Known issue on Windows | Quarto Templates | quarto_website: Simple Quarto Website Template | quarto_ggplot2: Quarto Report with Branded ggplot2 Figures | Shiny App Templates | shiny_basic: Simple Histogram Visualization Shiny App | shiny_kmeans: Simple K-means Clustering Visualization Shiny App | shiny_complex: Complex Histogram Visualization Shiny App | shiny_wastewater: Wastewater Data Visualization Shiny App | Other Templates | rmarkdown: R Markdown Template for PDF or HTML Reports

Overview | Getting Started | Step 1: Initialize and Load Brand Configuration | Step 2: Set the ggplot2 Theme | Step 3: Create ggplot2 Visualizations | Step 4: Add Brand Logo (Optional) | Step 5: Interactive Plots with plotly | Step 6: Advanced Theming | Step 7: Reset Theme | Best Practices | Troubleshooting | Common Issues | Solutions | Conclusion

Introduction to rbranding | Initialization | Updating Your Brand File | Example Usage | Using Templates

Introduction | Step 1: Getting State FIPS Codes | Step 2: Listing Counties | Step 3: Retrieving Population Data | Step 4: Visualizing Age Distribution | Step 5: Comparing Multiple Counties | Step 6: Using City-Level Data (getCityData) | Example 1: Default 5-year Age Groups | Example 2: Custom Age Groups for School-Based Analysis | Visualizing the Comparison | Summary

Introduction | Data Structure | Model Specification | Model Choice | Parameters | Specifying parameters | Abx Antibiotic use | AbxRate Antibiotic rates | InUnit In unit infection rate | Acquisition Model | Progression Model | Clearance Model | Out of Unit Importation | In Situ | Testing | Surveillance Testing | Clinical Testing | All Together | Running the Model | Analyzing MCMC Results | Converting Parameters to Data Frame | Trace Plots | Posterior Distributions | Summary Statistics

Facility Basic Reproduction Number $R_0$ | The S matrix; pre-invasion susceptible state transitions | The C matrix; colonized state transitions | The A matrix; susceptible-to-colonized state transitions and relative susceptibility | The transm vector: transmission rates | The initS vector: susceptible state admission distribution | facilityR0 function call with $h(t)=0$ | The mgf function: moment generating function associated with $h(t)\neq0$ | facilityR0 function call with $h(t)\neq0$ | Facility model equilibrium | The R matrix: recovery rates | The init vector: admission state distribution | facilityeq function call with $h(t)\neq0$ | facilityeq function call with $h(t)=0$

Introduction | Core Concept | Basic Usage | Key Requirements | What Happens When You Click? | Next Steps

Three-Component Example | Adding More Component Types | Summary Tables | Managing Complex State | Performance Tips | Troubleshooting Multiple Components

Introduction | Key Features | Basic Plotly Linking | Simple Example | Important Note: Enabling Visual Highlighting | Essential Plotly Parameters | The key Parameter | The source Parameter | Chart Types Support | Scatter Plots | Bar Charts | Line Charts | Multi-trace Charts | Advanced Integration | Multiple Plotly Charts | Mixed Component Types | Selection Highlighting | How It Works | Visual Customization | Troubleshooting | Common Issues | Best Practices | Complete Example | Summary

Introduction | Key Features | Basic SF Integration | Advanced SF Integration with Custom Handlers | Working with Different Geometry Types | Benefits of SF Integration | 1. Automatic Coordinate Extraction | 2. Preserved Geometry | 3. Mixed Data Types | 4. Developer-Friendly | Troubleshooting | Common Issues: | Debugging SF Integration: | Next Steps

Introduction: Why a Different Approach for Modules? | The Three-Step Pattern for Modular Linking | Step 1: Create the Map Module (map_module.R) | Step 2: Create the Table Module (table_module.R) | Step 3: Assemble the Main App (app.R)

Introduction to epitraxr | EpiTrax Data | Disease Lists | Generating Reports: Standard Mode | Generating Reports: Piped Mode (recommended)

Overview | Pipe Setup | Create an epitrax object | Add Disease Lists | Add Config | Convenient Setup | Running Report Generators | Exporting Reports | Setup Filesystem | Export to CSV | Full Pipe: Putting It All Together

Customizing Click Behaviors | Custom Leaflet Click Handler | Custom DT Click Handler | Global Selection Callback | Best Practices | Advanced Example: Conditional Behavior

Introduction | Offspring distribution | pNextGenSize(x,y,R,k) function | Dispersion effects | Final size distribution | Estimates from outbreak cluster data | Control reproduction number | Final size and number of generations | Risk assessment | Exceedance probability | Extinction probability and escape risk | Risk of outbreak duration | Outbreak size before extinction