Simple Incorporation of Interactions into Additive Models

Often, the functional form of covariate effects in an additive model varies across groups defined by levels of a categorical variable. This structure represents a factor-by-curve interaction. This article presents penalized spline models that incorporate factor-by-curve interactions into additive models. A mixed model formulation for penalized splines allows for straightforward model fitting and smoothing parameter selection. We illustrate the proposed model by applying it to pollen ragweed data in which seasonal trends vary by year.     

Laplace approximation in measurement error models

Likelihood analysis for regression models with measurement errors in explanatory variables typically involves integrals that do not have a closed-form solution. In this case, numerical methods such as Gaussian quadrature are generally employed. However, when the dimension of the integral is large, these methods become computationally demanding or even unfeasible. This paper proposes the use of the Laplace approximation to deal with measurement error problems when the likelihood function involves high-dimensional integrals. The cases considered are generalized linear models with multiple covariates measured with error and generalized linear mixed models with measurement error in the covariates. The asymptotic order of the approximation and the asymptotic properties of the Laplace-based estimator for these models are derived. The method is illustrated using simulations and real-data analysis.     

Stochastic Approximation Boosting for Incomplete Data Problems

Summary Boosting is a powerful approach to fitting regression models. This article describes a boosting algorithm for likelihood‐based estimation with incomplete data. The algorithm combines boosting with a variant of stochastic approximation that uses Markov chain Monte Carlo to deal with the missing data. Applications to fitting generalized linear and additive models with missing covariates are given. The method is applied to the Pima Indians Diabetes Data where over half of the cases contain missing values.     

Association of twenty-three plasma elements with fasting serum glucose among Chinese population from four areas with different pollution level

BackgroundAssociation between fasting serum glucose (FSG) and certain mineral elements has been extensively reported. Investigation regarding multi-element exposure among subjects with different exposure level is warranted to confirm the association and further explore dose-dependent relationship.MethodsA total of 3488 participants were recruited from four counties of Hunan province, South China. Basic characteristics were collected by face to face interview and 23 elements in plasma were determined by inductively coupled plasma mass spectrometry. We applied fully adjusted generalized linear regression model and multivariable restricted cubic spline function to test the association and dose-response relationship of FSG with 23 elements.ResultsThe results indicated that FSG was positively associated with plasma⁷⁸selenium level [regression coefficient (β), 0.001; 95 % confidence interval (CI), 0.001, 0.001] in a dose-dependent manner, robust to the adjustment for suspected covariates and stratification by age, gender, BMI and smoking status. A negative association was found between FSG and plasma ²⁰⁸lead (β, -0.004; 95 % CI, -0.016, -0.002), ⁵²chromium (β, -0.002; 95 % CI, -0.004, -0.001) and ⁴⁷titanium (β, -0.001; 95 % CI, -0.002, -0.001).Conclusion⁷⁸selenium was positively while ²⁰⁸lead, ⁵²chromium and ⁴⁷titanium were negatively associated with FSG in the present study. However, prospective studies are needed to confirm the results.     

Prediction of plant species distribution in lowland river valleys in Belgium: modelling species response to site conditions

In ecological modelling, limitations in data and their applicability for predictive modelling are more rule than exception. Often modelling has to be performed on sub-optimal data, as explicit and controlled collection of (more) appropriate data would not be feasible. An example of predictive ecological modelling is given with application of generalized additive and generalized linear models fitted to presence–absence records of plant species and site condition data from four nutrient-poor Flemish lowland valleys. Standard regression procedures are used for modelling, although explanatory and response data do not meet all the assumptions implicit in these procedures. Data were non-randomly collected and are spatially autocorrelated; model residuals retain part of that correlation. The scale of most site-condition records does not match the scale of the response variable (species distribution). Hence, interpolated and up-scaled explanatory variables are used. Data are aggregated from distinct phytogeographical regions to allow for generalized models, applicable to a wider population of river valleys in the same region. Nevertheless, ecologically sound models are obtained, which predict well the distribution of most plant species for the Flemish river valleys considered.     

Random effects modeling of multiple binomial responses using the multivariate binomial logit-normal distribution

The multivariate binomial logit-normal distribution is a mixture distribution for which, (i) conditional on a set of success probabilities and sample size indices, a vector of counts is independent binomial variates, and (ii) the vector of logits of the parameters has a multivariate normal distribution. We use this distribution to model multivariate binomial-type responses using a vector of random effects. The vector of logits of parameters has a mean that is a linear function of explanatory variables and has an unspecified or partly specified covariance matrix. The model generalizes and provides greater flexibility than the univariate model that uses a normal random effect to account for positive correlations in clustered data. The multivariate model is useful when different elements of the response vector refer to different characteristics, each of which may naturally have its own random effect. It is also useful for repeated binary measurement of a single response when there is a nonexchangeable association structure, such as one often expects with longitudinal data or when negative association exists for at least one pair of responses. We apply the model to an influenza study with repeated responses in which some pairs are negatively associated and to a developmental toxicity study with continuation-ratio logits applied to an ordinal response with clustered observations.     

Generalized models vs. classification tree analysis: Predicting spatial distributions of plant species at different scales

Abstract. Statistical models of the realized niche of species are increasingly used, but systematic comparisons of alternative methods are still limited. In particular, only few studies have explored the effect of scale in model outputs. In this paper, we investigate the predictive ability of three statistical methods (generalized linear models, generalized additive models and classification tree analysis) using species distribution data at three scales: fine (Catalonia), intermediate (Portugal) and coarse (Europe). Four Mediterranean tree species were modelled for comparison. Variables selected by models were relatively consistent across scales and the predictive accuracy of models varied only slightly. However, there were slight differences in the performance of methods. Classification tree analysis had a lower accuracy than the generalized methods, especially at finer scales. The performance of generalized linear models also increased with scale. At the fine scale GLM with linear terms showed better accuracy than GLM with quadratic and polynomial terms. This is probably because distributions at finer scales represent a linear sub‐sample of entire realized niches of species. In contrast to GLM, the performance of GAM was constant across scales being more data‐oriented. The predictive accuracy of GAM was always at least equal to other techniques, suggesting that this modelling approach is more robust to variations of scale because it can deal with any response shape.     

广义Logistic模型的捕获优化问题

以王寿松所提出的广义Ｌｏｇｉｓｔｉｃ模型为基础,讨论单种群生物资源的捕获优化问题,分析了被开发生物种群的动力学性质。在单位捕获努力量假定下,以最大可持续捕获量为管理目标,确定了线性捕获下的最优捕获策略,得到了最优捕获努力量,最大可持续收获及相应的最优种群水平的显式表达式,包括著名的Ｓｃｈａｅｆｅｒ模型作为特例,推广了相应的结果。     

A new association test based on disease allele selection for case–control genome-wide association studies

Background

Current robust association tests for case–control genome-wide association study (GWAS) data are mainly based on the assumption of some specific genetic models. Due to the richness of the genetic models, this assumption may not be appropriate. Therefore, robust but powerful association approaches are desirable.

Results

In this paper, we propose a new approach to testing for the association between the genotype and phenotype for case–control GWAS. This method assumes a generalized genetic model and is based on the selected disease allele to obtain a p-value from the more powerful one-sided test. Through a comprehensive simulation study we assess the performance of the new test by comparing it with existing methods. Some real data applications are also used to illustrate the use of the proposed test.

Conclusions

Based on the simulation results and real data application, the proposed test is powerful and robust.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-358) contains supplementary material, which is available to authorized users.     

On the asymptotics of marginal regression splines with longitudinal data

There have been studies on how the asymptotic efficiency ofa nonparametric function estimator depends on the handling ofthe within-cluster correlation when nonparametric regressionmodels are used on longitudinal or cluster data. In particular,methods based on smoothing splines and local polynomial kernelsexhibit different behaviour. We show that the generalized estimationequations based on weighted least squares regression splinesfor the nonparametric function have an interesting property:the asymptotic bias of the estimator does not depend on theworking correlation matrix, but the asymptotic variance, andtherefore the mean squared error, is minimized when the truecorrelation structure is specified. This property of the asymptoticbias distinguishes regression splines from smoothing splines.     

Semiparametric models for missing covariate and response data in regression models

We consider a class of semiparametric models for the covariate distribution and missing data mechanism for missing covariate and/or response data for general classes of regression models including generalized linear models and generalized linear mixed models. Ignorable and nonignorable missing covariate and/or response data are considered. The proposed semiparametric model can be viewed as a sensitivity analysis for model misspecification of the missing covariate distribution and/or missing data mechanism. The semiparametric model consists of a generalized additive model (GAM) for the covariate distribution and/or missing data mechanism. Penalized regression splines are used to express the GAMs as a generalized linear mixed effects model, in which the variance of the corresponding random effects provides an intuitive index for choosing between the semiparametric and parametric model. Maximum likelihood estimates are then obtained via the EM algorithm. Simulations are given to demonstrate the methodology, and a real data set from a melanoma cancer clinical trial is analyzed using the proposed methods.     

Modeling repeated count data subject to informative dropout

In certain diseases, outcome is the number of morbid events over the course of follow-up. In epilepsy, e.g., daily seizure counts are often used to reflect disease severity. Follow-up of patients in clinical trials of such diseases is often subject to censoring due to patients dying or dropping out. If the sicker patients tend to be censored in such trials, estimates of the treatment effect that do not incorporate the censoring process may be misleading. We extend the shared random effects approach of Wu and Carroll (1988, Biometrics 44, 175-188) to the setting of repeated counts of events. Three strategies are developed. The first is a likelihood-based approach for jointly modeling the count and censoring processes. A shared random effect is incorporated to introduce dependence between the two processes. The second is a likelihood-based approach that conditions on the dropout times in adjusting for informative dropout. The third is a generalized estimating equations (GEE) approach, which also conditions on the dropout times but makes fewer assumptions about the distribution of the count process. Estimation procedures for each of the approaches are discussed, and the approaches are applied to data from an epilepsy clinical trial. A simulation study is also conducted to compare the various approaches. Through analyses and simulations, we demonstrate the flexibility of the likelihood-based conditional model for analyzing data from the epilepsy trial.     

离散广义LOGISTIC模型的渐进性态和混沌现象

1引言自Li－Yorke的著名论文《3一周期意味混饨》问世以来,人们对一维离散模型进行了大量细致的研究工作,其中Logistic模型研究的最为彻底,并由此得到一系列普遍适用的理论结果［‘’2］文【3jIw接地对广义LOgistiC模型的稳定性及其吸引域进行了细致的研究,但其结论尚有不完善之处．在研究其周期解及混炖现象时,仅在IUI＜1时对其近似模型进行了初步讨论·这里参数C＞0为种群内禀生长率,U＞一1表示种群对环境（包括营养资源等）利用率程度的参数．显然,当U—0时,模型（2）可化为LOgistiC模型（1）．本文将直接对模型（2）进行…     

广义Kolmogorov模型的Lyapunov函数构造新算法及其应用

本文对广义Kolmogorov模型,给出构造Lyapunov函数的新算法,在文献1中只对其中某些特殊类型给出几种特殊的构造方法,而本文给出的是这类模型的一般新算法,应用较广泛。