vignettes/mysimulator.R

In ahgroup/DSAIRM: Dynamical Systems Approach to Immune Response Modeling

#' Basic Bacteria model
#'
#' A basic bacteria infection model with 2 compartments
#'
#' @details The model includes bacteria and an immune response. The processes are bacteria growth, death and killing, and immune response activation and decay. This is a predator-prey type model.
#' This code is based on a dynamical systems model created by the modelbuilder package.
#' The model is implemented here as a set of ordinary differential equations,
#' using the deSolve package.
#' @param B : starting value for Bacteria
#' @param I : starting value for Immune Response
#' @param g : maximum rate of bacteria growth
#' @param Bmax : bacteria carrying capacity
#' @param dB : bacteria death rate
#' @param k : bacteria kill rate
#' @param r : immune response growth rate
#' @param s : immune response saturation
#' @param dI : immune response decay rate
#' @param tstart : Start time of simulation
#' @param tfinal : Final time of simulation
#' @param dt : Time step
#' @param ... other arguments for possible pass-through
#' @return The function returns the output as a list.
#' The time-series from the simulation is returned as a dataframe saved as list element \code{ts}.
#' The \code{ts} dataframe has one column per compartment/variable. The first column is time.
#' @examples
#' # To run the simulation with default parameters:
#' result <- mysimulator()
#' @section 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.
#' @section Model Author: Andreas Handel
#' @section Model creation date: 2018-12-21
#' @export

mysimulator <- function(B = 10, I = 1, g = 1, Bmax = 1e+06, dB = 0.1, k = 1e-07, r = 1e3, dI = 1, s = 1e3, tstart = 0, tfinal = 30, dt = 0.01)
{
  #Block of ODE equations for deSolve
  basicbacteria_ode_fct <- function(t, y, parms)
  {
    with( as.list(c(y,parms)), { #lets us access variables and parameters stored in y and parms by name
    #StartODES
    #Bacteria : bacteria growth : bacteria death : immune response killing :
    dB = g*B*(1-B/Bmax) -dB*B -k*B*I
    #Immune Response : immune response growth : immune response decay :
    dI = r*B*I/(s+B) -dI*I
    #EndODES
    list(c(dB,dI))
  } ) } #close with statement, end ODE code block

  #Main function code block
  timevec=seq(tstart,tfinal,by=dt)
  vars = c(B = B, I = I)
  pars = c(g = g, Bmax = Bmax, dB =dB, k = k, r=r,dI=dI)
  odeout = deSolve::ode(y = vars, parms = pars, times = timevec,  func = basicbacteria_ode_fct)
  result <- list()
  result$ts <- as.data.frame(odeout)
  return(result)
}