inst/extdata/deprecated/suscept_func.R

In kylieainslie/MoreVac: Modelling Repeat Vaccination

### MoReVac - Modelling Repeat Vaccination ###
### Agent-based model of repeat vaccination in birth cohort


#' Susceptibility function
#'
#' This function initializes the population before running the model.
#' @param inf_history Number years since last infection
#' @param vac_history Number of years since last vaccination
#' @param gamma Vaccine efficacy
#' @param drift_x Amount of drift from infection
#' @param drift_v Amount of drift from vaccination
#' @param version Which susceptibility function to use: 1 = either-or, 2 = multiplicative
#' @return Numeric value of susceptibility
#' @keywords morevac
#' @export
suscept_func <- function(inf_history, vac_history = 999, gamma = 0.4, drift_x = 0.2, drift_v = 0.2, version = 1){
  # version = 1 is either-or
  # version = 2 is multiplicative

  if(is.na(inf_history)){inf_history<-999}
  if(is.na(vac_history)){vac_history<-999}

  vac_ind <- 0
  if(vac_history == 0){vac_ind <- 1}
  # never infected
  if (drift_x > 0 & drift_v > 0){
    if (inf_history >= 999){
      if (vac_history > 1/drift_v){ # never vaccinated or vaccinated long enough ago for drift to have diminished protection
        rtn <- 1
      } else if (vac_history <= 1/drift_v){ # vaccinated this year or within last few years
        rtn <- (vac_ind*gamma) + (vac_history*drift_v)
      }
    }

  # infected and drift>0
    if (inf_history < 999){
      if (vac_history > 1/drift_v){ # never vaccinated
        if (inf_history < 1/drift_x){
         rtn <- inf_history*drift_x
        } else if (inf_history >= 1/drift_x) {
          rtn <- 1
        }
      } else if (vac_history <= 1/drift_v){ # vaccinated
          if (version == 1){
            rtn <- min(inf_history*drift_x,(vac_ind*gamma)+(vac_history*drift_v)) # either-or
          } else if (version == 2) {
            rtn <- inf_history*drift_x * (gamma +(vac_history*drift_v)) # multiplicative
          }
      }
    }
  }
  # infected and drift=0
  if (drift_x == 0 & drift_v == 0){
    if (inf_history < 999){
      rtn <- 0
    }
  }

  return(rtn)

}