R/calcMeanAge.R

In nissandjac/PacifichakeMSE: Management strategy evaluation of Pacific hake

#' Title
#'
#' @param agemat matrix of ages
#' @param maxage maximum age to include in the calculation
#'
#' @return
#' @export
#'
#' @examples
#' p <- calcMeanAge(matrix(1,1), 5)
calcMeanAge <- function(agemat, maxage){
#' Calculate mean age in the population

  age <- 1:maxage
  dims <- dim(agemat)
  ## Adjust the agematrix to fit the maxage

  if(dims[1] == maxage){
    agecalc <- agemat
  }else{
    agecalc <- matrix(NA, maxage, dims[2])
    agecalc[1:(maxage-1),] <- agemat[1:(maxage-1),]
    agecalc[maxage,] <- colSums(agemat[maxage:dims[1],])
    agecalc <- agecalc/colSums(agecalc)
  }



  if(all(colSums(agecalc) != 1)){
    for(i in 1:dims[2]){
    agecalc[,i] <- agecalc[,i]/sum(agecalc[,i])
    }
  }

  agemean <- rep(0,dims[2])

  for(i in 1:dims[2]){
    agemean[i] <- sum(age*agecalc[,i])
  }



  return(agemean)
}