Statnote 37 : the negative binomial distribution

An organism living in water, and present at low density, may be distributed at random and therefore, samples taken from the water are likely to be distributed according to the Poisson distribution. The distribution of many organisms, however, is not random, individuals being either aggregated into clusters or more uniformly distributed. By fitting a Poisson distribution to data, it is only possible to test the hypothesis that an observed set of frequencies does not deviate significantly from an expected random pattern. Significant deviations from random, either as a result of increasing uniformity or aggregation, may be recognized by either rejection of the random hypothesis or by examining the variance/mean (V/M) ratio of the data. Hence, a V/M ratio not significantly different from unity indicates a random distribution, greater than unity a clustered distribution, and less then unity a regular or uniform distribution . If individual cells are clustered, however, the negative binomial distribution should provide a better description of the data. In addition, a parameter of this distribution, viz., the binomial exponent (k), may be used as a measure of the ‘intensity’ of aggregation present. Hence, this Statnote describes how to fit the negative binomial distribution to counts of a microorganism in samples taken from a freshwater environment.

Mixed Negative Binomial Distribution by Weighted Gamma Mixing Distribution

Павел Т. Стойнов - В тази работа се разглежда отрицателно биномното разпределение, известно още като разпределение на Пойа. Предполагаме, че смесващото разпределение е претеглено гама разпределение. Изведени са вероятностите в някои частни случаи. Дадени са рекурентните формули на Панжер.

A Characterization of the Negative Binomial Distribution

Only a few characterizations have been obtained in literatute for the negative binomial distribution (see Johnson et al., Chap. 5, 1992). In this article a characterization of the negative binomial distribution related to random sums is obtained which is motivated by the geometric distribution characterization given by Khalil et al. (1991). An interpretation in terms of an unreliable system is given.

On estimation and influence diagnostics for zero-inflated negative binomial regression models

The zero-inflated negative binomial model is used to account for overdispersion detected in data that are initially analyzed under the zero-Inflated Poisson model A frequentist analysis a jackknife estimator and a non-parametric bootstrap for parameter estimation of zero-inflated negative binomial regression models are considered In addition an EM-type algorithm is developed for performing maximum likelihood estimation Then the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes and some ways to perform global influence analysis are derived In order to study departures from the error assumption as well as the presence of outliers residual analysis based on the standardized Pearson residuals is discussed The relevance of the approach is illustrated with a real data set where It is shown that zero-inflated negative binomial regression models seems to fit the data better than the Poisson counterpart (C) 2010 Elsevier B V All rights reserved

The negative binomial-beta Weibull regression model to predict the cure of prostate cancer

In this article, for the first time, we propose the negative binomial-beta Weibull (BW) regression model for studying the recurrence of prostate cancer and to predict the cure fraction for patients with clinically localized prostate cancer treated by open radical prostatectomy. The cure model considers that a fraction of the survivors are cured of the disease. The survival function for the population of patients can be modeled by a cure parametric model using the BW distribution. We derive an explicit expansion for the moments of the recurrence time distribution for the uncured individuals. The proposed distribution can be used to model survival data when the hazard rate function is increasing, decreasing, unimodal and bathtub shaped. Another advantage is that the proposed model includes as special sub-models some of the well-known cure rate models discussed in the literature. We derive the appropriate matrices for assessing local influence on the parameter estimates under different perturbation schemes. We analyze a real data set for localized prostate cancer patients after open radical prostatectomy.

A Note on Bayesian Estimation for the Negative-Binomial Model

2000 Mathematics Subject Classification: 62F15.

Robust Estimates of the Negative Binomial Model

We consider robust parametric procedures for univariate discrete distributions, focusing on the negative binomial model. The procedures are based on three steps: ?First, a very robust, but possibly inefficient, estimate of the model parameters is computed. ?Second, this initial model is used to identify outliers, which are then removed from the sample. ?Third, a corrected maximum likelihood estimator is computed with the remaining observations. The final estimate inherits the breakdown point (bdp) of the initial one and its efficiency can be significantly higher. Analogous procedures were proposed in [1], [2], [5] for the continuous case. A comparison of the asymptotic bias of various estimates under point contamination points out the minimum Neyman's chi-squared disparity estimate as a good choice for the initial step. Various minimum disparity estimators were explored by Lindsay [4], who showed that the minimum Neyman's chi-squared estimate has a 50% bdp under point contamination; in addition, it is asymptotically fully efficient at the model. However, the finite sample efficiency of this estimate under the uncontaminated negative binomial model is usually much lower than 100% and the bias can be strong. We show that its performance can then be greatly improved using the three step procedure outlined above. In addition, we compare the final estimate with the procedure described in

Distribution patterns of infection with multiple types of human papillomaviruses and their association with risk factors

Background: Infection with multiple types of human papillomavirus (HPV) is one of the main risk factors associated with the development of cervical lesions. In this study, cervical samples collected from 1,810 women with diverse sociocultural backgrounds, who attended to their cervical screening program in different geographical regions of Colombia, were examined for the presence of cervical lesions and HPV by Papanicolau testing and DNA PCR detection, respectively. Principal Findings: The negative binomial distribution model used in this study showed differences between the observed and expected values within some risk factor categories analyzed. Particularly in the case of single infection and coinfection with more than 4 HPV types, observed frequencies were smaller than expected, while the number of women infected with 2 to 4 viral types were higher than expected. Data analysis according to a negative binomial regression showed an increase in the risk of acquiring more HPV types in women who were of indigenous ethnicity (+37.8%), while this risk decreased in women who had given birth more than 4 times (-31.1%), or were of mestizo (-24.6%) or black (-40.9%) ethnicity. Conclusions: According to a theoretical probability distribution, the observed number of women having either a single infection or more than 4 viral types was smaller than expected, while for those infected with 2-4 HPV types it was larger than expected. Taking into account that this study showed a higher HPV coinfection rate in the indigenous ethnicity, the role of underlying factors should be assessed in detail in future studies.

Spatial distribution of Diaphorina citri Kuwayama (Hemiptera: Psyllidae) in citrus orchards

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

DISTRIBUTION OF THE NUMBER OF EURYTREMA SP EGGS PER GRAM OF FECES IN NATURALLY INFECTED CATTLE

Eurytrema sp. egg counts (epg) in the feces of naturally infected cattle were performed and the technique employed showed 94.2% probability of detecting positive cases of the infection with a single examination independently of the host parasite burden. It was also demonstrated that the epg of Eurytrema sp. follows a negative binomial distribution model and is characterized by its small magnitude.

Density and spatial distribution of Atta sexdens rubropilosa and Atta laevigata colonies (Hym., Formicidae) in Eucalyptus spp. forests

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Spatial Distribution of Euschistus heros (F.) (Hemiptera: Pentatomidae) in Soybean

Soybean bugs are major crop pests that cause significant reduction in harvest yield and influence grain quality. The aim of this study was to verify the spatial distribution of Euschistus heros (F.) (Hemiptera: Pentatomidae) in conventional and transgenic soybean cultivars. The experiment was conducted during the 2010-2011 crop season in UNESP/FCAV, Jaboticabal, SP, Brazil, in two fields of 10,000-m2 area that were subdivided into 100 plots (10 m × 10 m). The cultivars sown were M 7908 RR and its isoline M-SOY 8001. The number of the first to fifth instars and the number of adults were determined. To evaluate insect dispersion in the area, the following indices were used: variance/mean ratio, Morisita index, Green coefficient, and the k exponent of the negative binomial distribution. To study probabilistic models to describe the spatial distribution of the insects, the adjustments of the Poisson and negative binomial distributions were tested. The first to third instars showed aggregated spatial distribution, whereas the fourth and fifth instars, and adults, isolated or grouped, showed variation in the arrangement, ranging from moderately aggregated to randomly dispersed. During the adjustment of probability distributions, the negative binomial distribution model showed adjustment for the first to third instars, fourth and fifth instars, adults, and fourth and fifth instars plus adults. © 2013 Sociedade Entomológica do Brasil.

A Poisson mixed model with nonnormal random effect distribution

In this paper, we propose a random intercept Poisson model in which the random effect is assumed to follow a generalized log-gamma (GLG) distribution. This random effect accommodates (or captures) the overdispersion in the counts and induces within-cluster correlation. We derive the first two moments for the marginal distribution as well as the intraclass correlation. Even though numerical integration methods are, in general, required for deriving the marginal models, we obtain the multivariate negative binomial model from a particular parameter setting of the hierarchical model. An iterative process is derived for obtaining the maximum likelihood estimates for the parameters in the multivariate negative binomial model. Residual analysis is proposed and two applications with real data are given for illustration. (C) 2011 Elsevier B.V. All rights reserved.

Differential expression analysis for sequence count data via mixtures of negative binomials

The recent advent of Next-generation sequencing technologies has revolutionized the way of analyzing the genome. This innovation allows to get deeper information at a lower cost and in less time, and provides data that are discrete measurements. One of the most important applications with these data is the differential analysis, that is investigating if one gene exhibit a different expression level in correspondence of two (or more) biological conditions (such as disease states, treatments received and so on). As for the statistical analysis, the final aim will be statistical testing and for modeling these data the Negative Binomial distribution is considered the most adequate one especially because it allows for "over dispersion". However, the estimation of the dispersion parameter is a very delicate issue because few information are usually available for estimating it. Many strategies have been proposed, but they often result in procedures based on plug-in estimates, and in this thesis we show that this discrepancy between the estimation and the testing framework can lead to uncontrolled first-type errors. We propose a mixture model that allows each gene to share information with other genes that exhibit similar variability. Afterwards, three consistent statistical tests are developed for differential expression analysis. We show that the proposed method improves the sensitivity of detecting differentially expressed genes with respect to the common procedures, since it is the best one in reaching the nominal value for the first-type error, while keeping elevate power. The method is finally illustrated on prostate cancer RNA-seq data.