R/sutherland_trans_params.R

In seabbs/AssessBCGPolicyChange: Assess the Evidence Used to Motivate the 2005 Change in BCG Vaccination Policy

#' Estimate Transmission chain parameters using Sutherland et al.s Approach
#'
#' @param Sutherland Logical, defaults to \code{TRUE}. Whether or not to use Sutherland et al.'s
#' assumption for estimating the basic reproduction number.
#' @param Repro.No If \code{Sutherland} is \code{FALSE} sets the basic reproduction number used to estimate
#' the transmission chain parameters.
#' @param update_chains Logical, defaults to \code{FALSE}. Should the transmission chain model be updated or used as found in Sutherland et al.
#' @return A dlist containing the expected total secondary notifications (Expected.Total.Sec.Note),
#' the size of the first generation (Size.First.Gen) and the average interval to all secondary cases (Avg.Int.All.Sec).
#' @export
#' @inheritParams sutherland_model
#' @examples
#'
#'# Orginal model
#'sutherland_trans_params()
#'
#'# Updated model
#'sutherland_trans_params(update_chains = TRUE)
sutherland_trans_params <- function(Annual.TB.Decrease.Yearly = TB_decrease_as_matrix(sutherland_TB_decrease), Sym.Lag = sutherland_gen_time,
                                    Sutherland = TRUE, Repro.No = NULL,
                                    Cohort.Length = 5, update_chains = FALSE)
{

  if (!update_chains) {
    ################################## Calculate parameters for secondary notifcations model
    ################ Expected Total no. notifications
    if (Sutherland) {
      Expected.Total.Sec.Note <- (1 - rowMeans(Annual.TB.Decrease.Yearly))^Sym.Lag
    }else {
      Expected.Total.Sec.Note <- rep(Repro.No, nrow(Annual.TB.Decrease.Yearly))
      names(Expected.Total.Sec.Note) <- rownames(Annual.TB.Decrease.Yearly)
    }

    ############### Size of first Gen
    Size.First.Gen <- Expected.Total.Sec.Note / (Expected.Total.Sec.Note + 1)
    names(Size.First.Gen) <- rownames(Annual.TB.Decrease.Yearly)
    ############### average interval to all secondary notifications
  }else{

    # Define the size of the first generation ---------------------------------
    Size.First.Gen <- (1 - rowMeans(Annual.TB.Decrease.Yearly)) ^ Sym.Lag

    # Define expected total notifications -------------------------------------
    Expected.Total.Sec.Note <- Size.First.Gen / (1 - Size.First.Gen)

  }


  Avg.Int.All.Sec <- Sym.Lag/(1 - Size.First.Gen)
  names(Avg.Int.All.Sec) <- rownames(Annual.TB.Decrease.Yearly)

  out <- list(Expected.Total.Sec.Note, Size.First.Gen, Avg.Int.All.Sec)
  names(out) <- c("Expected.Total.Sec.Note", "Size.First.Gen", "Avg.Int.All.Sec")
  return(out)
}