auxiliary/stratification_functionality_testing/stratified_models/simulate_COVAX1_vaccine_ode.R

In ahgroup/modelbuilder: Building Compartmental Simulation Models Without Coding

#' COVAX1_vaccine
#' 
#' @description A Covid vaccine model
#' 
#' @details The model includes susceptible, presymptomatic, asymptomatic, infected/symptomatic/ill, recovered, and deceased compartments.
#' 
#' This code was generated by the modelbuilder R package.  
#' The model is implemented as a set of ordinary differential equations using the deSolve package. 
#' The following R packages need to be loaded for the function to work: deSolve. 
#' 
#' Starting conditions for model variables 
#' @param Suv : starting value for Susceptible unvaccinated : numeric
#' @param Sv : starting value for Susceptible vaccinated : numeric
#' @param Puv : starting value for Presymptomatic unvaccinated : numeric
#' @param Pv : starting value for Presymptomatic vaccinated : numeric
#' @param Auv : starting value for Asymptomatic unvaccinated : numeric
#' @param Av : starting value for Asymptomatic vaccinated : numeric
#' @param Iuv : starting value for Ill unvaccinated : numeric
#' @param Iv : starting value for Ill vaccinated : numeric
#' @param Ruv : starting value for Recovered unvaccinated : numeric
#' @param Rv : starting value for Recovered vaccinated : numeric
#' @param Duv : starting value for Deceased unvaccinated : numeric
#' @param Dv : starting value for Deceased vaccinated : numeric
#' Values for model parameters : numeric 
#' @param nu_Suv : fraction symptomatic:  vaccinated : numeric
#' @param bP_Suv_Puv : transmission by presymptomatic: to  vaccinated from  vaccinated : numeric
#' @param bP_Suv_Pv : transmission by presymptomatic: to presymptomatic vaccinated from presymptomatic vaccinated : numeric
#' @param bA_Suv_Auv : transmission by asymptomatic: to  vaccinated from  vaccinated : numeric
#' @param bA_Suv_Av : transmission by asymptomatic: to asymptomatic vaccinated from asymptomatic vaccinated : numeric
#' @param bI_Suv_Iuv : transmission by ill: to  vaccinated from  vaccinated : numeric
#' @param bI_Suv_Iv : transmission by ill: to ill vaccinated from ill vaccinated : numeric
#' @param w_Ruv : immunity wane rate:  vaccinated : numeric
#' @param nu_Sv : fraction symptomatic: susceptible vaccinated : numeric
#' @param bP_Sv_Puv : transmission by presymptomatic: to susceptible vaccinated from susceptible vaccinated : numeric
#' @param bP_Sv_Pv : transmission by presymptomatic: to susceptible vaccinated from presymptomatic vaccinated : numeric
#' @param bA_Sv_Auv : transmission by asymptomatic: to susceptible vaccinated from susceptible vaccinated : numeric
#' @param bA_Sv_Av : transmission by asymptomatic: to susceptible vaccinated from asymptomatic vaccinated : numeric
#' @param bI_Sv_Iuv : transmission by ill: to susceptible vaccinated from susceptible vaccinated : numeric
#' @param bI_Sv_Iv : transmission by ill: to susceptible vaccinated from ill vaccinated : numeric
#' @param w_Rv : immunity wane rate: recovered vaccinated : numeric
#' @param sig_Puv : progression to symptomatic:  vaccinated : numeric
#' @param sig_Pv : progression to symptomatic: presymptomatic vaccinated : numeric
#' @param gA_Auv : recovery of asymptomatic:  vaccinated : numeric
#' @param gA_Av : recovery of asymptomatic: asymptomatic vaccinated : numeric
#' @param rho_Iuv : fraction dying:  vaccinated : numeric
#' @param gI_Iuv : leaving the symptomatic class:  vaccinated : numeric
#' @param rho_Iv : fraction dying: ill vaccinated : numeric
#' @param gI_Iv : leaving the symptomatic class: ill vaccinated : numeric
#' Values for model times : numeric 
#' @param tstart : Start time of simulation : numeric
#' @param tfinal : Final time of simulation : numeric
#' @param dt : Time step : numeric
#' @return The function returns the output as a list. 
#' The time-series from the simulation is returned as a dataframe saved as list element \code{ts}. 
#' The \code{ts} dataframe has one column per compartment/variable. The first column is time.   
#' @examples  
#' # To run the simulation with default parameters:  
#' result <- simulate_COVAX1_vaccine_ode() 
#' # To choose values other than the standard one, specify them like this:  
#' result <- simulate_COVAX1_vaccine_ode(Suv = 2000,Sv = 2000,Puv = 2,Pv = 2,Auv = 2,Av = 2,Iuv = 2,Iv = 2,Ruv = 0,Rv = 0,Duv = 0,Dv = 0) 
#' # You can display or further process the result, like this:  
#' plot(result$ts[,'time'],result$ts[,'Suv'],xlab='Time',ylab='Numbers',type='l') 
#' print(paste('Max number of Suv: ',max(result$ts[,'Suv']))) 
#' @section Warning: This function does not perform any error checking. So if you try to do something nonsensical (e.g. have negative values for parameters), the code will likely abort with an error message.
#' @section Model Author: COVAMOD consortium
#' @section Model creation date: 18536
#' @section Code Author: generated by the \code{modelbuilder} R package 
#' @section Code creation date: 2020-10-01
#' @export 
 
simulate_COVAX1_vaccine_ode <- function(Suv = 1000, Sv = 1000, Puv = 1, Pv = 1, Auv = 1, Av = 1, Iuv = 1, Iv = 1, Ruv = 0, Rv = 0, Duv = 0, Dv = 0, nu_Suv = 0.3, bP_Suv_Puv = 0.001, bP_Suv_Pv = 0.001, bA_Suv_Auv = 5e-04, bA_Suv_Av = 5e-04, bI_Suv_Iuv = 0.001, bI_Suv_Iv = 0.001, w_Ruv = 0.01, nu_Sv = 0.3, bP_Sv_Puv = 0.001, bP_Sv_Pv = 0.001, bA_Sv_Auv = 5e-04, bA_Sv_Av = 5e-04, bI_Sv_Iuv = 0.001, bI_Sv_Iv = 0.001, w_Rv = 0.01, sig_Puv = 0.2, sig_Pv = 0.2, gA_Auv = 0.125, gA_Av = 0.125, rho_Iuv = 0.01, gI_Iuv = 0.1, rho_Iv = 0.01, gI_Iv = 0.1, tstart = 0, tfinal = 100, dt = 0.1) 
{ 
  ############################## 
  #Block of ODE equations for deSolve 
  ############################## 
  COVAX1_vaccine_ode_fct <- function(t, y, parms) 
  {
    with( as.list(c(y,parms)), { #lets us access variables and parameters stored in y and parms by name 
    #StartODES
    #Susceptible unvaccinated : infection by presymptomatic leading to symptomatic infections, unvaccinated : infection by presymptomatic leading to symptomatic infections, unvaccinated : infection by presymptomatic leading to asymptomatic infections, unvaccinated : infection by presymptomatic leading to asymptomatic infections, unvaccinated : infection by asymptomatic leading to symptomatic infections, unvaccinated : infection by asymptomatic leading to symptomatic infections, unvaccinated : infection by asymptomatic leading to asymptomatic infections, unvaccinated : infection by asymptomatic leading to asymptomatic infections, unvaccinated : infection by symptomatic leading to symptomatic infections, unvaccinated : infection by symptomatic leading to symptomatic infections, unvaccinated : infection by symptomatic leading to asymptomatic infections, unvaccinated : infection by symptomatic leading to asymptomatic infections, unvaccinated : waning immunity, unvaccinated : waning immunity, unvaccinated :
    dSuv_mb = -nu_Suv*bP_Suv_Puv*Suv*Puv -nu_Suv*bP_Suv_Pv*Suv*Pv -(1-nu_Suv)*bP_Suv_Puv*Suv*Puv -(1-nu_Suv)*bP_Suv_Pv*Suv*Pv -nu_Suv*bA_Suv_Auv*Suv*Auv -nu_Suv*bA_Suv_Av*Suv*Av -(1-nu_Suv)*bA_Suv_Auv*Suv*Auv -(1-nu_Suv)*bA_Suv_Av*Suv*Av -nu_Suv*bI_Suv_Iuv*Suv*Iuv -nu_Suv*bI_Suv_Iv*Suv*Iv -(1-nu_Suv)*bI_Suv_Iuv*Suv*Iuv -(1-nu_Suv)*bI_Suv_Iv*Suv*Iv *w_Ruv*Ruv
    #Susceptible vaccinated : infection by presymptomatic leading to symptomatic infections, vaccinated : infection by presymptomatic leading to symptomatic infections, vaccinated : infection by presymptomatic leading to asymptomatic infections, vaccinated : infection by presymptomatic leading to asymptomatic infections, vaccinated : infection by asymptomatic leading to symptomatic infections, vaccinated : infection by asymptomatic leading to symptomatic infections, vaccinated : infection by asymptomatic leading to asymptomatic infections, vaccinated : infection by asymptomatic leading to asymptomatic infections, vaccinated : infection by symptomatic leading to symptomatic infections, vaccinated : infection by symptomatic leading to symptomatic infections, vaccinated : infection by symptomatic leading to asymptomatic infections, vaccinated : infection by symptomatic leading to asymptomatic infections, vaccinated : waning immunity, vaccinated : waning immunity, vaccinated :
    dSv_mb = -nu_Sv*bP_Sv_Puv*Sv*Puv -nu_Sv*bP_Sv_Pv*Sv*Pv -(1-nu_Sv)*bP_Sv_Puv*Sv*Puv -(1-nu_Sv)*bP_Sv_Pv*Sv*Pv -nu_Sv*bA_Sv_Auv*Sv*Auv -nu_Sv*bA_Sv_Av*Sv*Av -(1-nu_Sv)*bA_Sv_Auv*Sv*Auv -(1-nu_Sv)*bA_Sv_Av*Sv*Av -nu_Sv*bI_Sv_Iuv*Sv*Iuv -nu_Sv*bI_Sv_Iv*Sv*Iv -(1-nu_Sv)*bI_Sv_Iuv*Sv*Iuv -(1-nu_Sv)*bI_Sv_Iv*Sv*Iv *w_Rv*Rv
    #Presymptomatic unvaccinated : infection by presymptomatic, unvaccinated : infection by presymptomatic, unvaccinated : infection by ill, unvaccinated : infection by ill, unvaccinated : infection by asymptomatic, unvaccinated : infection by asymptomatic, unvaccinated : progression to symptoms, unvaccinated : progression to symptoms, unvaccinated :
    dPuv_mb = +nu_Suv*bP_Suv_Puv*Suv*Puv +nu_Suv*bP_Suv_Pv*Suv*Pv +nu_Suv*bA_Suv_Auv*Suv*Auv +nu_Suv*bA_Suv_Av*Suv*Av +nu_Suv*bI_Suv_Iuv*Suv*Iuv +nu_Suv*bI_Suv_Iv*Suv*Iv -sig_Puv*Puv
    #Presymptomatic vaccinated : infection by presymptomatic, vaccinated : infection by presymptomatic, vaccinated : infection by ill, vaccinated : infection by ill, vaccinated : infection by asymptomatic, vaccinated : infection by asymptomatic, vaccinated : progression to symptoms, vaccinated : progression to symptoms, vaccinated :
    dPv_mb = +nu_Sv*bP_Sv_Puv*Sv*Puv +nu_Sv*bP_Sv_Pv*Sv*Pv +nu_Sv*bA_Sv_Auv*Sv*Auv +nu_Sv*bA_Sv_Av*Sv*Av +nu_Sv*bI_Sv_Iuv*Sv*Iuv +nu_Sv*bI_Sv_Iv*Sv*Iv -sig_Pv*Pv
    #Asymptomatic unvaccinated : infection by presymptomatic, unvaccinated : infection by presymptomatic, unvaccinated : infection by ill, unvaccinated : infection by ill, unvaccinated : infection by asymptomatic, unvaccinated : infection by asymptomatic, unvaccinated : recovery, unvaccinated : recovery, unvaccinated :
    dAuv_mb = +(1-nu_Suv)*bP_Suv_Puv*Suv*Puv +(1-nu_Suv)*bP_Suv_Pv*Suv*Pv +(1-nu_Suv)*bA_Suv_Auv*Suv*Auv +(1-nu_Suv)*bA_Suv_Av*Suv*Av +(1-nu_Suv)*bI_Suv_Iuv*Suv*Iuv +(1-nu_Suv)*bI_Suv_Iv*Suv*Iv -gA_Auv*Auv
    #Asymptomatic vaccinated : infection by presymptomatic, vaccinated : infection by presymptomatic, vaccinated : infection by ill, vaccinated : infection by ill, vaccinated : infection by asymptomatic, vaccinated : infection by asymptomatic, vaccinated : recovery, vaccinated : recovery, vaccinated :
    dAv_mb = +(1-nu_Sv)*bP_Sv_Puv*Sv*Puv +(1-nu_Sv)*bP_Sv_Pv*Sv*Pv +(1-nu_Sv)*bA_Sv_Auv*Sv*Auv +(1-nu_Sv)*bA_Sv_Av*Sv*Av +(1-nu_Sv)*bI_Sv_Iuv*Sv*Iuv +(1-nu_Sv)*bI_Sv_Iv*Sv*Iv -gA_Av*Av
    #Ill unvaccinated : progression to symptoms, unvaccinated : progression to symptoms, unvaccinated : progression to death, unvaccinated : progression to death, unvaccinated : progression to recovery, unvaccinated : progression to recovery, unvaccinated :
    dIuv_mb = +sig_Puv*Puv -rho_Iuv*gI_Iuv*Iuv -(1-rho_Iuv)*gI_Iuv*Iuv
    #Ill vaccinated : progression to symptoms, vaccinated : progression to symptoms, vaccinated : progression to death, vaccinated : progression to death, vaccinated : progression to recovery, vaccinated : progression to recovery, vaccinated :
    dIv_mb = +sig_Pv*Pv -rho_Iv*gI_Iv*Iv -(1-rho_Iv)*gI_Iv*Iv
    #Recovered unvaccinated : recovery of asymptomatics, unvaccinated : recovery of asymptomatics, unvaccinated : recovery of ill, unvaccinated : recovery of ill, unvaccinated : waning immunity, unvaccinated : waning immunity, unvaccinated :
    dRuv_mb = +gA_Auv*Auv +(1-rho_Iuv)*gI_Iuv*Iuv -w_Ruv*Ruv
    #Recovered vaccinated : recovery of asymptomatics, vaccinated : recovery of asymptomatics, vaccinated : recovery of ill, vaccinated : recovery of ill, vaccinated : waning immunity, vaccinated : waning immunity, vaccinated :
    dRv_mb = +gA_Av*Av +(1-rho_Iv)*gI_Iv*Iv -w_Rv*Rv
    #Deceased unvaccinated : death, unvaccinated : death, unvaccinated :
    dDuv_mb = +rho_Iuv*gI_Iuv*Iuv
    #Deceased vaccinated : death, vaccinated : death, vaccinated :
    dDv_mb = +rho_Iv*gI_Iv*Iv
    #EndODES
    list(c(dSuv_mb,dSv_mb,dPuv_mb,dPv_mb,dAuv_mb,dAv_mb,dIuv_mb,dIv_mb,dRuv_mb,dRv_mb,dDuv_mb,dDv_mb)) 
  } ) } #close with statement, end ODE code block 
 
  ############################## 
  #Main function code block 
  ############################## 
  #Creating named vectors 
  varvec_mb = c(Suv = Suv, Sv = Sv, Puv = Puv, Pv = Pv, Auv = Auv, Av = Av, Iuv = Iuv, Iv = Iv, Ruv = Ruv, Rv = Rv, Duv = Duv, Dv = Dv) 
  parvec_mb = c(nu_Suv = nu_Suv, bP_Suv_Puv = bP_Suv_Puv, bP_Suv_Pv = bP_Suv_Pv, bA_Suv_Auv = bA_Suv_Auv, bA_Suv_Av = bA_Suv_Av, bI_Suv_Iuv = bI_Suv_Iuv, bI_Suv_Iv = bI_Suv_Iv, w_Ruv = w_Ruv, nu_Sv = nu_Sv, bP_Sv_Puv = bP_Sv_Puv, bP_Sv_Pv = bP_Sv_Pv, bA_Sv_Auv = bA_Sv_Auv, bA_Sv_Av = bA_Sv_Av, bI_Sv_Iuv = bI_Sv_Iuv, bI_Sv_Iv = bI_Sv_Iv, w_Rv = w_Rv, sig_Puv = sig_Puv, sig_Pv = sig_Pv, gA_Auv = gA_Auv, gA_Av = gA_Av, rho_Iuv = rho_Iuv, gI_Iuv = gI_Iuv, rho_Iv = rho_Iv, gI_Iv = gI_Iv) 
  timevec_mb = seq(tstart, tfinal,by = dt) 
  #Running the model 
  simout = deSolve::ode(y = varvec_mb, parms = parvec_mb, times = timevec_mb,  func = COVAX1_vaccine_ode_fct, rtol = 1e-12, atol = 1e-12) 
  #Setting up empty list and returning result as data frame called ts 
  result <- list() 
  result$ts <- as.data.frame(simout) 
  return(result) 
}