ESTIMATING WITHIN-SCHOOL CONTACT NETWORKS TO UNDERSTAND INFLUENZA TRANSMISSION

Many epidemic models approximate social contact behavior by assuming random mixing within mixing groups (e.g., homes, schools, and workplaces). The effect of more realistic social network structure on estimates of epidemic parameters is an open area of exploration. We develop a detailed statistical model to estimate the social contact network within a high school using friendship network data and a survey of contact behavior. Our contact network model includes classroom structure, longer durations of contacts to friends than non-friends and more frequent contacts with friends, based on reports in the contact survey. We performed simulation studies to explore which network structures are relevant to influenza transmission. These studies yield two key findings. First, we found that the friendship network structure important to the transmission process can be adequately represented by a dyad-independent exponential random graph model (ERGM). This means that individual-level sampled data is sufficient to characterize the entire friendship network. Second, we found that contact behavior was adequately represented by a static rather than dynamic contact network. We then compare a targeted antiviral prophylaxis intervention strategy and a grade closure intervention strategy under random mixing and network-based mixing. We find that random mixing overestimates the effect of targeted antiviral prophylaxis on the probability of an epidemic when the probability of transmission in 10 minutes of contact is less than 0.004 and underestimates it when this transmission probability is greater than 0.004. We found the same pattern for the final size of an epidemic, with a threshold transmission probability of 0.005. We also find random mixing overestimates the effect of a grade closure intervention on the probability of an epidemic and final size for all transmission probabilities. Our findings have implications for policy recommendations based on models assuming random mixing, and can inform further development of network-based models.     

ESTIMATING DISTRIBUTION FUNCTIONS FROM SURVEY DATA WITH LIMITED BENCHMARK INFORMATION

The model-based approach to estimation of finite population distribution functions introduced in Chambers & Dunstan (1986) is extended to the case where only summary information is available for the auxiliary size variable. Monte Carlo results indicate that this ‘limited information’ extension is almost as efficient as the ‘full information’ method proposed in the above reference. These results also indicate that the model-based confidence intervals generated by either of these methods have superior coverage properties to more conventional design-based confidence intervals.     

ESTIMATING BAYESIAN NETWORKS FOR HIGH‐DIMENSIONAL DATA WITH COMPLEX MEAN STRUCTURE AND RANDOM EFFECTS

The estimation of Bayesian networks given high‐dimensional data, in particular gene expression data, has been the focus of much recent research. Whilst there are several methods available for the estimation of such networks, these typically assume that the data consist of independent and identically distributed samples. It is often the case, however, that the available data have a more complex mean structure, plus additional components of variance, which must then be accounted for in the estimation of a Bayesian network. In this paper, score metrics that take account of such complexities are proposed for use in conjunction with score‐based methods for the estimation of Bayesian networks. We propose first, a fully Bayesian score metric, and second, a metric inspired by the notion of restricted maximum likelihood. We demonstrate the performance of these new metrics for the estimation of Bayesian networks using simulated data with known complex mean structures. We then present the analysis of expression levels of grape‐berry genes adjusting for exogenous variables believed to affect the expression levels of the genes. Demonstrable biological effects can be inferred from the estimated conditional independence relationships and correlations amongst the grape‐berry genes.     

NONPARAMETRIC METHOD FOR ESTIMATING THE SIZE OF AN OPEN POPULATION USING MARGINAL DATA FROM REPEATED MULTIPLE LISTS

Kernel smoothing methods are used to extend the Poisson log‐linear approach to the estimation of the size of population using multiple lists to an open population when the multiple lists are recorded at each time point. The data is marginal as only the lists at each time point are available and the transitions of individuals between lists at different time points are not observable. Our analysis is motivated by and applied to data on the number of drug addicts in the Hong Kong Special Administrative Region.     

ESTIMATING PROCESSES OF COUNTS FROM CROSS-SECTIONAL AGGREGATE DATA, WITH AN APPLICATION TO MULTISTATE LIFE TABLES AND HEALTH EXPECTANCIES

This paper discusses the estimation of time‐dependent probabilities of a finite state‐space discrete‐time process using aggregate cross‐sectional data. A large‐sample version of multistate logistic regression is described and shown to be useful for analysing multistate life tables. The technique is applied to the estimation of disability‐free, severely disabled and other disabled survival curves and health expectancies in Australia, based on data from national health surveys in 1988, 1993 and 1998. A conclusion is that there has been a general upward trend in the future time expected to be spent in a state of disability, the picture being more pessimistic for males than females. For example, during 1988‐1998 the estimated increase in male life expectancy at birth of 2.7 years is decomposed as a decrease of 1.2 years in disability‐free health (life) expectancy and increases of 1.3 and 2.6 years, respectively, in states of severe disability and other disability.     

ESTIMATING POPULATION SIZE FROM CAPTURE-RECAPTURE EXPERIMENTS IN CONTINUOUS TIME

Estimates for the size of a closed population are given for multiple recapture studies in continuous time. The estimates are derived by a method of moments for martingales. An estimate and associated standard error of the population size are derived for a homogeneous population when the capture rates are permitted to depend on time in an unspecified manner. Corresponding results are obtained when the capture rates vary among individuals as well. Explicit expressions are given for these estimates and standard errors which involve only simple computation.     

NONPARAMETRIC QUANTILE ESTIMATION FROM RECORD-BREAKING DATA

Sometimes, in industrial quality control experiments and destructive stress testing, only values smaller than all previous ones are observed. Here we consider nonparametric quantile estimation, both the ‘sample quantile function’ and kernel-type estimators, from such record-breaking data. For a single record-breaking sample, consistent estimation is not possible except in the extreme tails of the distribution. Hence replication is required, and for m. such independent record-breaking samples the quantile estimators are shown to be strongly consistent and asymptotically normal as m-→∞. Also, for small m, the mean-squared errors, biases and smoothing parameters (for the smoothed estimators) are investigated through computer simulations.     

ESTIMATING A LOGIT MODEL WITH RANDOMIZED DATA: THE CASE OF COCAINE USE

In his influential book, Maddala (1983) suggests combining randomized response survey data with other personal information to estimate logit models predicting immoral, unpopular, or unlawful behaviour. This study is one of the first to implement this technique using real data. Models of college students' recent cocaine use are estimated with academic performance and socio-economic characteristics as determinants. Parameter estimates obtained from randomized response surveys are compared to those obtained using conventional, direct question surveys. The results indicate that randomized response estimates provide useful information on the degree to which inferences regarding the determinants of cocaine use are sensitive to survey type.     

ASYMPTOTIC DISTRIBUTIONS OF SEMIPARAMETRIC MAXIMUM LIKELIHOOD ESTIMATORS WITH ESTIMATING EQUATIONS FOR GROUP-CENSORED DATA

Semiparametric maximum likelihood estimation with estimating equations (SMLE) is more flexible than traditional methods; it has fewer restrictions on distributions and regression models. The required information about distribution and regression structures is incorporated in estimating equations of the SMLE to improve the estimation quality of non‐parametric methods. The likelihood of SMLE for censored data involves complicated implicit functions without closed‐form expressions, and the first derivatives of the log‐profile‐likelihood cannot be expressed as summations of independent and identically distributed random variables; it is challenging to derive asymptotic properties of the SMLE for censored data. For group‐censored data, the paper shows that all the implicit functions are well defined and obtains the asymptotic distributions of the SMLE for model parameters and lifetime distributions. With several examples the paper compares the SMLE, the regular non‐parametric likelihood estimation method and the parametric MLEs in terms of their asymptotic efficiencies, and illustrates application of SMLE. Various asymptotic distributions of the likelihood ratio statistics are derived for testing the adequacy of estimating equations and a partial set of parameters equal to some known values.     

ONE-SIDED ESTIMATING AND TESTING PROBLEMS FOR LOCATION MODELS FROM GROUPED SAMPLES

This article deals with one-sided problems for location models from grouped samples. Suppose the support region of a density function, which does not depend on parameters, is divided into some disjointed intervals, grouped samples are the number of observations falling in each intervals respectively. The studying of grouped samples may be dated back to the beginning of the century, in which only one sample location and/or scale models is considered. This article considers one-sided estimating and testing problems for location models. Some methods for computing the maximum likelihood estimates of the parameters subject to order restrictions are proposed and a numerical example by the method is given.     

TIGHT UPPER CONFIDENCE LIMITS FROM DISCRETE DATA

Consider the problem of finding an upper 1 –α confidence limit for a scalar parameter of interest ø in the presence of a nuisance parameter vector θ when the data are discrete. Approximate upper limits T may be found by approximating the relevant unknown finite sample distribution by its limiting distribution. Such approximate upper limits typically have coverage probabilities below, sometimes far below, 1 –α for certain values of (θ, ø). This paper remedies that defect by shifting the possible values t of T so that they are as small as possible subject both to the minimum coverage probability being greater than or equal to 1 –α, and to the shifted values being in the same order as the unshifted ts. The resulting upper limits are called ‘tight’. Under very weak and easily checked regularity conditions, a formula is developed for the tight upper limits.     

ESTIMATING THE PARAMETERS OF NORMAL AND LOGISTIC DISTRIBUTIONS FROM CENSORED SAMPLES1

Let g(z) be the ratio of the ordinate and the probability integral of the distribution of a variate z. The relation g(z)～+βz is used to derive (i) estimators μ_r and s?_r of the parameters of a truncated normal distribution and (ii) estimators μ_c and s?_c of the mean and standard deviation of a logistic distribution from doubly censored samples. The variances and eovariances of these estimators are obtained. They are shown to be nearly as efficient as the maximum likelihood estimators and easier to compute.     

ESTIMATING A RATIO OF MEANS FROM BIVARIATE COUNTS WITH APPLICATIONS IN STEREOLOGY

In survey sampling and in stereology, it is often desirable to estimate the ratio of means θ= E(Y)/E(X) from bivariate count data (X, Y) with unknown joint distribution. We review methods that are available for this problem, with particular reference to stereological applications. We also develop new methods based on explicit statistical models for the data, and associated model diagnostics. The methods are tested on a stereological dataset. For point‐count data, binomial regression and bivariate binomial models are generally adequate. Intercept‐count data are often overdispersed relative to Poisson regression models, but adequately fitted by negative binomial regression.     

ASYMPTOTIC PROPERTIES OF AN OPTIMAL ESTIMATING FUNCTION APPROACH TO THE ANALYSIS OF MARK RECAPTURE DATA

ABSTRACT

A drawback of non parametric estimators of the size of a closed population in the presence of heterogeneous capture probabilities has been their lack of analytic tractability. Here we show that the martingale estimating function/sample coverage approach to estimating the size of a closed population with heterogeneous capture probabilities is mathematically tractable and develop its large sample properties.     

ANALYSIS OF DATA FROM A SINGLE EPIDEMIC1

A model with nonrandom latent and infectious periods is suggested for epidemics in a large community. This permits a relatively complete statistical analysis of data from the spread of a single epidemic. An attractive feature of such models is the possibility of exploring how the rate of spread of the disease depends on the number of susceptibles and infectives. An application to smallpox data is included.     

CSISZAR DIVERGENCE FROM CONSTANT FAILURE RATE MODEL FOR GROUPED DATA

We propose a measure of divergence in failure rates of a system from the constant failure rate model for a grouped data situation. We use this measure to compare the divergences of several systems from the constant failure rate model and find the asymptotic distributions of the test statistics. Several applications are discussed to illustrate the procedure. In the context of testing the goodness-of-fit with the constant failure rate model, we conduct a simulation study which shows that this procedure compares favorably with the Pearson chi-square test and the likelihood ratio test procedures.     

ESTIMATION OF LLUCH'S EXTENDED LINEAR EXPENDITURE SYSTEM FROM CROSS-SECTIONAL DATA1

Complete sets of demand relations may be fitted using varying types of sample information and varying a priori specifications. In this paper the identification and estimation of Lluch's extended linear expenditure system (ELES) from cross-sectional data alone is investigated. Under the most favourable conditions of data availability, all of the parameters of the ELES model are identified, and are estimable by the method of reduced form least squares. This is the case where observations on permanent income are available for the consuming units of the cross section and where, in addition, prices are recorded (even though they do not vary from one consuming unit to the next). Under the least favourable conditions only the marginal budget shares are identified. This corresponds to the case where no data on permanent income, or on savings, are available. The conventional ordinary least squares estimators of the marginal budget shares are, under these conditions, biased and inconsistent. Expressions are developed for the large-sample biases.     

CONTINUOUS-TIME FILTERS FOR STATE ESTIMATION FROM POINT PROCESS MODELS OF NEURAL DATA

Neural spike trains, the primary communication signals in the brain, can be accurately modeled as point processes. For many years, significant theoretical work has been done on the construction of exact and approximate filters for state estimation from point process observations in continuous-time. We have previously developed approximate filters for state estimation from point process observations in discrete-time and applied them in the study of neural systems. Here, we present a coherent framework for deriving continuous-time filters from their discrete-counterparts. We present an accessible derivation of the well-known unnormalized conditional density equation for state evolution, construct a new continuous-time filter based on a Gaussian approximation, and propose a method for assessing the validity of the approximation following an approach by Brockett and Clark. We apply these methods to the problem of reconstructing arm reaching movements from simulated neural spiking activity from the primary motor cortex. This work makes explicit the connections between adaptive point process filters for analyzing neural spiking activity in continuous-time, and standard continuous-time filters for state estimation from continuous and point process observations.     

A NOTE ON ESTIMATING THE LOCATION AND SCALE PARAMETERS OF THE EXPONENTIAL DISTRIBUTION FROM A CENSORED SAMPLE

   
Replacing f (x)/F (x) by α+β(x- θ)/σ in the maximum likelihood equations ∂L/∂θ and ∂L/∂σ calculated from a censored sample, a pair of estimators θ^e and σ^e, is obtained. The variances and covariances of these estimators are calculated and compared with the corresponding values for the best linear unbiassed (BLU) estimators.     

USING LINEAR PREDICTORS TO IMPUTE ALLELE FREQUENCIES FROM SUMMARY OR POOLED GENOTYPE DATA

Recently-developed genotype imputation methods are a powerful tool for detecting untyped genetic variants that affect disease susceptibility in genetic association studies. However, existing imputation methods require individual-level genotype data, whereas in practice it is often the case that only summary data are available. For example this may occur because, for reasons of privacy or politics, only summary data are made available to the research community at large; or because only summary data are collected, as in DNA pooling experiments. In this article, we introduce a new statistical method that can accurately infer the frequencies of untyped genetic variants in these settings, and indeed substantially improve frequency estimates at typed variants in pooling experiments where observations are noisy. Our approach, which predicts each allele frequency using a linear combination of observed frequencies, is statistically straight-forward, and related to a long history of the use of linear methods for estimating missing values (e.g. Kriging). The main statistical novelty is our approach to regularizing the covariance matrix estimates, and the resulting linear predictors, which is based on methods from population genetics. We find that, besides being both fast and flexible - allowing new problems to be tackled that cannot be handled by existing imputation approaches purpose-built for the genetic context - these linear methods are also very accurate. Indeed, imputation accuracy using this approach is similar to that obtained by state-of-the art imputation methods that use individual-level data, but at a fraction of the computational cost.