R/getParameters_OM.R

In nissandjac/PacifichakeMSE: Management strategy evaluation of Pacific hake

#' Create a list of parameters for TMB
#'
#' @param trueparms  should the model use the assesment parameters
#' @param mod r4ss object with a stock assessment
#' @param df list of parameters
#'
#' @return
#' @export
#'
#' @examples
getParameters_OM <- function(trueparms = TRUE, mod = NA,df = NA){


  if (trueparms == TRUE){
    # (those with NA for Active_Cnt are not estimated)
    pars <- mod$parameters[,c("Value","Active_Cnt")]
    pars <- pars[is.na(pars$Active_Cnt) == 0,] # Remove parameters that are not estimated
    nms <- rownames(pars)

    ### Get the Rdev params
    ninit.idx <- grep('Early_Init', nms)
    PSEL <- matrix(0,5, length(1991:mod$endyr))

    fish_ages <- c('P3','P4', 'P5', 'P6', 'P7')

    for(i in 1:length(fish_ages)){ # Generalize later
      idx <- grep(paste('AgeSel_',fish_ages[i],'_F',sep = ''), nms)

      nms[idx[2:length(idx)]] # Something wrong with the naming corrections.
      PSEL[i,] <- pars$Value[idx[2:length(idx)]]
    }



    parms <- list( # Just start all the simluations with the same initial conditions
      logRinit = pars$Value[which(nms == "SR_LN(R0)")],
      logh = log(pars$Value[which(nms == "SR_BH_steep")]),
      logMinit = log(pars$Value[which(nms == "NatM_p_1_Fem_GP_1")]),
      logSDsurv = log(pars$Value[which(nms == "Q_extraSD_Acoustic_Survey(2)")]),
      #logSDR = log(1.4),
      logphi_catch = pars$Value[which(nms =="ln(EffN_mult)_1")],
      # logphi_survey = log(10),
      # logSDF = log(0.1),
      # Selectivity parameters
      psel_fish = pars$Value[81:85], # Find a way to identify these
      psel_surv = pars$Value[86:89],
      initN = rev(pars$Value[ninit.idx]),
      Rin = pars$Value[c(grep('Early_Recr', rownames(pars)),grep('Main_Recr', rownames(pars)))], # Perhaps should be 75 - check
      # F0 = mod$derived_quants$Value[grep('F_',rownames(mod$derived_quants))][1:df$tEnd],
      PSEL = PSEL,
      F0 = mod$catch$F[2:length(mod$catch$F)]

    )



  }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)
}