auxiliary/stratification_functionality_testing/base_models/COVAX1_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$title = 'COVAX1'
 mbmodel$description = 'A Covid vaccine model'
 mbmodel$author = 'COVAMOD consortium'
 mbmodel$date = Sys.Date()
 mbmodel$details = 'The model includes susceptible, presymptomatic, asymptomatic, infected/symptomatic/ill, recovered, and deceased compartments.'

 #Information for all variables
 var = vector('list',6)
 id = 0
 id = id + 1
 var[[id]]$varname = 'S'
 var[[id]]$vartext = 'Susceptible'
 var[[id]]$varval = 1000
 var[[id]]$flows = c('-nu*bP*S*P', '-(1-nu)*bP*S*P', '-nu*bA*S*A', '-(1-nu)*bA*S*A', '-nu*bI*S*I', '-(1-nu)*bI*S*I', 'w*R')
 var[[id]]$flownames = c('infection by presymptomatic leading to symptomatic infections', 'infection by presymptomatic leading to asymptomatic infections', 'infection by asymptomatic leading to symptomatic infections', 'infection by asymptomatic leading to asymptomatic infections', 'infection by symptomatic leading to symptomatic infections', 'infection by symptomatic leading to asymptomatic infections', 'waning immunity')

 id = id + 1
 var[[id]]$varname = 'P'
 var[[id]]$vartext = 'Presymptomatic'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+nu*bP*S*P', '+nu*bA*S*A', '+nu*bI*S*I', '-sig*P')
 var[[id]]$flownames = c('infection by presymptomatic', 'infection by ill', 'infection by asymptomatic', 'progression to symptoms')

 id = id + 1
 var[[id]]$varname = 'A'
 var[[id]]$vartext = 'Asymptomatic'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+(1-nu)*bP*S*P', '+(1-nu)*bA*S*A', '+(1-nu)*bI*S*I', '-gA*A')
 var[[id]]$flownames = c('infection by presymptomatic', 'infection by ill', 'infection by asymptomatic', 'recovery')

 id = id + 1
 var[[id]]$varname = 'I'
 var[[id]]$vartext = 'Ill'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+sig*P', '-rho*gI*I', '-(1-rho)*gI*I')
 var[[id]]$flownames = c('progression to symptoms', 'progression to death', 'progression to recovery')

 id = id + 1
 var[[id]]$varname = 'R'
 var[[id]]$vartext = 'Recovered'
 var[[id]]$varval = 0
 var[[id]]$flows = c('+gA*A', '+(1-rho)*gI*I', '-w*R')
 var[[id]]$flownames = c('recovery of asymptomatics', 'recovery of ill', 'waning immunity')

 id = id + 1
 var[[id]]$varname = 'D'
 var[[id]]$vartext = 'Deceased'
 var[[id]]$varval = 0
 var[[id]]$flows = c('+rho*gI*I')
 var[[id]]$flownames = c('death')

 mbmodel$var = var

 #Information for all parameters
 par = vector('list',9)
 id = 0
 id = id + 1
 par[[id]]$parname = 'bP'
 par[[id]]$partext = 'transmission by presymptomatic'
 par[[id]]$parval = 0.001

 id = id + 1
 par[[id]]$parname = 'bA'
 par[[id]]$partext = 'transmission by asymptomatic'
 par[[id]]$parval = 5e-04

 id = id + 1
 par[[id]]$parname = 'bI'
 par[[id]]$partext = 'transmission by ill'
 par[[id]]$parval = 0.001

 id = id + 1
 par[[id]]$parname = 'nu'
 par[[id]]$partext = 'fraction symptomatic'
 par[[id]]$parval = 0.3

 id = id + 1
 par[[id]]$parname = 'sig'
 par[[id]]$partext = 'progression to symptomatic'
 par[[id]]$parval = 0.2

 id = id + 1
 par[[id]]$parname = 'gA'
 par[[id]]$partext = 'recovery of asymptomatic'
 par[[id]]$parval = 0.125

 id = id + 1
 par[[id]]$parname = 'gI'
 par[[id]]$partext = 'leaving the symptomatic class'
 par[[id]]$parval = 0.1

 id = id + 1
 par[[id]]$parname = 'rho'
 par[[id]]$partext = 'fraction dying'
 par[[id]]$parval = 0.01

 id = id + 1
 par[[id]]$parname = 'w'
 par[[id]]$partext = 'immunity wane rate'
 par[[id]]$parval = 0.01

 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