLs on the formation of mouse cholesterol gallstones were demonstrated by analyzing an mouse dataset.

GEE-based zero-inflated generalized Poisson model for clustered over or under-dispersed count data

ABSTRACTThe zero-inflated regression models such as zero-inflated Poisson (ZIP), zero-inflated negative binomial (ZINB) or zero-inflated generalized Poisson (ZIGP) regression models can model the count data with excess zeros. The ZINB model can handle over-dispersed and the ZIGP model can handle the over or under-dispersed count data with excess zeros as well. Moreover, the count data may be correlated because of data collection procedure or special study design. The clustered sampling approach is one of the examples in which the correlation among subjects could be defined. In such situations, a marginal model using generalized estimating equation (GEE) approach can incorporate these correlations and lead up to the relationships at the population level. In this study, the GEE-based zero-inflated generalized Poisson regression model was proposed to fit over and under-dispersed clustered count data with excess zeros.

PENERAPAN REGRESI ZERO INFLATED GENERALIZED POISSON (ZIGP) PADA DATA OVERDISPERSION

Zero Inflated Generalized Poisson (ZIGP) is a regression model used to analyze Poisson distributed discrete data which contains mostly zero and tends to experience overdispersion (varians value greater than the mean value). The purpose of this research is to find out the best model and the factors which influence the maternal mortality in Bali Province in year 2016 by using ZIGP regression model. The data used in this research was data from health profile Bali Province with the object totally 57 district rate data has proportion of zeros value more than 50% on the response variable. The analysis result of ZIGP data on maternal mortality cannot modeled using the ZIGP so ZIGP regression model became ZIP model . The best model which resulted from ZIP regression got one free variable which have significant impact towards the total number of maternal mortality. This significant variabel is the percentage of mother did visiting to K1.

Zero-inflated Conway-Maxwell Poisson Distribution to Analyze Discrete Data.

In this paper, we study the zero-inflated Conway-Maxwell Poisson (ZICMP) distribution and develop a regression model. Score and likelihood ratio tests are also implemented for testing the inflation/deflation parameter. Simulation studies are carried out to examine the performance of these tests. A data example is presented to illustrate the concepts. In this example, the proposed model is compared to the well-known zero-inflated Poisson (ZIP) and the zero- inflated generalized Poisson (ZIGP) regression models. It is shown that the fit by ZICMP is comparable or better than these models.

Empirical null estimation using zero-inflated discrete mixture distributions and its application to protein domain data.

In recent mutation studies, analyses based on protein domain positions are gaining popularity over gene-centric approaches since the latter have limitations in considering the functional context that the position of the mutation provides. This presents a large-scale simultaneous inference problem, with hundreds of hypothesis tests to consider at the same time. This article aims to select significant mutation counts while controlling a given level of Type I error via False Discovery Rate (FDR) procedures. One main assumption is that the mutation counts follow a zero-inflated model in order to account for the true zeros in the count model and the excess zeros. The class of models considered is the Zero-inflated Generalized Poisson (ZIGP) distribution. Furthermore, we assumed that there exists a cut-off value such that smaller counts than this value are generated from the null distribution. We present several data-dependent methods to determine the cut-off value. We also consider a two-stage procedure based on screening process so that the number of mutations exceeding a certain value should be considered as significant mutations. Simulated and protein domain data sets are used to illustrate this procedure in estimation of the empirical null using a mixture of discrete distributions. Overall, while maintaining control of the FDR, the proposed two-stage testing procedure has superior empirical power.

Marginalized zero-inflated generalized Poisson regression

ABSTRACTThe generalized Poisson (GP) regression model has been used to model count data that exhibit over-dispersion or under-dispersion. The zero-inflated GP (ZIGP) regression model can additionally handle count data characterized by many zeros. However, the parameters of ZIGP model cannot easily be used for inference on overall exposure effects. In order to address this problem, a marginalized ZIGP is proposed to directly model the population marginal mean count. The parameters of the marginalized zero-inflated GP model are estimated by the method of maximum likelihood. The regression model is illustrated by three real-life data sets.

Applicability of Zero-Inflated Models to Fit the Torrential Rainfall Count Data with Extra Zeros in South Korea

Several natural disasters occur because of torrential rainfalls. The change in global climate most likely increases the occurrences of such downpours. Hence, it is necessary to investigate the characteristics of the torrential rainfall events in order to introduce effective measures for mitigating disasters such as urban floods and landslides. However, one of the major problems is evaluating the number of torrential rainfall events from a statistical viewpoint. If the number of torrential rainfall occurrences during a month is considered as count data, their frequency distribution could be identified using a probability distribution. Generally, the number of torrential rainfall occurrences has been analyzed using the Poisson distribution (POI) or the Generalized Poisson Distribution (GPD). However, it was reported that POI and GPD often overestimated or underestimated the observed count data when additional or fewer zeros were included. Hence, in this study, a zero-inflated model concept was applied to solve this problem existing in the conventional models. Zero-Inflated Poisson (ZIP) model, Zero-Inflated Generalized Poisson (ZIGP) model, and the Bayesian ZIGP model have often been applied to fit the count data having additional or fewer zeros. However, the applications of these models in water resource management have been very limited despite their efficiency and accuracy. The five models, namely, POI, GPD, ZIP, ZIGP, and Bayesian ZIGP, were applied to the torrential rainfall data having additional zeros obtained from two rain gauges in South Korea, and their applicability was examined in this study. In particular, the informative prior distributions evaluated via the empirical Bayes method using ten rain gauges were developed in the Bayesian ZIGP model. Finally, it was suggested to avoid using the POI and GPD models to fit the frequency of torrential rainfall data. In addition, it was concluded that the Bayesian ZIGP model used in this study provided the most accurate results for the count data having additional zeros. Moreover, it was recommended that the ZIP model could be an alternative from a practical viewpoint, as the Bayesian approach used in this study was considerably complex.

Parameter change test for zero-inflated generalized Poisson autoregressive models

In this paper, we consider the problem of testing for parameter change in zero-inflated generalized Poisson (ZIGP) autoregressive models. We verify that the ZIGP process is stationary and ergodic and that the conditional maximum likelihood estimator (CMLE) is strongly consistent and asymptotically normal. Based on these results, we construct CMLE- and residual-based cumulative sum tests and show that their limiting null distributions are a function of independent Brownian bridges. The simulation results are provided for illustration. A real data analysis is performed on some crime data of Australia.

Two new bivariate zero-inflated generalized Poisson distributions with a flexible correlation structure

To model correlated bivariate count data with extra zero observations, this paper proposes two new bivariate zero-inflated generalized Poisson (ZIGP) distributions by incorporating a multiplicative factor (or dependency parameter) λ, named as Type I and Type II bivariate ZIGP distributions, respectively. The proposed distributions possess a flexible correlation structure and can be used to fit either positively or negatively correlated and either over- or under-dispersed count data, comparing to the existing models that can only fit positively correlated count data with over-dispersion. The two marginal distributions of Type I bivariate ZIGP share a common parameter of zero inflation while the two marginal distributions of Type II bivariate ZIGP have their own parameters of zero inflation, resulting in a much wider range of applications. The important distributional properties are explored and some useful statistical inference methods including maximum likelihood estimations of parameters, standard errors estimation, bootstrap confidence intervals and related testing hypotheses are developed for the two distributions. A real data are thoroughly analyzed by using the proposed distributions and statistical methods. Several simulation studies are conducted to evaluate the performance of the proposed methods.

Two new bivariate zero-inflated generalized Poisson distributions with a flexible correlation structure

To model correlated bivariate count data with extra zero observations, this paper proposes two new bivariate zero-inflated generalized Poisson (ZIGP) distributions by incorporating a multiplicative factor (or dependency parameter) λ, named as Type I and Type II bivariate ZIGP distributions, respectively. The proposed distributions possess a flexible correlation structure and can be used to fit either positively or negatively correlated and either over- or under-dispersed count data, comparing to the existing models that can only fit positively correlated count data with over-dispersion. The two marginal distributions of Type I bivariate ZIGP share a common parameter of zero inflation while the two marginal distributions of Type II bivariate ZIGP have their own parameters of zero inflation, resulting in a much wider range of applications. The important distributional properties are explored and some useful statistical inference methods including maximum likelihood estimations of parameters, standard errors estimation, bootstrap confidence intervals and related testing hypotheses are developed for the two distributions. A real data are thoroughly analyzed by using the proposed distributions and statistical methods. Several simulation studies are conducted to evaluate the performance of the proposed methods.

Two-part zero-inflated negative binomial regression model for quantitative trait loci mapping with count trait.

Poisson regression models provide a standard framework for quantitative trait locus (QTL) mapping of count traits. In practice, however, count traits are often over-dispersed relative to the Poisson distribution. In these situations, the zero-inflated Poisson (ZIP), zero-inflated generalized Poisson (ZIGP) and zero-inflated negative binomial (ZINB) regression may be useful for QTL mapping of count traits. Added genetic variables to the negative binomial part equation, may also affect extra zero data. In this study, to overcome these challenges, I apply two-part ZINB model. The EM algorithm with Newton-Raphson method in the M-step uses for estimating parameters. An application of the two-part ZINB model for QTL mapping is considered to detect associations between the formation of gallstone and the genotype of markers.

Bayesian zero-inflated generalized Poisson regression model: estimation and case influence diagnostics

Count data with excess zeros arises in many contexts. Here our concern is to develop a Bayesian analysis for the zero-inflated generalized Poisson (ZIGP) regression model to address this problem. This model provides a useful generalization of zero-inflated Poisson model since the generalized Poisson distribution is overdispersed/underdispersed relative to Poisson. Due to the complexity of the ZIGP model, Markov chain Monte Carlo methods are used to develop a Bayesian procedure for the considered model. Additionally, some discussions on the model selection criteria are presented and a Bayesian case deletion influence diagnostics is investigated for the joint posterior distribution based on the Kullback–Leibler divergence. Finally, a simulation study and a psychological example are given to illustrate our methodology.

Score test for testing zero-inflated Poisson regression against zero-inflated generalized Poisson alternatives

In several cases, count data often have excessive number of zero outcomes. This zero-inflated phenomenon is a specific cause of overdispersion, and zero-inflated Poisson regression model (ZIP) has been proposed for accommodating zero-inflated data. However, if the data continue to suggest additional overdispersion, zero-inflated negative binomial (ZINB) and zero-inflated generalized Poisson (ZIGP) regression models have been considered as alternatives. This study proposes the score test for testing ZIP regression model against ZIGP alternatives and proves that it is equal to the score test for testing ZIP regression model against ZINB alternatives. The advantage of using the score test over other alternative tests such as likelihood ratio and Wald is that the score test can be used to determine whether a more complex model is appropriate without fitting the more complex model. Applications of the proposed score test on several datasets are also illustrated.

The accuracy of self-reported fisheries data: Oregon trawl logbook fishing locations and retained catches

Self-reporting of information is an inexpensive means for collecting data on fishing or other human activities, but the accuracy of self-reported data can be difficult to measure. Logbooks that record fishing activities are a common form of self-reporting that can provide vast amounts of information about a fishery. Using logbook data from trawlers from Oregon ports operating along the US Pacific coast during 1987–2001, this study examined (a) the consistency of reported tow locations and bottom depths and (b) the accuracy of reported retained catches of four groundfish species groups. Because logbook data during this period played no direct role in fishery management or stock assessments, there were no obvious incentives for trawl captains to deliberately report false logbook information. To evaluate consistency between tow locations and corresponding bottom depths, each tow was assigned to a 100-m bottom depth-band based on the reported tow location on a digital chart. The depth-bands based on the tow locations were then compared one-to-one with the depths reported in the logbooks and analysed to determine factors (e.g., year, quarter, vessel) contributing to the consistency between the reported locations and depths. Consistency was highest in the shallowest depth-bands and there was a strong interaction between depth and vessel. To evaluate the accuracy of the retained catches reported by the captains, the tow-by-tow logbook data were summed to the fishing-trip-level and compared to the official landing weights, recorded at the fish processing plants when the catches were off-loaded and weighed. The logbook weights relative to the corresponding official landing weights were analysed using zero-inflated generalized Poisson (ZIGP) regression models to determine factors (year, quarter, vessel) that were important explanatory variables. The analysis found strong year, quarter, and vessel effects for all three parts of the ZIGP: the mean value, the dispersion, and the proportion of zeros. The vessel effect was strongest. In a combined analysis, based on results from the other two analyses, vessels that were consistent in recording their depths and fishing locations had only a weak tendency to be accurate in recording their catches.