Introduction | What this guide covers | Installation | The pipeline at a glance | Step 1: Generate or import data | Using the built-in test data generator | Importing real STEPS data | Step 2: Auto-detect STEPS variables | Version 3.1 vs 3.2 variable codes | Column mapping for non-standard datasets | Step 3: Clean and derive indicators | What the cleaning step does | Configurable indicator thresholds | Step 3b: Data quality diagnostics | Step 4: Set up the survey design | Step 5: Compute indicators | All indicators at once | Domain-specific functions | Custom weighted estimates | Step 6: Build publication-ready tables | Summary tables (Both Sexes only) | Detailed WHO 3-panel tables (Men | Women | Both Sexes) | Step 7: Create visualisations | Overview chart | Sex-stratified dashboard | Age-stratified trends | Forest plot | Risk profile radar chart | Saving plots | WHO STEPS colour palette and theme | Step 8: Generate Word reports | What each report contains | One-command pipeline | Working with real STEPS data | Preparing your data file | Handling custom variable names | Adjusting age range | Complete worked example | Interactive Shiny app | WHO standard definitions used | FAQ | Further resources | Session info

Introduction | Supported file formats | Minimum required variables | Essential (required) | Strongly recommended | Step 1: Behavioural risk factors | Step 2: Physical measurements | Step 3: Biochemical measurements | Health history (H-codes) | How auto-detection works | Common data issues and solutions | Issue: Sex coded as numeric without labels | Issue: Yes/No variables coded inconsistently | Issue: Glucose values in mg/dL instead of mmol/L | Issue: Multiple datasets for different STEPS steps | Issue: Missing sampling weights | Issue: Variables detected as wrong type | Pre-flight checklist | Quick diagnostic script | Further reading

Acknowledgements | Overview | Validation criteria | Indicators compared | Results summary | Detailed results by country | Moldova 2021 | Mongolia 2019 | Georgia 2016 | Afghanistan 2018 | Algeria 2016 | Ukraine 2019 | Ecuador 2018 | Cabo Verde 2020 | Bahamas 2019 | Analysis of mismatches | Key methodological alignments | Running the validation yourself | Reproducibility notes | References

Overview | Launching the app | Tab 1: Data & Settings | Uploading a data file | Using demo data | Column overrides | Survey settings | Tab 2: Clean | Tab 3: Design | Tab 4: Indicators | Tab 5: Visualise | Available charts | Tab 6: Reports | What happens when you click Generate | Two reports | Summary Report | Detailed Data Book | Additional downloads | Tips and troubleshooting | The app shows an error on upload | Charts don't display or show "figure margins too large" | Physical Activity shows "not available" | Some tables are empty in the Data Book | Can I customise the report templates? | Comparison: Shiny app vs R scripting

Why Background Mortality Matters | Method 1: SMR Adjustment | The Scenario -- Heart Failure Cohort | The Formula | Worked Example | Method 2: DEALE (Declining Exponential Approximation of Life Expectancy) | The Scenario -- Rare Disease with Known Life Expectancy | Method 3: Gompertz Parameterization | When to Use | Method 4: Linear Interpolation | References

When to Use Batch Conversion | Supported Conversion Types | Example: PLATO Trial Parameters | Step 1: Prepare Your CSV | Step 2: Upload and Configure | Step 3: Run and Review | Step 4: Download | Example Output | Tips | References

Overview | Tutorial: 5-Year BIA for a New Oral Anticoagulant | The Scenario | The Framework | In ParCC | Reading the Output | Interpreting Year 1 | Key Modelling Decisions | Time Horizon | Uptake Trajectory | Discounting | Population Dynamics | ISPOR Good Practice Checklist | References

Overview | Tutorial 1: Rate to Probability | The Scenario -- Anticoagulant Safety (RE-LY Trial) | Why Simple Division is Wrong | The Formula | Worked Example | In ParCC | Tutorial 2: Time Rescaling | The Scenario -- UKPDS Risk Engine | Tutorial 3: Odds to Probability | The Scenario -- Logistic Regression Output | The Conversion | References

Overview | Part A: Dirichlet for Transition Matrices | The Problem | The Dirichlet Solution | Sampling via Gamma Decomposition | In ParCC | When to Use Dirichlet vs Independent Betas | Part B: Log-Logistic Survival | The Log-Logistic Distribution | Calibration Method | Choosing the Right Survival Distribution | Extrapolation Warning | References

ICER (Incremental Cost-Effectiveness Ratio) | The Formula | The Scenario -- New Diabetes Drug | Interpretation | Net Monetary Benefit (iNMB) | Value-Based Pricing (Headroom Analysis) | The Scenario -- SepsiQuick (Point-of-Care Test for Sepsis) | The Formulas | Worked Example | What If You Price Above the Headroom? | References

What is ParCC? | Installation | Launching the Application | The Lab Notebook Workflow | Application Overview | Parameter Estimation | Uncertainty Analysis | Financial Adjustments | Decision Outputs | Next Steps | References

Overview | Tutorial A: Extracting a Hazard Ratio from a Log-rank Test | The Scenario -- Adjuvant Chemotherapy in Colon Cancer | The Peto Approximation | In ParCC | Alternative: From a p-value | Tutorial B: Computing NNT for a Formulary Decision | The Scenario -- Hospital P&T Committee | The Formula | Other Input Modes | NNT vs NNH | When to Use These Tools | References

Overview | Tutorial: Preparing Data for an NMA in Depression | The Scenario | Step 1: Convert OR to RR (Zhang & Yu Method) | Why This Matters | Step 2: Convert SMD to log(OR) (Chinn Method) | Step 3: Convert log(OR) to log(RR) | When to Use These Conversions | The Rare-Disease Approximation | References

Why PSA Needs the Right Distribution | Tutorial 1: Utilities with Beta Distribution | The Scenario -- EQ-5D Utility in COPD | The Method of Moments | Worked Example | Tutorial 2: Costs with Gamma Distribution | The Scenario -- Surgery Cost (AIIMS Costing Study) | Tutorial 3: Hazard Ratios with LogNormal Distribution | The Scenario -- HR from Network Meta-Analysis | The Method | When SE is Missing: The Rule of 4 | References

ParCC Vignette Library | Getting Started | Core Conversions | Hazard Ratio Conversion (NEW in v1.3.0) | Survival Extrapolation | Background Mortality | Probabilistic Sensitivity Analysis | Economic Evaluation | Batch Processing | Key References

Overview | Tutorial: Is a US Drug Affordable in India? | The Scenario | Why Market Exchange Rates Are Wrong | The PPP Approach | In ParCC | Reading the Output | WTP Threshold Assessment | Implications for Pricing | Override Values | Supported Countries (30) | Important Caveats | References

The Problem | Method 1: Exponential (From Median Survival) | When to Use | The Scenario -- Metastatic Colorectal Cancer | Worked Example | Method 2: Weibull (From Two KM Points) | The Scenario -- NSCLC (CheckMate 017) | The Formula | Interpretation | Generating Markov Trace | References

The Problem | The Three-Step Method | Worked Example 1: PLATO Trial (Ticagrelor vs Aspirin) | CV Death Conversion | With 95% Confidence Interval | Worked Example 2: High Event Rate (Oncology) | Worked Example 3: Rescaling to Monthly Cycles | Batch Conversion | Example CSV format: | Multi-HR Comparison | Key Assumptions and Limitations | References