denim (version 1.2.2)

sim: Simulator for deterministic discrete time model with memory

Description

Simulation function that call the C++ simulator

Usage

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

Value

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

Arguments

transitions

output of function denim_dsl() or a list of transitions follows this format "transition" = expression

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

Examples

# model can be defined using denim DSL
transitions <- denim_dsl({
   S -> I = beta * S * I / N
   I -> R = d_gamma(1/3, 2)
})

# or as a list
transitions <- list(
   "S -> I" = "beta * S * I / N",
   "I -> R" = d_gamma(1/3, 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)