Preliminaries | Factorial (Multi-Split) Designs | Example 1: A Two-by-Two Factorial Trial | Example 2: Larger Factorial Grids | Example 3: Asymmetric Factorial Designs | Example 4: Factorial Designs from Row-Level Data | Example 5: Pooling Twice into a Single Cohort | Example 6: Factorial Layouts via the DOT Engine | Hierarchical (Nested) Exclusion Reasons | Example 7: Manual Nested Reasons | Example 8: Two-Column Reasons from Row-Level Data | Example 9: Nested Reasons via the DOT Engine | Visual Customization | Example 10: Custom Font Sizes | Example 11: Custom Colors | Example 12: Font Family | Example 13: Regional Number Formatting | Global Options | Multi-Line Phase Labels | Example 14: Wrapped Phase Labels | Example 15: Explicit Line Breaks | Further Reading

Preliminaries | Operating Modes | CONSORT — Randomized Controlled Trials | Example 1: Data-Driven Two-Arm Trial | Example 2: Data-Driven Three-Arm Trial | Example 3: Manual Mode | Example 4: Count-First Display Mode | STROBE — Observational Cohort Studies | Example 5: Single-Arm Cohort | Example 6: Exposure-Stratified Cohort | STARD — Diagnostic Accuracy Studies | Example 7: Index Test and Reference Standard | Cohort Extraction | Inspecting the Diagram Structure | Saving to File | Further Reading

Preliminaries | Generating DOT Output | Example 1: Basic DOT String | Example 2: Multi-Arm Trial (CONSORT) | Example 3: Systematic Review (PRISMA) | Customizing DOT Output | Example 4: Changing Node Colors | Example 5: Count-First Layout | Example 6: Rich (HTML) Formatting | Example 7: Times Typography | Example 8: Adding Graphviz Attributes | Font Formatting Notes | The plot() Method | Bullets vs. Indentation | Saving to File | Advanced Rendering Options | Saving as HTML | Saving as PNG | Choosing Between Engines | Further Reading

Preliminaries | Manual Entry | Example 1: Screening Validation Study | Example 2: Per-Stratum Exclusion Reasons | Data-Driven Flow | Example 3: Data-Driven Split and Recombine | Cohort Extraction | Re-Splitting after Recombination | Example 4: Risk Stratification Followed by Randomization | Design Considerations | Saving to File | Further Reading

Preliminaries | PRISMA — Three-Column Layout | Example 1: Full Three-Column PRISMA Diagram | Example 2: Three-Column Count-First Layout | PRISMA — Two-Column Layout | Example 3: Two-Column Sources | PRISMA — Single-Column Layout | Example 4: Flat Source List | MOOSE — Observational Meta-Analysis | Example 5: MOOSE Flow Diagram | Source Group Structure | Saving to File | Further Reading

Preliminaries | Factorial (Multi-Split) Designs | Example 1: A Two-by-Two Factorial Trial | Example 2: Larger Factorial Grids | Example 3: Asymmetric Factorial Designs | Example 4: Factorial Designs from Row-Level Data | Example 5: Pooling Twice into a Single Cohort | Example 6: Factorial Layouts via the DOT Engine | Hierarchical (Nested) Exclusion Reasons | Example 7: Manual Nested Reasons | Example 8: Two-Column Reasons from Row-Level Data | Example 9: Nested Reasons via the DOT Engine | Visual Customization | Example 10: Custom Font Sizes | Example 11: Custom Colors | Example 12: Font Family | Example 13: Regional Number Formatting | Global Options | Multi-Line Phase Labels | Example 14: Wrapped Phase Labels | Example 15: Explicit Line Breaks | Further Reading

Preliminaries | Operating Modes | CONSORT — Randomized Controlled Trials | Example 1: Data-Driven Two-Arm Trial | Example 2: Data-Driven Three-Arm Trial | Example 3: Manual Mode | Example 4: Count-First Display Mode | STROBE — Observational Cohort Studies | Example 5: Single-Arm Cohort | Example 6: Exposure-Stratified Cohort | STARD — Diagnostic Accuracy Studies | Example 7: Index Test and Reference Standard | Cohort Extraction | Inspecting the Diagram Structure | Saving to File | Further Reading

Preliminaries | Generating DOT Output | Example 1: Basic DOT String | Example 2: Multi-Arm Trial (CONSORT) | Example 3: Systematic Review (PRISMA) | Customizing DOT Output | Example 4: Changing Node Colors | Example 5: Count-First Layout | Example 6: Rich (HTML) Formatting | Example 7: Times Typography | Example 8: Adding Graphviz Attributes | Font Formatting Notes | The plot() Method | Bullets vs. Indentation | Saving to File | Advanced Rendering Options | Saving as HTML | Saving as PNG | Choosing Between Engines | Further Reading

Preliminaries | Manual Entry | Example 1: Screening Validation Study | Example 2: Per-Stratum Exclusion Reasons | Data-Driven Flow | Example 3: Data-Driven Split and Recombine | Cohort Extraction | Re-Splitting after Recombination | Example 4: Risk Stratification Followed by Randomization | Design Considerations | Saving to File | Further Reading

Preliminaries | PRISMA — Three-Column Layout | Example 1: Full Three-Column PRISMA Diagram | Example 2: Three-Column Count-First Layout | PRISMA — Two-Column Layout | Example 3: Two-Column Sources | PRISMA — Single-Column Layout | Example 4: Flat Source List | MOOSE — Observational Meta-Analysis | Example 5: MOOSE Flow Diagram | Source Group Structure | Saving to File | Further Reading

Package Installation | From Repository | Verification | Dependencies | Required Dependencies | Optional Dependencies | LaTeX Configuration | TinyTeX (Recommended) | Alternative LaTeX Distributions | Required LaTeX Packages | Microsoft Office Export | Export Verification Procedure | Troubleshooting | LaTeX Not Found | Missing LaTeX Packages | Package Installation Failures | Write Permission Errors | System Requirements

Preliminaries | Supported Model Types | Univariable Screening | Example 1: Binary Outcome Screen (Logistic Regression) | Example 2: Filtering Screen by p-value | Example 3: Continuous Outcome Screen (Linear Regression) | Example 4: Time-to-Event Outcome Screen (Cox Regression) | Example 5: Retaining Model Objects | Multivariable Modeling | Example 6: Logistic Regression | Example 7: Linear Regression | Example 8: Cox Regression | Example 9: Poisson Regression | Example 10: Toggling Reference Rows for Factors | Example 11: Confidence Level | Example 12: Confidence Interval Method | Example 13: Raw Coefficients | Combined Analysis | Example 14: Screening-Based Selection | Example 15: All Predictors | Example 16: Custom Selection | Example 17: Controlling Output Columns | Example 18: Survival Analysis | Extended Model Types | Example 19: Negative Binomial | Example 20: Gamma Regression | Example 21: Random-Intercept Model | Example 22: GLMM for Binary Outcome | Example 23: GLMM for Count Outcome | Example 24: Cox Mixed-Effects Model | Example 25: Quasibinomial for Overdispersed Binary Data | Example 26: Conditional Logistic Model for Matched Data | Exporting Results | Best Practices | Variable Selection Strategy | Choosing the Right Model | Interpreting Results | Sample Size Considerations | Common Issues | Missing Data | Factor Reference Levels | Convergence Issues | Overdispersion Diagnostics | Mixed-Effects Model Convergence | Multinomial and Ordinal Outcomes | Further Reading

Preliminaries | Interaction Effects | Example 1: Two-Way Interaction | Example 2: Multiple Interactions | Example 3: Continuous × Categorical Interaction | Example 4: Interaction in fullfit() | Example 5: Testing Interaction Significance | Example 6: Forest Plot with Interactions | Mixed-Effects Models | Example 7: Random Intercepts (Linear Mixed) | Example 8: Random Intercepts (Logistic Mixed) | Example 9: Random Slopes | Example 10: Cox Mixed-Effects Model | Example 11: Forest Plot from Mixed Model | Example 12: Comparing Random-Effects Specifications | Stratification and Clustering | Example 13: Stratified Cox Model | Example 14: Cluster-Robust SEs | Weighted Regression | Example 15: Weighted Analysis | Advanced Univariable Screening Features | Example 16: Univariable Screening with Random Effects | Example 17: Cox Screening with Mixed Effects | Example 18: Forest Plot from Univariable Screening | Advanced Multivariate Regression Features | Example 19: Multi-Outcome with Interactions | Example 20: Multi-Outcome with Mixed Effects | Example 21: Survival Multi-Outcome with Mixed Effects | Complete Workflow Example | Best Practices | Interaction Analysis | Method Selection | Sample Size Considerations | Common Issues | Convergence Problems in Mixed Models | Interpreting Interactions | Forest Plots with Interactions | Further Reading

Preliminaries | Summary Statistics and Tests | Basic Usage | Example 1: Grouped Descriptive Table | Example 2: Ungrouped Summary Statistics | Customizing Summary Statistics | Example 3: Continuous Variables | Example 4: Categorical Variables | Example 5: Numeric Precision | Statistical Testing | Example 6: Disabling Automatic Test Selection | Example 7: Specifying Tests Manually | Handling Missing Data | Example 8: Including Missing Values | Example 9: Missing Value Denominators | Example 10: Custom Missing Value Label | Total Column Options | Example 11: Total Column Configuration | Complete Example | Accessing Raw Data | Survival Summary Tables | Exporting Tables | Best Practices | Variable Selection | Statistical Considerations | Formatting Recommendations | Common Issues | Empty Cells in Categorical Variables | Skewed Continuous Variables | Large Tables | Further Reading

Preliminaries | Creating Forest Plots from Model Objects | Example 1: Logistic Regression | Example 2: Linear Regression | Example 3: Cox Regression | Example 4: Automatic Model Detection | Creating Forest Plots from summata Output | Example 5: Direct Extraction from Fit Output | Example 6: Model Attribute from Fit Output | Display Options | Example 7: Indenting Factor Levels | Example 8: Condensing Binary Variables | Example 9: Toggle Zebra Striping | Example 10: Sample Size and Event Columns | Formatting Options | Example 11: Adjusting Numeric Precision | Example 12: Custom Reference Label | Example 13: Custom Effect Measure Label | Example 14: Custom Colors | Example 15: Change Font Sizes | Example 16: Table Width | Saving Forest Plots | Example 17: Recommended Dimensions | Example 18: Multiple Formats | Advanced Customization | Example 19: Combined Options | Example 20: Extensions with ggplot2 | Additional GLM Families | Example 21: Poisson Regression | Example 22: Negative Binomial Regression | Function Parameter Summary | Best Practices | Model Preparation | Visual Design | Publication Preparation | Common Issues | Long Variable Names | Overlapping Text | Missing Labels | Further Reading

Preliminaries | Quality Metrics and the Composite Model Score | Available Metrics | CMS Interpretation | Default CMS Weights by Model Type | Basic Usage | Example 1: Nested Model Comparison | Example 2: Linear Regression Models | Example 3: Cox Regression Models | Example 4: Count Models | Interaction Testing | Example 5: Single Interaction | Example 6: Multiple Interactions | Accessing Detailed Results | Example 7: Coefficient Comparison | Example 8: Fitted Model Objects | Example 9: Recommended Model | Custom CMS Weights | Example 10: Custom Weights | Application Scenarios | Scenario 1: Confounder Assessment | Scenario 2: Variable Selection Validation | Scenario 3: Parsimony Assessment | Exporting Results | Best Practices | When to Compare Models | Interpreting Results | Limitations | Common Issues | Non-Convergence | Differing Sample Sizes | Interpreting Close Scores | Further Reading

Preliminaries | Basic Usage | Example 1: Unadjusted Analysis | Example 2: Adjusted Analysis | Example 3: Unadjusted and Adjusted Comparison | Predictor Types | Example 4: Continuous Predictors | Example 5: Multilevel Categorical Predictors | Model Types | Example 6: Cox Regression | Example 7: Linear Regression | Example 8: Mixed-Effects Models | Advanced Features | Example 9: Interaction Terms | Example 10: Filtering by p-value | Example 11: Accessing Model Objects | Forest Plot Visualization | Example 12: Forest Plot for Logistic (Binary) Outcomes | Example 13: Customization Options | Example 14: Forest Plot for Continuous Outcomes | Example 15: Forest Plot for Survival Outcomes | Exporting Results | Tables | Forest Plots | Complete Workflow Example | Parameter Reference | Best Practices | Outcome Selection | Adjustment Strategy | Interpretation | Common Issues | Empty Results | Convergence Warnings | Many Factor Levels | Other Considerations | Multivariate Regression vs. Univariable Screening | Categorical Outcomes with More Than Two Levels | Further Reading

Preliminaries | Landmark Survival Estimates | Example 1: Basic Landmark Analysis | Example 2: Remove Median Survival Column | Survival Quantiles | Example 3: Survival Quartiles | Multiple Endpoints | Example 4: PFS and OS Comparison | Output Variations | Example 5: Cumulative Event Rates | Example 6: Including At-Risk Counts | Pairing with Kaplan-Meier Curves | Example 7: Coordinated Figure-Table Output | Exporting Tables | Best Practices | Time Point Selection | Reporting Recommendations | Further Reading

Preliminaries | CSV / TSV Export | Example 1: CSV Export | Example 2: TSV Export | Example 3: Semicolon-Delimited (European Locale) | PDF Export | Example 4: Basic Export | Example 5: With Caption | Example 6: With Formatting Options | Example 7: Page Layout | Example 8: Custom Margins | Example 9: Fit to Page Width | Example 10: Standalone Table | Microsoft Word Export | Example 11: Basic Export | Example 12: With Caption | Example 13: With Formatting Options | Example 14: Page Layout | Example 15: Dark Header Style | HTML Export | Example 16: Basic Export | Example 17: With Caption | Example 18: With Formatting Options | PowerPoint Export | Example 19: Basic Export | Example 20: With Slide Title | Example 21: With Formatting Options | Example 22: Custom Template | LaTeX Export | Example 23: Basic Export | Example 24: With Caption and Label | Example 25: With Booktabs Styling | RTF Export | Example 26: Basic Export | Example 27: With Formatting Options | Example 28: Page Layout | Automatic Format Detection | Common Formatting Parameters | Condensing Options | Format-Specific Parameters | PDF | Word/RTF/PowerPoint | HTML | LaTeX | PowerPoint (additional) | Best Practices | Format Selection | Page Layout Guidelines | Consistent Multi-Format Export | Troubleshooting | PDF Compilation Fails | Table Too Wide | Customizing flextable Output | Further Reading