Phase 1: Preparing pathogen data | Phase 2: Configuring the model | Method | Smoothing parameters | Dispersion parameters | Pathogen noise | Day of week effect | Worked example | Output | Phase 3: Fitting | Checking convergence | Phase 4: Deriving epidemiological quantities | Additional worked example: COVID-19

1. Load data | 2. process data | 3. Plot mass loss and rate of mass loss curves | 4. deconvolve data | 5. Examine outputs | 6. Plot deconvolved curves