Flexible Extended State-Space Epidemiological Models with Modern Inference

Documentation for package ‘EpiNova’ version 0.1.0

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