R: Flexible Extended State-Space Epidemiological Models with Modern Inference

# Flexible Extended State-Space Epidemiological Models with Modern Inference

## Documentation for package ‘EpiNova’ version 0.1.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

build_multipatch_SEIR | Build a mobility-coupled multi-patch SEIR ODE system
build_phi_pulse | Build a smooth quarantine pulse phi(t)
build_pi_exp | Build an exponential decay pi(t) = exp(-lambda t)
build_pi_spline | Build a natural cubic spline pi(t)
build_pi_step | Build a step-function pi(t) (reproduces eSIR Model 1 behaviour)
compose_pi | Compose multiple pi(t) functions multiplicatively
ensemble_forecast | Ensemble forecast via Bayesian Model Averaging (BMA)
EpiNova-ensemble | Ensemble Forecasting and Uncertainty Quantification
EpiNova-inference | Inference Engines for EpiNova
EpiNova-interventions | Flexible Intervention (pi) Functions
EpiNova-multipatch | Multi-patch Spatial SIR Models
EpiNova-ode | EpiNova: Flexible Epidemiological Compartmental Models
EpiNova-plotting | Visualisation Layer for EpiNova
estimate_Rt | Estimate time-varying effective reproduction number Rt
estimate_Rt_simple | Lightweight built-in Rt estimator (no extra packages needed)
fit_mle | Fit a EpiNova model by maximum likelihood
fit_smc | Sequential Monte Carlo (particle filter) inference
gp_cov_sqexp | Build a squared-exponential covariance matrix for GP pi(t)
gravity_mobility | Build a gravity-model mobility matrix
hubei_covid | Hubei Province COVID-19 data (Jan 13 - Feb 11, 2020)
plot_forecast | Plot forecast with uncertainty ribbon
plot_multipatch_snapshot | Multi-patch bar chart of infected proportion by patch
plot_Rt | Plot effective reproduction number Rt over time
plot_scenarios | Plot scenario comparison
plot_trajectory | Plot model trajectory with observed data
prep_proportions | Prepare population proportions from a hubei_covid-style list
project_scenarios | Project scenarios under alternative intervention strategies
score_forecast | Evaluate forecast calibration with proper scoring rules
solve_model | Solve a compartmental ODE model
solve_multipatch | Solve a multi-patch SEIR model