Simulator for deterministic discrete time model with memory

Simulation function that call the C++ simulator

Usage

sim(
  transitions,
  initialValues,
  parameters = NULL,
  simulationDuration,
  timeStep = 1,
  errorTolerance = 0.001
)

Arguments

transitions: a list of transitions follows this format "transition" = distribution()
initialValues: a vector contains the initial values of all compartments defined in the transitions, follows this format compartment_name = initial_value
parameters: a vector contains values of any parameters that are not compartments, usually parameters used in mathexp() functions
simulationDuration: duration of time to be simulate
timeStep: set the output time interval. For example, if simulationDuration = 10 means 10 days and timeStep = 0.1, the output will display results for each 0.1 daily interval
errorTolerance: set the threshold so that a cumulative distribution function can be rounded to 1. For example, if we want a cumulative probability of 0.999 to be rounded as 1, we set errorTolerance = 0.001 (1 - 0.999 = 0.001). Default is 0.001

Value

a data.frame with class denim that can be plotted with a plot() method

Examples

transitions <- list(
   "S -> I" = "beta * S * I / N",
   "I -> R" = d_gamma(3, 2)
)

initialValues <- c(
   S = 999, 
   I = 1, 
   R = 0
)

parameters <- c(
   beta = 0.012,
   N = 1000
)

simulationDuration <- 30
timeStep <- 0.01

mod <- sim(transitions = transitions, 
           initialValues = initialValues, 
           parameters = parameters, 
           simulationDuration = simulationDuration, 
           timeStep = timeStep)