Assessing competition among species through simultaneously modeling marginal counts and respective proportions
TL;DR: In this article, a community-based Poisson model with multivariate random effects is introduced to explicitly characterize marginal counts and respective proportions simultaneously, and the existence and strength of the competition among species can be assessed through their approach.
Abstract: Evolution processes of multiple competitive and non-competitive species have traditionally been handled using different methods. In particular, evolution processes of multiple competitive species have usually been evaluated by the continuous and discrete proportions analysis; however, such evolution processes cannot be solely characterized by their relative proportions in practice. In this paper, we introduce a community based Poisson model with multivariate random effects to explicitly characterize marginal counts and respective proportions simultaneously. Furthermore, our method provides a unified approach to handle evolution processes of competitive and non-competitive species. In fact, the existence and strength of the competition among species can be assessed through our approach. Unlike those marginal modelling methods, our approach explicitly predicts random effects. Our model inference does not rely on distributional assumption of observed multivariate random effects, and thus is more robust than traditional approaches assuming parametric random effects.
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TL;DR: In this article, the authors present a generalized linear model for categorical data, which is based on the Logit model, and use it to fit Logistic Regression models.
Abstract: Preface. 1. Introduction: Distributions and Inference for Categorical Data. 1.1 Categorical Response Data. 1.2 Distributions for Categorical Data. 1.3 Statistical Inference for Categorical Data. 1.4 Statistical Inference for Binomial Parameters. 1.5 Statistical Inference for Multinomial Parameters. Notes. Problems. 2. Describing Contingency Tables. 2.1 Probability Structure for Contingency Tables. 2.2 Comparing Two Proportions. 2.3 Partial Association in Stratified 2 x 2 Tables. 2.4 Extensions for I x J Tables. Notes. Problems. 3. Inference for Contingency Tables. 3.1 Confidence Intervals for Association Parameters. 3.2 Testing Independence in Two Way Contingency Tables. 3.3 Following Up Chi Squared Tests. 3.4 Two Way Tables with Ordered Classifications. 3.5 Small Sample Tests of Independence. 3.6 Small Sample Confidence Intervals for 2 x 2 Tables . 3.7 Extensions for Multiway Tables and Nontabulated Responses. Notes. Problems. 4. Introduction to Generalized Linear Models. 4.1 Generalized Linear Model. 4.2 Generalized Linear Models for Binary Data. 4.3 Generalized Linear Models for Counts. 4.4 Moments and Likelihood for Generalized Linear Models . 4.5 Inference for Generalized Linear Models. 4.6 Fitting Generalized Linear Models. 4.7 Quasi likelihood and Generalized Linear Models . 4.8 Generalized Additive Models . Notes. Problems. 5. Logistic Regression. 5.1 Interpreting Parameters in Logistic Regression. 5.2 Inference for Logistic Regression. 5.3 Logit Models with Categorical Predictors. 5.4 Multiple Logistic Regression. 5.5 Fitting Logistic Regression Models. Notes. Problems. 6. Building and Applying Logistic Regression Models. 6.1 Strategies in Model Selection. 6.2 Logistic Regression Diagnostics. 6.3 Inference About Conditional Associations in 2 x 2 x K Tables. 6.4 Using Models to Improve Inferential Power. 6.5 Sample Size and Power Considerations . 6.6 Probit and Complementary Log Log Models . 6.7 Conditional Logistic Regression and Exact Distributions . Notes. Problems. 7. Logit Models for Multinomial Responses. 7.1 Nominal Responses: Baseline Category Logit Models. 7.2 Ordinal Responses: Cumulative Logit Models. 7.3 Ordinal Responses: Cumulative Link Models. 7.4 Alternative Models for Ordinal Responses . 7.5 Testing Conditional Independence in I x J x K Tables . 7.6 Discrete Choice Multinomial Logit Models . Notes. Problems. 8. Loglinear Models for Contingency Tables. 8.1 Loglinear Models for Two Way Tables. 8.2 Loglinear Models for Independence and Interaction in Three Way Tables. 8.3 Inference for Loglinear Models. 8.4 Loglinear Models for Higher Dimensions. 8.5 The Loglinear Logit Model Connection. 8.6 Loglinear Model Fitting: Likelihood Equations and Asymptotic Distributions . 8.7 Loglinear Model Fitting: Iterative Methods and their Application . Notes. Problems. 9. Building and Extending Loglinear/Logit Models. 9.1 Association Graphs and Collapsibility. 9.2 Model Selection and Comparison. 9.3 Diagnostics for Checking Models. 9.4 Modeling Ordinal Associations. 9.5 Association Models . 9.6 Association Models, Correlation Models, and Correspondence Analysis . 9.7 Poisson Regression for Rates. 9.8 Empty Cells and Sparseness in Modeling Contingency Tables. Notes. Problems. 10. Models for Matched Pairs. 10.1 Comparing Dependent Proportions. 10.2 Conditional Logistic Regression for Binary Matched Pairs. 10.3 Marginal Models for Square Contingency Tables. 10.4 Symmetry, Quasi symmetry, and Quasiindependence. 10.5 Measuring Agreement Between Observers. 10.6 Bradley Terry Model for Paired Preferences. 10.7 Marginal Models and Quasi symmetry Models for Matched Sets . Notes. Problems. 11. Analyzing Repeated Categorical Response Data. 11.1 Comparing Marginal Distributions: Multiple Responses. 11.2 Marginal Modeling: Maximum Likelihood Approach. 11.3 Marginal Modeling: Generalized Estimating Equations Approach. 11.4 Quasi likelihood and Its GEE Multivariate Extension: Details . 11.5 Markov Chains: Transitional Modeling. Notes. Problems. 12. Random Effects: Generalized Linear Mixed Models for Categorical Responses. 12.1 Random Effects Modeling of Clustered Categorical Data. 12.2 Binary Responses: Logistic Normal Model. 12.3 Examples of Random Effects Models for Binary Data. 12.4 Random Effects Models for Multinomial Data. 12.5 Multivariate Random Effects Models for Binary Data. 12.6 GLMM Fitting, Inference, and Prediction. Notes. Problems. 13. Other Mixture Models for Categorical Data . 13.1 Latent Class Models. 13.2 Nonparametric Random Effects Models. 13.3 Beta Binomial Models. 13.4 Negative Binomial Regression. 13.5 Poisson Regression with Random Effects. Notes. Problems. 14. Asymptotic Theory for Parametric Models. 14.1 Delta Method. 14.2 Asymptotic Distributions of Estimators of Model Parameters and Cell Probabilities. 14.3 Asymptotic Distributions of Residuals and Goodnessof Fit Statistics. 14.4 Asymptotic Distributions for Logit/Loglinear Models. Notes. Problems. 15. Alternative Estimation Theory for Parametric Models. 15.1 Weighted Least Squares for Categorical Data. 15.2 Bayesian Inference for Categorical Data. 15.3 Other Methods of Estimation. Notes. Problems. 16. Historical Tour of Categorical Data Analysis . 16.1 Pearson Yule Association Controversy. 16.2 R. A. Fisher s Contributions. 16.3 Logistic Regression. 16.4 Multiway Contingency Tables and Loglinear Models. 16.5 Recent and Future? Developments. Appendix A. Using Computer Software to Analyze Categorical Data. A.1 Software for Categorical Data Analysis. A.2 Examples of SAS Code by Chapter. Appendix B. Chi Squared Distribution Values. References. Examples Index. Author Index. Subject Index. Sections marked with an asterisk are less important for an overview.
4,650 citations
TL;DR: In this article, a generalization of Henderson's joint likelihood, called a hierarchical or h-likelihood, for inferences from hierarchical generalized linear models is proposed, where the distribution of these components is not restricted to be normal; this allows a broader class of models, which includes generalized linear mixed models.
Abstract: We consider hierarchical generalized linear models which allow extra error components in the linear predictors of generalized linear models. The distribution of these components is not restricted to be normal; this allows a broader class of models, which includes generalized linear mixed models. We use a generalization of Henderson's joint likelihood, called a hierarchical or h-likelihood, for inferences from hierarchical generalized linear models. This avoids the integration that is necessary when marginal likelihood is used. Under appropriate conditions maximizing the h-likelihood gives fixed effect estimators that are asymptotically equivalent to those obtained from the use of marginal likelihood; at the same time we obtain the random effect estimates that are asymptotically best unbiased predictors. An adjusted profile h-likelihood is shown to give the required generalization of restricted maximum likelihood for the estimation of dispersion components. A scaled deviance test for the goodness of fit, a model selection criterion for choosing between various dispersion models and a graphical method for checking the distributional assumption of random effects are proposed. The ideas of quasi-likelihood and extended quasi-likelihood are generalized to the new class. We give examples of the Poisson-gamma, binomial-beta and gamma-inverse gamma hierarchical generalized linear models. A resolution is proposed for the apparent difference between population-averaged and subject-specific models. A unified framework is provided for viewing and extending many existing methods.
825 citations
TL;DR: This work introduces a family of multivariate binary distributions with certain conditional linear property that is particularly useful for efficient and easy simulation of correlated binary variables with a given marginal mean vector and correlation matrix.
Abstract: SUMMARY We introduce a family of multivariate binary distributions with certain conditional linear property. This family is particularly useful for efficient and easy simulation of correlated binary variables with a given marginal mean vector and correlation matrix.
215 citations
TL;DR: In this paper, a general approach for logit random effects modeling of clustered ordinal and nominal responses is presented, where the maximum likelihood estimation utilizes adaptive Gauss-Hermite quadrature within a quasi-Newton maximization algorithm.
Abstract: This article presents a general approach for logit random effects modelling of clustered ordinal and nominal responses. We review multinomial logit random effects models in a unified form as multivariate generalized linear mixed models. Maximum likelihood estimation utilizes adaptive Gauss-Hermite quadrature within a quasi-Newton maximization algorithm. For cases in which this is computationally infeasible, we generalize a Monte Carlo EM algorithm. We also generalize a pseudo-likelihood approach that is simpler but provides poorer approximations for the likelihood. Besides the usual normality structure for random effects, we also present a semi-parametric approach treating the random effects in a non-parametric manner. An example comparing reviews of movie critics uses adjacent-categories logit models and a related baseline-category logit model.
181 citations
TL;DR: In this article, a Poisson model was proposed for nested random effects Cox proportional hazards models, where the principal results depend only on the first and second moments of the unobserved random effects.
Abstract: SUMMARY We propose a Poisson modelling approach to nested random effects Cox proportional hazards models. An important feature of this approach is that the principal results depend only on the first and second moments of the unobserved random effects. The orthodox best linear unbiased predictor approach to random effects Poisson modelling techniques enables us to justify appropriate consistency and optimality. The explicit expressions for the random effects given by our approach facilitate incorporation of a relatively large number of random effects. The use of the proposed methods is illustrated through the reanalysis of data from a large-scale cohort study of particulate air pollution and mortality previously reported by Pope et al. (1995).
111 citations