auxiliary/modelfiles/DSAIDE/Environmental_Transmission_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$title = 'Environmental Transmission model'
 mbmodel$description = 'An SIR model including environmental transmission'
 mbmodel$author = 'Andreas Handel'
 mbmodel$date = Sys.Date()
 mbmodel$details = 'The model includes susceptible, infected, recovered and environmental pathogen compartments. Infection can occur through direct contact with infected or through contact with pathogen in the environment. Infected individuals shed into the environment, pathogen decays there.'

 #Information for all variables
 var = vector('list',4)
 var[[1]]$varname = 'S'
 var[[1]]$vartext = 'Susceptible'
 var[[1]]$varval = 1000
 var[[1]]$flows = c('+n', '-m*S', '-bI*I*S', '-bP*P*S')
 var[[1]]$flownames = c('births', 'natural death', 'direct infection', 'environmental infection')

 var[[2]]$varname = 'I'
 var[[2]]$vartext = 'Infected'
 var[[2]]$varval = 1
 var[[2]]$flows = c('+bI*I*S', '+bP*P*S', '-m*I', '-g*I')
 var[[2]]$flownames = c('direct infection', 'environmental infection', 'natural death', 'recovery of infected')

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

 var[[4]]$varname = 'P'
 var[[4]]$vartext = 'Pathogen in environment'
 var[[4]]$varval = 0
 var[[4]]$flows = c('+q*I', '-c*P')
 var[[4]]$flownames = c('shedding by infected', 'decay')

 mbmodel$var = var

 #Information for all parameters
 par = vector('list',7)
 par[[1]]$parname = 'bI'
 par[[1]]$partext = 'direct transmission rate'
 par[[1]]$parval = 0.004

 par[[2]]$parname = 'bP'
 par[[2]]$partext = 'environmental transmission rate'
 par[[2]]$parval = 0

 par[[3]]$parname = 'n'
 par[[3]]$partext = 'birth rate'
 par[[3]]$parval = 0

 par[[4]]$parname = 'm'
 par[[4]]$partext = 'natural death rate'
 par[[4]]$parval = 0

 par[[5]]$parname = 'g'
 par[[5]]$partext = 'recovery rate'
 par[[5]]$parval = 2

 par[[6]]$parname = 'q'
 par[[6]]$partext = 'rate at which infected hosts shed pathogen into the environment'
 par[[6]]$parval = 0

 par[[7]]$parname = 'c'
 par[[7]]$partext = 'rate at which pathogen in the environment decays'
 par[[7]]$parval = 0

 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 = 60

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

 mbmodel$time = time