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trivial — MY module

Source: R/adult-MY-trivial.R
trivial_MY.Rd

The trivial MY module configures two trace functions:

  • infectious biting: $$F_{fqZ}(t, V) = fqZ \times F_S(t, V_s) \times F_T(t, V_t) \times F_K(t, V_k)$$

  • egg laying: $$F_G(t, V) = G \times F_S(t,V_s) \times F_T(t, V_t) \times F_K(t, V_k)$$

where

  • \(G\) or eggs is the mean egg laying rate

  • \(fqZ\) or fqZ is the mean number of infectious bites on humans, per patch

  • \(F_S(t,V_s)\) or F_season is a seasonal pattern function

  • \(F_T(t,V_t)\) or F_trend is a trend pattern function

  • \(F_K(t,V_k)\) or F_shock is a perturbation function

The variables \(V_s\), \(V_t\), and \(V_t\) are called by get_variables, which dispatches on the class of season_par or trend_par or shock_par.

The implementation assumes that only one of these functions gets used.

Parameters

eggs

the mean number of eggs laid, per day

Z

the mean density of infectious mosquitoes

f

the blood feeding rate

q

the human fraction

F_season

a seasonal pattern function, \({F_S(t,V_s)}\)

F_trend

a trend function, \(F_T(t,V_t)\)

F_shock

a shock function, \(F_K(t,V_k)\)

season_par

dispatches get_variables to get \(V_s\)

trend_par

dispatches get_variables to get \(V_t\)

shock_par

dispatches get_variables to get \(V_k\)

The default values are F_season=F_trend=F_shock=F_one and the classes of the objects season_par and trend_par and shock_par are all 'list'

For the bionomic parameters, f=q=Z=eggs=1.

Get

  • get_MY_pars — the trivial method returns all the parameters

  • get_mean_forcing — returns Z

  • get_f — returns f

  • get_q — returns q

  • get_season — returns season_par

  • get_trend — returns trend_par

  • get_shock — returns shock_par

Note: use get_MY_pars to inspect eggs

Change

  • change_MY_pars — change bionomic parameters by name

  • change_mean_forcing — changes Z

  • change_F_season — changes F_season

  • change_F_trend — changes F_trend

  • change_F_shock — changes F_shock

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