Basic Bacteria model - discrete — simulate_basicbacteria

A basic bacteria infection model with 2 compartments, implemented as discrete time simulation. The model tracks bacteria and an immune response dynamics. The processes modeled are bacteria growth, death and killing by the immune response, and immune response activation and decay.

simulate_basicbacteria_discrete(
  B = 10,
  I = 1,
  g = 1,
  Bmax = 1e+06,
  dB = 0.1,
  k = 1e-07,
  r = 0.001,
  dI = 1,
  tstart = 0,
  tfinal = 30,
  dt = 0.01
)

Arguments

B: : starting value for bacteria : numeric
I: : starting value for immune response : numeric
g: : maximum rate of bacteria growth : numeric
Bmax: : bacteria carrying capacity : numeric
dB: : bacteria death rate : numeric
k: : rate of bacteria killing by immune reesponse : numeric
r: : immune response growth rate : numeric
dI: : immune response decay rate : numeric
tstart: : start time of simulation : numeric
tfinal: : final time of simulation : numeric
dt: : time step : numeric

Value

The function returns the output as a list. The time-series from the simulation is returned as a dataframe saved as list element ts. The ts dataframe has one column per compartment/variable. The first column is time.

Details

The model includes bacteria and an immune response. The processes are bacteria growth, death and killing by the immune response, and immune response activation and decay. This is a predator-prey type model. The model is implemented as a set of discrete-time, deterministic equations, coded as a for-loop. This code is part of the DSAIRM R package. For additional model details, see the corresponding app in the DSAIRM package.

Warning

This function does not perform any error checking. So if you try to do something nonsensical (e.g. have negative values for parameters), the code will likely abort with an error message.

Examples

# To run the simulation with default parameters:
result <- simulate_basicbacteria_discrete()