R/bednet-lemenach.R

In dd-harp/MicroMoB: Discrete Time Systems for Robust Analytics for Malaria Policy (RAMP), and Transmission Dynamics and Control of Mosquito-Borne Pathogens Transmission

# specialized methods for the Le Menach model of ITN based vector control

# https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-6-10
#' @title Modify baseline values due to vector control
#' @description Implements [BedNetEffectSizes] for the Le Menach ITN model of vector control
#' @inheritParams BedNetEffectSizes
#' @return a named [list]
#' @importFrom stats pexp
#' @export
BedNetEffectSizes.lemenach <- function(t, pars, s){
  with(pars$ITNefsz, with(pars$MYZpar[[s]],{
    n <- length(f)

    for (i in seq_len(n)) {
      tau0 <- (1/f[i]) * tau0_frac

      p0 <- pexp(q = g[i]*tau0, lower.tail = FALSE)
      Q0 <- q[i]
      W <- (1-Q0) + Q0*(1-phi) + Q0*phi*ss
      Z <- Q0*phi*r

      tau_phi <- tau0
      tau_phi[1] <- tau0[1]/(1-Z)

      f_phi <- 1 / sum(tau_phi) # feeding rate under control

      p_phi <- p0
      p_phi[1] <- (p0[1] * W) / (1 - Z*p0[1])

      g_phi <- -f_phi*log(prod(p_phi)) # mortality under control
      q_phi <- (Q0*(1-phi) + Q0*phi*ss)/W # human feeding fraction under control

      pars$MYZpar[[s]]$f[i] <- f_phi
      pars$MYZpar[[s]]$q[i] <- q_phi
      pars$MYZpar[[s]]$g[i] <- g_phi
    }

    return(pars)
}))}



#' @title Make parameters for Le Menach ITN model of vector control
#' @description This model of ITN based vector control was originally described in \url{https://malariajournal.biomedcentral.com/articles/10.1186/1475-2875-6-10}.
#' @param pars a [list]
#' @param tau0_frac a [numeric] vector giving the proportion of time spent
#' in host seeking/bloodfeeding and resting/oviposition
#' @param r probability of mosquito being repelled upon contact with ITN
#' @param s probability of mosquito successfully feeding upon contact with ITN
#' @param F_phi a [function] that takes as argument `t` and `pars` and returns the level of ITN coverage at that time
#' @return none
#' @export
setup_itn_lemenach <- function(pars, tau0_frac = c(0.68/3, 2.32/3), r = 0.56, s = 0.03, F_phi = function(t, pars){.8} ) {
  stopifnot(sum(tau0_frac) == 1)
  stopifnot(F_phi(0, pars) >= 0)
  stopifnot(F_phi(0, pars) <= 1)

  efsz <- list()
  class(efsz) <- 'lemenach'
  efsz$tau0_frac <- tau0_frac
  efsz$r <- r
  efsz$ss <- s
  pars$ITNefsz <- efsz

  coverage = list()
  class(coverage) <- "lemenach"
  coverage$F_phi = F_phi
  pars$ITNeff = coverage

  return(pars)
}

#' @title Modify baseline values due to vector control
#' @description Implements [BedNetEffectSizes] for the Le Menach ITN model of vector control
#' @inheritParams BedNetEffectSizes
#' @return a named [list]
#' @importFrom stats pexp
#' @export
BedNetEffects.lemenach <- function(t, pars, s){
  pars$ITNefsz$phi <- pars$ITNeff$F_phi(t, pars)
  return(pars)
}