R/mda_parameters.R

In mrc-ide/malariasimulation: An individual based model for malaria

#' @title Parameterise a Mass Drug Administration
#' @param parameters a list of parameters to modify
#' @param drug the index of the drug to administer
#' @param timesteps a vector of timesteps for each round of mda
#' @param coverages a vector of the proportion of the target population who receive each
#' round
#' @param min_ages a vector of minimum ages of the target population for each round exclusive (in timesteps)
#' @param max_ages a vector of maximum ages of the target population for each round exclusive (in timesteps)
#' @export
set_mda <- function(
  parameters,
  drug,
  timesteps,
  coverages,
  min_ages,
  max_ages
  ) {
  stopifnot(all(coverages >= 0) && all(coverages <= 1))
  if(length(coverages) != length(timesteps)){
    stop("coverages and timesteps do no align")
  }
  if(length(min_ages) != length(timesteps)){
    stop("minimum ages and timesteps do no align")
  }
  if(length(max_ages) != length(timesteps)){
    stop("maximum ages and timesteps do no align")
  }
  
  parameters$mda <- TRUE
  parameters$mda_drug <- drug
  parameters$mda_timesteps <- timesteps
  parameters$mda_coverages <- coverages
  parameters$mda_min_ages <- min_ages
  parameters$mda_max_ages <- max_ages
  parameters
}

#' @title Parameterise a Seasonal Malaria Chemoprevention
#' @param parameters a list of parameters to modify
#' @param drug the index of the drug to administer
#' @param timesteps a vector of timesteps for each round of smc
#' @param coverages a vector of the proportion of the target population who receive each
#' round
#' @param min_ages a vector of minimum ages of the target population for each round exclusive (in timesteps)
#' @param max_ages a vector of maximum ages of the target population for each round exclusive (in timesteps)
#' drug
#' @export
set_smc <- function(
  parameters,
  drug,
  timesteps,
  coverages,
  min_ages,
  max_ages
  ) {
  stopifnot(all(coverages >= 0) && all(coverages <= 1))
  if(length(coverages) != length(timesteps)){
    stop("coverages and timesteps do no align")
  }
  if(length(min_ages) != length(timesteps)){
    stop("minimum ages and timesteps do no align")
  }
  if(length(max_ages) != length(timesteps)){
    stop("maximum ages and timesteps do no align")
  }
  
  parameters$smc <- TRUE
  parameters$smc_drug <- drug
  parameters$smc_timesteps <- timesteps
  parameters$smc_coverages <- coverages
  parameters$smc_min_ages <- min_ages
  parameters$smc_max_ages <- max_ages
  parameters
}

#' @title Parameterise a perennial malaria chemoprevention (PMC, formerly IPIi)
#' @param parameters a list of parameters to modify
#' @param drug the index of the drug to administer
#' @param timesteps a vector of timesteps for each change in coverage
#' @param coverages a vector of proportions of the target population to receive
#' the intervention
#' @param ages a vector of ages at which PMC is administered (in timesteps)
#' @export
set_pmc <- function(
    parameters,
    drug,
    timesteps,
    coverages,
    ages
) {
  stopifnot(all(coverages >= 0) && all(coverages <= 1))
  if(length(coverages) != length(timesteps)){
    stop("coverages and timesteps do no align")
  }
  # check that the drug is valid
  stopifnot((drug > 0) && (drug <= length(parameters$drug_rel_c)))
  
  parameters$pmc <- TRUE
  parameters$pmc_drug <- drug
  parameters$pmc_timesteps <- timesteps
  parameters$pmc_coverages <- coverages
  parameters$pmc_ages <- ages
  parameters
}