trivial — XH module

The trivial module outputs the net infectiousness, \(\kappa\), by calling a trace function, $$F_\kappa(t) = \kappa S(t) T(t) K(t)$$ where

• \(\kappa\) or kappa is the mean net infectiousness

• \(S(t)\) or F_season is a seasonal pattern

• \(T(t)\) or F_trend is a trend pattern

• \(K(t)\) or F_shock is a perturbation

Note: \(0 \leq F_\kappa(t) \leq 1\)

Parameters

kappa

the net infectiousness

season_par

parameters for make_function: F_season=make_par(season_par)

trend_par

parameters for make_function: F_trend=make_par(trend_par)

shock_par

parameters for make_function: F_shock=make_par(shock_par)

The default setup option is season_par = trend_par = shock_par = makepar_F_one().

Get

• get_XH_pars — the trivial method returns all the parameters

Change

• change_XH_pars — change parameters by name

Notes

1. The module has no state variables.

2. The size of an object saved by saveRDS balloons if it saves a function, so saveXDS function strips the functions and readRDS remakes the function from the stored parameters. F_season, F_trend, and F_shock can be set up manually by passing any user defined function. If so, the user should use saveRDS and readRDS rather than saveXDS and readXDS

3. Setup expects that membership= c(1:nPatches), but any membership vector works.