R/getParameters_csv.R

In nissandjac/PacifichakeMSE: Management strategy evaluation of Pacific hake

#' Title
#'
#' @param trueparms true of random parameter initialization
#'
#' @return
#' @export
#'
#' @examples
getParameters_csv <- function(trueparms = TRUE){
#' Export EM parameters for TMB based on csv files with parameters
#


  if (trueparms == TRUE){

    initN <- read.csv('inst/extdata/Ninit_MLE.csv')[,1]
    Rdev <- read.csv('inst/extdata/Rdev_MLE.csv')[,1]
    PSEL <- as.matrix(read.csv('inst/extdata/p_MLE.csv'))
    F0 <- assessment$F0

    # assessment <- read.csv('data/asssessment_MLE.csv')
    # assessment <- assessment[assessment$year > 1965 &assessment$year < 2018 ,]

    parms <- list( # Just start all the simluations with the same initial conditions
      logRinit = 14.5614,
      logh = log(0.861909),
      logMinit = log(0.213686),
      logSDsurv = log(0.257246),
      #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 = rev(initN),
      Rin = Rdev[1:(length(Rdev)-1)],
      PSEL = PSEL,
      F0 = F0

)



}else{

  PSEL <- matrix(0,5, length(1991:years[length(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)
}