auxiliary/modelfiles/DSAIDE/Host_Heterogeneity_Model_file.R

In ahgroup/modelbuilder: Building Compartmental Simulation Models Without Coding

############################## 
#R script to generate a modelbuilder model object with code. 
#This file was generated on 2020-10-05 08:14:29 
############################## 
 
 mbmodel = list() #create empty list 
 
 #Model meta-information
 mbmodel$title = 'Host Heterogeneity Model'
 mbmodel$description = 'An SIR type model stratified for two different types of hosts.'
 mbmodel$author = 'Andreas Handel, Alexis Vittengl'
 mbmodel$date = Sys.Date()
 mbmodel$details = 'This model tracks susceptibles, infected and recovered of 2 different types. Think of those types as e.g. males/females, children/adults, etc. The model includes infection, recovery and waning immunity processes for both hosts.' 

 #Information for all variables
 var = vector('list',6)
 id = 0
 id = id + 1
 var[[id]]$varname = 'S1'
 var[[id]]$vartext = 'Susceptible type 1 hosts'
 var[[id]]$varval = 1000
 var[[id]]$flows = c('-b11*S1*I1', '-b12*S1*I2', '+w1*R1')
 var[[id]]$flownames = c('Susceptible 1 hosts infected by infected 1 hosts', 'Susceptible 1 hosts infected by infected 2 hosts', 'Loss of immunity by recovered 1 hosts')
 
 id = id + 1
 var[[id]]$varname = 'I1'
 var[[id]]$vartext = 'Infected type 1 hosts'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+b11*S1*I1', '+b12*S1*I2', '-g1*I1')
 var[[id]]$flownames = c('Susceptible 1 hosts infected by infected 1 hosts', 'Susceptible 1 hosts infected by infected 2 hosts', 'Infected 1 hosts recovery')
 
 id = id + 1
 var[[id]]$varname = 'R1'
 var[[id]]$vartext = 'Recovered type 1 hosts'
 var[[id]]$varval = 0
 var[[id]]$flows = c('+g1*I1', '-w1*R1')
 var[[id]]$flownames = c('Infected 1 hosts recovery', 'Loss of immunity by recovered 1 hosts')
 
 id = id + 1
 var[[id]]$varname = 'S2'
 var[[id]]$vartext = 'Susceptible type 2 hosts'
 var[[id]]$varval = 200
 var[[id]]$flows = c('-b21*S2*I1', '-b22*S2*I2', '+w2*R2')
 var[[id]]$flownames = c('Susceptible 2 hosts infected by infected 1 hosts', 'Susceptible 2 hosts infected by infected 2 hosts', 'Loss of immunity by recovered 2 hosts')
 
 id = id + 1
 var[[id]]$varname = 'I2'
 var[[id]]$vartext = 'Infected type 2 hosts'
 var[[id]]$varval = 1
 var[[id]]$flows = c('+b21*S2*I1', '+b22*S2*I2', '-g2*I2')
 var[[id]]$flownames = c('Susceptible 2 hosts infected by infected 1 hosts', 'Susceptible 2 hosts infected by infected 2 hosts', 'Infected 2 hosts recovery')
 
 id = id + 1
 var[[id]]$varname = 'R2'
 var[[id]]$vartext = 'Recovered type 2 hosts'
 var[[id]]$varval = 0
 var[[id]]$flows = c('+g2*I2', '-w2*R2')
 var[[id]]$flownames = c('Infected 2 hosts recovery', 'Loss of immunity by recovered 2 hosts')
 
 mbmodel$var = var
 
 #Information for all parameters
 par = vector('list',8)
 id = 0
 id = id + 1
 par[[id]]$parname = 'b11'
 par[[id]]$partext = 'rate of transmission to susceptible type 1 host from infected type 1 host'
 par[[id]]$parval = 0.002
 
 id = id + 1
 par[[id]]$parname = 'b12'
 par[[id]]$partext = 'rate of transmission to susceptible type 1 host from infected type 2 host'
 par[[id]]$parval = 0
 
 id = id + 1
 par[[id]]$parname = 'b21'
 par[[id]]$partext = 'rate of transmission to susceptible type 2 host from infected type 1 host'
 par[[id]]$parval = 0
 
 id = id + 1
 par[[id]]$parname = 'b22'
 par[[id]]$partext = 'rate of transmission to susceptible type 2 host from infected type 2 host'
 par[[id]]$parval = 0.01
 
 id = id + 1
 par[[id]]$parname = 'g1'
 par[[id]]$partext = 'the rate at which infected type 1 hosts recover'
 par[[id]]$parval = 1
 
 id = id + 1
 par[[id]]$parname = 'g2'
 par[[id]]$partext = 'the rate at which infected type 2 hosts recover'
 par[[id]]$parval = 1
 
 id = id + 1
 par[[id]]$parname = 'w1'
 par[[id]]$partext = 'the rate at which type 1 host immunity wanes'
 par[[id]]$parval = 0
 
 id = id + 1
 par[[id]]$parname = 'w2'
 par[[id]]$partext = 'the rate at which type 2 host immunity wanes'
 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 = 60
 
 id = id + 1
 time[[id]]$timename = 'dt'
 time[[id]]$timetext = 'Time step'
 time[[id]]$timeval = 0.1
 
 mbmodel$time = time