The R package mice imputes incomplete multivariate data by chained equations. The software mice 1.0 appeared in the year 2000 as an S-PLUS library, and in 2001 as an R package. mice 1.0 introduced predictor selection, passive imputation and automatic pooling. This article documents mice, which extends the functionality of mice 1.0 in several ways. In mice, the analysis of imputed data is made completely general, whereas the range of models under which pooling works is substantially extended. mice adds new functionality for imputing multilevel data, automatic predictor selection, data handling, post-processing imputed values, specialized pooling routines, model selection tools, and diagnostic graphs. Imputation of categorical data is improved in order to bypass problems caused by perfect prediction. Special attention is paid to transformations, sum scores, indices and interactions using passive imputation, and to the proper setup of the predictor matrix. mice can be downloaded from the Comprehensive R Archive Network. This article provides a hands-on, stepwise approach to solve applied incomplete data problems.

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mice: Multivariate Imputation by Chained Equations in R

An essential textbook for any student or researcher in biology needing to design experiments, sample programs or analyse the resulting data The text begins with a revision of estimation and hypothesis testing methods, covering both classical and Bayesian philosophies, before advancing to the analysis of linear and generalized linear models Topics covered include linear and logistic regression, simple and complex ANOVA models (for factorial, nested, block, split-plot and repeated measures and covariance designs), and log-linear models Multivariate techniques, including classification and ordination, are then introduced Special emphasis is placed on checking assumptions, exploratory data analysis and presentation of results The main analyses are illustrated with many examples from published papers and there is an extensive reference list to both the statistical and biological literature The book is supported by a website that provides all data sets, questions for each chapter and links to software

/pdf/experimental-design-and-data-analysis-for-biologists-8ybva8d53x.pdf

Experimental Design and Data Analysis for Biologists

Models for the analysis of longitudinal data must recognize the relationship between serial observations on the same unit. Multivariate models with general covariance structure are often difficult to apply to highly unbalanced data, whereas two-stage random-effects models can be used easily. In two-stage models, the probability distributions for the response vectors of different individuals belong to a single family, but some random-effects parameters vary across individuals, with a distribution specified at the second stage. A general family of models is discussed, which includes both growth models and repeated-measures models as special cases. A unified approach to fitting these models, based on a combination of empirical Bayes and maximum likelihood estimation of model parameters and using the EM algorithm, is discussed. Two examples are taken from a current epidemiological study of the health effects of air pollution.

Random-effects models for longitudinal data

Objectives:Implementation of the International Statistical Classification of Disease and Related Health Problems, 10th Revision (ICD-10) coding system presents challenges for using administrative data. Recognizing this, we conducted a multistep process to develop ICD-10 coding algorithms to define C

https://czresearch.com/dropbox/Quan_MedCare_2005v43p1130.pdf

Coding algorithms for defining comorbidities in ICD-9-CM and ICD-10 administrative data.

Recent scientific work has established both a theoretical basis and strong empirical evidence for a causal impact of social relationships on health. Prospective studies, which control for baseline health status, consistently show increased risk of death among persons with a low quantity, and sometimes low quality, of social relationships. Experimental and quasi-experimental studies of humans and animals also suggest that social isolation is a major risk factor for mortality from widely varying causes. The mechanisms through which social relationships affect health and the factors that promote or inhibit the development and maintenance of social relationships remain to be explored.

https://science.sciencemag.org/content/sci/241/4865/540.full.pdf

Social relationships and health.

1. CONCEPTS AND EXAMPLES OF RESEARCH. Concepts. Examples. Concluding Remarks. References. 2. CLASSIFICATION OF VARIABLES AND THE CHOICE OF ANALYSIS. Classification of Variables. Overlapping of Classification Schemes. Choice of Analysis. References. 3. BASIC STATISTICS: A REVIEW. Preview. Descriptive Statistics. Random Variables and Distributions. Sampling Distributions of t, ?O2, and F. Statistical Inference: Estimation. Statistical Inference: Hypothesis Testing. Error Rate, Power, and Sample Size. Problems. References. 4. INTRODUCTION TO REGRESSION ANALYSIS. Preview. Association versus Causality. Statistical versus Deterministic Models. Concluding Remarks. References. 5. STRAIGHT-LINE REGRESSION ANALYSIS. Preview. Regression with a Single Independent Variable. Mathematical Properties of a Straight Line. Statistical Assumptions for a Straight-line Model. Determining the Best-fitting Straight Line. Measure of the Quality of the Straight-line Fit and Estimate ?a2. Inferences About the Slope and Intercept. Interpretations of Tests for Slope and Intercept. Inferences About the Regression Line ?YY|X = ?O0 + ?O1X . Prediction of a New Value of Y at X0. Problems. References. 6. THE CORRELATION COEFFICIENT AND STRAIGHT-LINE REGRESSION ANALYSIS. Definition of r. r as a Measure of Association. The Bivariate Normal Distribution. r and the Strength of the Straight-line Relationship. What r Does Not Measure. Tests of Hypotheses and Confidence Intervals for the Correlation Coefficient. Testing for the Equality of Two Correlations. Problems. References. 7. THE ANALYSIS-OF-VARIANCE TABLE. Preview. The ANOVA Table for Straight-line Regression. Problems. 8. MULTIPLE REGRESSION ANALYSIS: GENERAL CONSIDERATIONS. Preview. Multiple Regression Models. Graphical Look at the Problem. Assumptions of Multiple Regression. Determining the Best Estimate of the Multiple Regression Equation. The ANOVA Table for Multiple Regression. Numerical Examples. Problems. References. 9. TESTING HYPOTHESES IN MULTIPLE REGRESSION. Preview. Test for Significant Overall Regression. Partial F Test. Multiple Partial F Test. Strategies for Using Partial F Tests. Tests Involving the Intercept. Problems. References. 10. CORRELATIONS: MULTIPLE, PARTIAL, AND MULTIPLE PARTIAL. Preview. Correlation Matrix. Multiple Correlation Coefficient. Relationship of RY|X1, X2, !KXk to the Multivariate Normal Distribution. Partial Correlation Coefficient. Alternative Representation of the Regression Model. Multiple Partial Correlation. Concluding Remarks. Problems. References. 11. CONFOUNDING AND INTERACTION IN REGRESSION. Preview. Overview. Interaction in Regression. Confounding in Regression. Summary and Conclusions. Problems. References. 12. DUMMY VARIABLES IN REGRESSION. Preview. Definitions. Rule for Defining Dummy Variables. Comparing Two Straight-line Regression Equations: An Example. Questions for Comparing Two Straight Lines. Methods of Comparing Two Straight Lines. Method I: Using Separate Regression Fits to Compare Two Straight Lines. Method II: Using a Single Regression Equation to Compare Two Straight Lines. Comparison of Methods I and II. Testing Strategies and Interpretation: Comparing Two Straight Lines. Other Dummy Variable Models. Comparing Four Regression Equations. Comparing Several Regression Equations Involving Two Nominal Variables. Problems. References. 13. ANALYSIS OF COVARIANCE AND OTHER METHODS FOR ADJUSTING CONTINUOUS DATA. Preview. Adjustment Problem. Analysis of Covariance. Assumption of Parallelism: A Potential Drawback. Analysis of Covariance: Several Groups and Several Covariates. Comments and Cautions. Summary Problems. Reference. 14. REGRESSION DIAGNOSTICS. Preview. Simple Approaches to Diagnosing Problems in Data. Residual Analysis: Detecting Outliers and Violations of Model Assumptions. Strategies of Analysis. Collinearity. Scaling Problems. Diagnostics Example. An Important Caution. Problems. References. 15. POLYNOMIAL REGRESSION. Preview. Polynomial Models. Least-squares Procedure for Fitting a Parabola. ANOVA Table for Second-order Polynomial Regression. Inferences Associated with Second-order Polynomial Regression. Example Requiring a Second-order Model. Fitting and Testing Higher-order Model. Lack-of-fit Tests. Orthogonal Polynomials. Strategies for Choosing a Polynomial Model. Problems. 16. SELECTING THE BEST REGRESSION EQUATION. Preview. Steps in Selecting the Best Regression Equation. Step 1: Specifying the Maximum Model. Step 2: Specifying a Criterion for Selecting a Model. Step 3: Specifying a Strategy for Selecting Variables. Step 4: Conducting the Analysis. Step 5: Evaluating Reliability with Split Samples. Example Analysis of Actual Data. Issues in Selecting the Most Valid Model. Problems. References. 17. ONE-WAY ANALYSIS OF VARIANCE. Preview. One-way ANOVA: The Problem, Assumptions, and Data Configuration. for One-way Fixed-effects ANOVA. Regression Model for Fixed-effects One-way ANOVA Fixed-effects Model for One-way ANOVA. Random-effects Model for One-way ANOVA. -comparison Procedures for Fixed-effects One-way ANOVA. a Multiple-comparison Technique. Orthogonal Contrasts and Partitioning an ANOVA Sum of Squares. Problems. References. 18. RANDOMIZED BLOCKS: SPECIAL CASE OF TWO-WAY ANOVA. Preview. Equivalent Analysis of a Matched-pairs Experiment. Principle of Blocking. Analysis of a Randomized-blocks Experiment. ANOVA Table for a Randomized-blocks Experiment. Models for a Randomized-blocks Experiment. Fixed-effects ANOVA Model for a Randomized-blocks Experiment. Problems. References. 19. TWO-WAY ANOVA WITH EQUAL CELL NUMBERS. Preview. Using a Table of Cell Means. General Methodology. F Tests for Two-way ANOVA. Regression Model for Fixed-effects Two-way ANOVA. Interactions in Two-way ANOVA. Random- and Mixed-effects Two-way ANOVA Models. Problems. References. 20. TWO-WAY ANOVA WITH UNEQUAL CELL NUMBERS. Preview. Problem with Unequal Cell Numbers: Nonorthogonality. Regression Approach for Unequal Cell Sample Sizes. Higher-way ANOVA. Problems. References. 21. THE METHOD OF MAXIMUM LIKELIHOOD. Preview. The Principle of Maximum Likelihood. Statistical Inference Using Maximum Likelihood. Summary. Problems. 22. LOGISTIC REGRESSION ANALYSIS. Preview. The Logistic Model. Estimating the Odds Ratio Using Logistic Regression. A Numerical Example of Logistic Regression. Theoretical Considerations. An Example of Conditional ML Estimation Involving Pair-matched Data with Unmatched Covariates. Summary. Problems. References. 23. POLYTOMOUS AND ORDINAL LOGISTIC REGRESSION. Preview. Why Not Use Binary Regression? An Example of Polytomous Logistic Regression: One Predictor, Three Outcome Categories. An Example: Extending the Polytomous Logistic Model to Several Predictors. Ordinal Logistic Regression: Overview. A "Simple" Hypothetical Example: Three Ordinal Categories and One Dichotomous Exposure Variable. Ordinal Logistic Regression Example Using Real Data with Four Ordinal Categories and Three Predictor Variables. Summary. Problems. References. 24. POISSON REGRESSION ANALYSIS. Preview. The Poisson Distribution. Example of Poisson Regression. Poisson Regression: General Considerations. Measures of Goodness of Fit. Continuation of Skin Cancer Data Example. A Second Illustration of Poisson Regression Analysis. Summary. Problems. References. 25. ANALYSIS OF CORRELATED DATA PART 1: THE GENERAL LINEAR MIXED MODEL. Preview. Examples. General Linear Mixed Model Approach. Example: Study of Effects of an Air Polluion Episode on FEV1 Levels. Summary!XAnalysis of Correlated Data: Part 1. Problems. References. 26. ANALYSIS OF CORRELATED DATA PART 2: RANDOM EFFECTS AND OTHER ISSUES. Preview. Random Effects Revisited. Results for Random Effects Models Applied to Air Pollution Study Data. Second Example!XAnalysis of Posture Measurement Data. Recommendations about Choice of Correlation Structure. Analysis of Data for Discrete Outcomes. Problems. References. 27. SAMPLE SIZE PLANNING FOR LINEAR AND LOGISTIC REGRESSION AND ANALYSIS OF VARIANCE. Preview. Review: Sample Size Calculations for Comparisons of Means and Proportions. Sample Size Planning for Linear Regression. Sample Size Planning for Logistic Regression. Power and Sample Size Determination for Linear Models: A General Approach. Sample Size Determination for Matched Case-control Studies with a Dichotomous Outcome. Practical Considerations and Cautions. Problems. References. Appendix A. Appendix B. Appendix C. Solutions to Exercises. Index.

/pdf/applied-regression-analysis-and-other-multivariable-methods-2gj8f32ss1.pdf

Applied Regression Analysis and Other Multivariable Methods

Key Issues in Epidemiologic Research: An Overview. OBJECTIVES AND METHODS OR EPIDEMIOLOGIC RESEARCH. Fundamentals of Epidemiologic Research. Types of Epidemiologic Research. Design Options in Observational Studies. Typology of Observational Study Designs. Measures of Disease Frequency: Incidence. Other Measures of Disease Frequency. Measures of Association. Measures of Potential Impact and Summary of the Measures. VALIDITY OF EPIDEMIOLOGIC RESEARCH. Validity: General Considerations. Selection Bias. Information Bias. Confounding. Confounding Involving Several Risk Factors. PRINCIPLES AND PROCEDURES OF EPIDEMIOLOGIC ANALYSIS. Statistical Inferences About Effect Measures: Simple Analysis. Overview of Options for Control of Extraneous Factors. Stratified Analysis. Matching in Epidemiologic Studies. Interaction, Effect Modification, and Synergism. Modeling: Theoretical Considerations. Modeling: Analysis Strategy. Applications of Modeling with No Interaction. Applications of Logistic Regression with Interaction, Using Unconditional ML Estimation. Applications of Modeling: Conditional Likelihood Estimation. Appendices. Index.

Epidemiologic Research: Principles and Quantitative Methods.

Epidemiologic Research: Principles and Quantitative Methods

Introduction to Survival Analysis.- Kaplan-Meier Survival Curves and the Log-Rank Test.- The Cox Proportional Hazards Model and Its Characteristics.- Evaluating the Proportional Hazards Assumption.- The Stratified Cox Procedure.- Extension of the Cox Proportional Hazards Model for Time-Dependent Variables.- Parametric Survival Models.- Recurrent Events Survival Analysis.- Competing Risks Survival Analysis.

Survival Analysis: A Self-Learning Text

to Logistic Regression.- Important Special Cases of the Logistic Model.- Computing the Odds Ratio in Logistic Regression.- Maximum Likelihood Techniques: An Overview.- Statistical Inferences Using Maximum Likelihood Techniques.- Modeling Strategy Guidelines.- Modeling Strategy for Assessing Interaction and Confounding.- Additional Modeling Strategy Issues.- Assessing Goodness of Fit for Logistic Regression.- Assessing Discriminatory Performance of a Binary Logistic Model: ROC Curves.- Analysis of Matched Data Using Logistic Regression.- Polytomous Logistic Regression.- Ordinal Logistic Regression.- Logistic Regression for Correlated Data: GEE.- GEE Examples.- Other Approaches for Analysis of Correlated Data.

David G. Kleinbaum

Papers

Applied Regression Analysis and Other Multivariable Methods

Epidemiologic Research: Principles and Quantitative Methods.

Epidemiologic Research: Principles and Quantitative Methods

Survival Analysis: A Self-Learning Text

Logistic Regression. A Self- Learning Text