auxiliary/stratification_functionality_testing/base_models/SIRSd_model_file.R

In ahgroup/modelbuilder: Building Compartmental Simulation Models Without Coding

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

 mbmodel = list() #create empty list

 #Model meta-information
 mbmodel$title = 'SIRSd2'
 mbmodel$description = 'A SIRSd model with 3 compartments. Processes are infection, recovery, births deaths and waning immunity.'
 mbmodel$author = 'Andreas Handel'
 mbmodel$date = Sys.Date()
 mbmodel$details = 'The model includes susceptible, infected, and recovered compartments. The processes which are modeled are infection, recovery, natural births and deaths and waning immunity.'

 #Information for all variables
 var = vector('list',3)
 id = 0
 id = id + 1
 var[[id]]$varname = 'S'
 var[[id]]$vartext = 'Susceptible'
 var[[id]]$varval = 1000
 var[[id]]$flows = c('-b*S*I', '+w*R', '+n', '-mS*S')
 var[[id]]$flownames = c('infection', 'waning immunity', 'births', 'natural deaths of S')

 id = id + 1
 var[[id]]$varname = 'I'
 var[[id]]$vartext = 'Infected'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+b*S*I', '-g*I', '-mI*I')
 var[[id]]$flownames = c('infection', 'recovery', 'natural deaths of I')

 id = id + 1
 var[[id]]$varname = 'R'
 var[[id]]$vartext = 'Recovered'
 var[[id]]$varval = 0
 var[[id]]$flows = c('+g*I', '-w*R', '-mR*R')
 var[[id]]$flownames = c('recovery', 'waning immunity', 'natural deaths of R')

 mbmodel$var = var

 #Information for all parameters
 par = vector('list',7)
 id = 0
 id = id + 1
 par[[id]]$parname = 'b'
 par[[id]]$partext = 'infection rate'
 par[[id]]$parval = 0.002

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

 id = id + 1
 par[[id]]$parname = 'w'
 par[[id]]$partext = 'waning immunity rate'
 par[[id]]$parval = 1

 id = id + 1
 par[[id]]$parname = 'n'
 par[[id]]$partext = 'birth rate'
 par[[id]]$parval = 0

 id = id + 1
 par[[id]]$parname = 'mS'
 par[[id]]$partext = 'death rate of S'
 par[[id]]$parval = 0

 id = id + 1
 par[[id]]$parname = 'mI'
 par[[id]]$partext = 'death rate of I'
 par[[id]]$parval = 0

 id = id + 1
 par[[id]]$parname = 'mR'
 par[[id]]$partext = 'death rate of R'
 par[[id]]$parval = 0

 mbmodel$par = par

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

 id = id + 1
 time[[id]]$timename = 'tfinal'
 time[[id]]$timetext = 'Final time of simulation'
 time[[id]]$timeval = 100

 id = id + 1
 time[[id]]$timename = 'dt'
 time[[id]]$timetext = 'Time step'
 time[[id]]$timeval = 0.1

 mbmodel$time = time