inst/extdata/depricated/seir_ode.R

In kylieainslie/vacamole: Deterministic Age-Structured SEIR model with Vaccination

#' SEIR ODE model of vaccination with 2 doses and delay to protection
#' @param times vector of times
#' @param init list of inititial states
#' @param params list of parameter values
#' @return List of summary results
#' @keywords vacamole
#' @export
# Define model -----------------------------------------------------
seir_ode <- function(times,init,params){
  with(as.list(c(params,init)), {
    # determine vaccination rate
      if (t>tv && S/N>(1-uptake) && sum(Shold,Sv) < total_dose1){
        alpha <- vac_per_day
      } else {
        alpha <- 0
      }
    
      if (t>tv2 && S/N>(1-uptake) && sum(Shold2,Sv2) < total_dose2){ 
        alpha2 <- vac_per_day2
      } else {
        alpha2 <- 0
      }
    
    ################################################################
    # ODEs:
    if (constant_foi){
      lambda <- beta*init_inf/N
    } else{lambda <- beta * (I + Iv + Iv2)/N}
    
      dS <- -lambda * S - alpha * S/N
      dShold <- alpha * S/N - (1/delay) * Shold - lambda * Shold
      dSv <- (1/delay) * Shold - eta * lambda * Sv - ifelse(Sv>0,alpha2 * Sv/(Sv+Ev+Iv+Rv), alpha2*0)
      dShold2 <- ifelse(Sv>0,alpha2 * Sv/(Sv+Ev+Iv+Rv), alpha2*0) - (1/delay2) * Shold2 - eta * lambda * Shold2
      dSv2 <- (1/delay2) * Shold2 - eta2 * lambda * Sv2
      dE <- lambda * (S + Shold) - sigma * E
      dEv <- eta * lambda * (Sv + Shold2) - sigma * Ev
      dEv2 <- eta2 * lambda * Sv2 - sigma * Ev2 
      dI <- sigma * E - (gamma + h) * I 
      dIv <- sigma * Ev - (gamma + h) * Iv  
      dIv2 <- sigma * Ev2 - (gamma + h) * Iv2
      dH <- h * (I + Iv + Iv2) - (d + r) * H
      dHv <- h * Iv - (d + r) * Hv
      dHv2 <- h * Iv2 - (d + r) * Hv2
      dD <- d * (H + Hv + Hv2) 
      dR <- gamma * I + r * H 
      dRv <- gamma * Iv + r * Hv
      dRv2 <- gamma * Iv2 + r * Hv2 
      
    ################################################################
    
    dt <- 1
    list(c(dt,dS,dShold,dSv,dShold2,dSv2,dE,dEv,dEv2,
           dI,dIv,dIv2,dH,dHv,dHv2,dD,dR,dRv,dRv2))
  })
}