A multi-year endemic parameter set that sustains low-level transmission
and produces recurring seasonal + quadrennial waves via environmental
persistence.
The object is generated by make_simulation_endemic_config_files.R (sim_endemic) and saved in the package as config_simulation_endemic.
Format
A named list with the same structure as config_default but spanning five years of daily timesteps.
Details
| Aspect | Setting |
| Time span | 1 Jan 2020 – 31 Dec 2024 (about 1 826 days). |
| Locations | “FOO” (8 k), “BAR” (12 k), “BAZ” (20 k). |
| Initial mix | 10 % susceptible, 30 % first-dose vaccinated, ~60 % recovered, ~0.1 % infectious (at least 1 exposed and at least 1 infectious each site). |
| Transmission | Site-specific human-to-human \(\beta\): 0.18, 0.30, 0.24, plus environmental \(\beta\) of half those values, with a first-harmonic seasonal forcing of amplitude 0.2 and a random phase per site. |
| Environment | Suitability \(\psi_{jt}\) = 0.45 + annual 0.25 sin (2\(\pi\) t/365 + \(\phi_j\)) + quadrennial 0.15 sin (2\(\pi\) t/1 460 + \(\phi_j\)/2), with a random phase \(\phi_j\) per site; values clipped to [0,1] (shipped range about 0.06–0.85). psi_star_* are the identity. |
| Environmental half-life | decay_days_long = 365 days (~1 year); decay_days_short = 1. |
| Immunity waning | \(\omega_1 \approx 1/180\) d (0.0056), \(\omega_2 \approx 1/300\) d (0.0033). |
| Mobility | \(\tau_i\) = 0.005, 0.002, 0.006 per day. |
| Observed data | reported_cases / reported_deaths hold one simulated realisation of the model itself (run_simulation() on this config), not real surveillance. |
| Seed | set.seed(999999999) for full reproducibility. |
Together, the longer environmental survival and waning immunity allow susceptibles to replenish, generating periodic endemic outbreaks without the explosive dynamics of the epidemic toy set.
See also
config_simulation_epidemic – one-year outbreak scenario.
config_default – comprehensive default configuration.
make_simulation_endemic_config_files.R (sim_endemic)– generator script.