R/E_num.R

In n8thangreen/i-sense-model:

#' Event Joint Probabilities
#'
#' These are the joint probabilities, not the step by step conditional probabilities
#'
#' @param p_GP.H1N1 Probability
#' @param p_GP.notH1N1 Probability
#' @param p_NPFS.H1N1 Probability
#' @param p_NPFS.notH1N1 Probability
#' @param p_notseekcare_H1N1 Probability
#' @param p_Sx Probability
#' @param p_flu Probability
#' @param p_GP.Rx Probability
#' @param p_GP.collect Probability
#' @param p_NPFS.collect Probability
#' @param p_start Probability
#' @param p_complete Probability
#' @param p_hosp Probability
#' @param p_hosp_complete Probability
#' @param p_death Probability
#' @param spec_NPFS Test performance
#' @param sens_NPFS Test performance
#' @param spec_GP Test performance
#' @param sens_GP Test performance
#'
E_num <-  function(p_GP.H1N1 = 0.1,
                   p_GP.notH1N1 = 0.1,
                   p_NPFS.H1N1 = 0.1,
                   p_NPFS.notH1N1 = 0.1,
                   p_notseekcare_H1N1 = 0.1,
                   p_Sx = 0.5,
                   p_flu = 0.1,
                   p_GP.Rx = 0.3,

                   # treatment
                   p_GP.collect = 0.5,
                   p_NPFS.collect = 0.5,
                   p_start = 0.5,
                   p_complete = 0.5,
                   p_hosp = 0.5,
                   p_hosp_complete = 0.25,
                   p_death = 0.5,

                   # test performance
                   spec_NPFS = 0,
                   sens_NPFS = 1,
                   spec_GP = 0,
                   sens_GP = 1)
{

  Sx <- p_flu*p_Sx

  # ILI cases going to NPFS
  ILI_NPFS <- Sx*(p_NPFS.notH1N1 + p_NPFS.H1N1)

  # ILI cases going to GP
  ILI_GP <- Sx*(p_GP.notH1N1 + p_GP.H1N1)

  # NPFS authorisations _after_ test
  new_NPFS <- Sx*(p_NPFS.notH1N1*(1 - spec_NPFS) + p_NPFS.H1N1*sens_NPFS)

  # GP prescriptions _after_ test
  new_GP <- Sx*(p_GP.notH1N1*(1 - spec_GP) + p_GP.H1N1*sens_GP)

  # treatment collections GP
  collection_GP <- new_GP*p_GP.Rx*p_GP.collect

  # treatment collections NPFS
  collection_NPFS <- new_NPFS*p_NPFS.collect

  # treatments completed
  complete_Tx <- (collection_GP + collection_NPFS)*p_start*p_complete

  # treatments completed H1N1
  complete_Tx_H1N1 <- Sx*(p_NPFS.H1N1*sens_NPFS*p_NPFS.collect + p_GP.H1N1*sens_GP*p_GP.Rx*p_GP.collect)*p_start*p_complete

  # Sx H1N1 cases
  SxH1N1 <- Sx*(p_NPFS.H1N1 + p_GP.H1N1 + p_notseekcare_H1N1)

  # hospitalisation
  complete_hosp <- complete_Tx_H1N1*p_hosp_complete
  notcomplete_hosp <- (SxH1N1 - complete_Tx_H1N1)*p_hosp
  hosp <- complete_hosp + notcomplete_hosp

  # death in hospital
  death <- hosp*p_death

  return(c(flu = p_flu,
           ILI_NPFS = ILI_NPFS,
           ILI_GP = ILI_GP,
           new_NPFS = new_NPFS,
           new_GP = new_GP,
           collection_GP = collection_GP,
           collection_NPFS = collection_NPFS,
           complete = complete_Tx,
           complete_H1N1 = complete_Tx_H1N1,
           SxH1N1 = SxH1N1,
           hosp = hosp,
           death = death))
}