auxiliary/archive/test-models/mbsir.R

In andreashandel/modeldiagram: Easy Creation of ggplot2 Based Figures of Flow Diagrams

# R script to generate a modelbuilder model object with code.

mbmodel = list() #create empty list

#Model meta-information
mbmodel$title = 'SIR model'
mbmodel$description = 'A basic SIR model with 3 compartments and infection and recovery processes'
mbmodel$author = 'Andreas Handel'
mbmodel$date = Sys.Date()
mbmodel$details = 'The model includes susceptible, infected, and recovered compartments. The two processes that are modeled are infection and recovery.'

#Information for all variables
var = vector('list',3)
var[[1]]$varname = 'S'
var[[1]]$vartext = 'Susceptible'
var[[1]]$varval = 1000
var[[1]]$flows = c('-b*S*I')
var[[1]]$flownames = c('infection of susceptibles')

var[[2]]$varname = 'I'
var[[2]]$vartext = 'Infected'
var[[2]]$varval = 1
var[[2]]$flows = c('+b*S*I', '-g*I')
var[[2]]$flownames = c('infection of susceptibles', 'recovery of infected')

var[[3]]$varname = 'R'
var[[3]]$vartext = 'Recovered'
var[[3]]$varval = 0
var[[3]]$flows = c('+g*I')
var[[3]]$flownames = c('recovery of infected')

mbmodel$var = var

#Information for all parameters
par = vector('list',2)
par[[1]]$parname = 'b'
par[[1]]$partext = 'infection rate'
par[[1]]$parval = 0.002

par[[2]]$parname = 'g'
par[[2]]$partext = 'recovery rate'
par[[2]]$parval = 1

mbmodel$par = par

#Information for time parameters
time = vector('list',3)
time[[1]]$timename = 'tstart'
time[[1]]$timetext = 'Start time of simulation'
time[[1]]$timeval = 0

time[[2]]$timename = 'tfinal'
time[[2]]$timetext = 'Final time of simulation'
time[[2]]$timeval = 100

time[[3]]$timename = 'dt'
time[[3]]$timetext = 'Time step'
time[[3]]$timeval = 0.1

mbmodel$time = time

mbsir <- mbmodel