R/getParameters.R

In nissandjac/PacifichakeMSE: Management strategy evaluation of Pacific hake

#' Load parameters for tmb model
#'
#' @param trueparms use the correct parameters for initial distribution?
#' @param df data frame of OM parameters and life history
#'
#' @return
#' @export
#'
#' @examples
#' example here
getParameters <- function(trueparms = TRUE, df){


  if (trueparms == TRUE){
    # (those with NA for Active_Cnt are not estimated)
    ### Get the Rdev params
    df$parms



  }else{

    PSEL <- matrix(0,5, length(1991:df$years[length(df$years)]))
    initN <- rep(0,df$nage-1)
    F0 <- rep(0.01, df$tEnd)
    Rdev <- rep(0, df$tEnd-1)
    #Rdev <- read.csv('Rdev_MLE.csv')[,1]


    parms <- list( # Just start all the simluations with the same initial conditions
      logRinit = 16,
      logh = log(0.7),
      logMinit = log(0.3),
      logSDsurv = log(0.3),
      # logSDR = log(1.4),
      logphi_catch = log(0.8276),
      # logphi_survey = log(11.33),
      # logSDF = log(0.1),
      # Selectivity parameters
      psel_fish = c(2.486490, 0.928255,0.392144,0.214365,0.475473),
      psel_surv = c(0.568618,-0.216172,0.305286 ,0.373829),
      initN = initN,
      Rin = Rdev,
      F0 = F0,
      PSEL = PSEL
    )


  }
  return(parms)
}