R/map_SS_MAS.R

In cstawitz/RMAS: Read and Write Input and Output for MAS Model

#'Function mapping SS values to MAS
#'@name map_SS_MAS
#'@author Christine Stawitz
#'@description Function to map names between different stock assessment models
#'@param toMAS boolean; if this will be written to a MAS-style JSON input
#'@param in_name string; the string to map to a new name
#'@return new_name - the mapped name
#'
#'@example map_SS_MAS("SR_LN(R0)")
map_SS_MAS <-function(toMAS = TRUE, in_name){
  if(toMAS){
    new_name <- switch(in_name, "L_at_Amin_Fem_GP_1" = "lmin",
           "L_at_Amax_Fem_GP_1" = "lmax",
           "L_at_Amin__GP_1" = "lmin",
           "Wtlen_1_Fem" = "alpha_f",
           "Wtlen_2_Fem" = "beta_f",
           "NatM_p_1_Fem_GP_1" = "M",
           "SR_LN(R0)" = "R0",
           "SR_BH_steep" = "h",
           "SR_sigmaR" = "sigma_r",
           "SR_autocorr" = "rho",
           "VonBert_K_Fem_GP_1" = "c",
           "AgeSel_P1_Fishery(1)" = "a50",
           "AgeSel_P2_Fishery(1)" = "s",
           "AgeSel_P1_Acoustic_Survey(2)" = "a50",
           "AgeSel_P2_Acoustic_Survey(2)" = "s",
           in_name
           )
  } else{
    new_name <- switch(in_name, "L_at_Amin_Fem_GP_1" = "lmin",
                       "L_at_Amax_Fem_GP_1" = "lmax",
                       "L_at_Amin__GP_1" = "lmin",
                       "Wtlen_1_Fem" = "alpha_f",
                       "Wtlen_2_Fem" = "beta_f",
                       "NatM_p_1_Fem_GP_1" = "M",
                       "SR_LN(R0)" = "R0",
                       "SR_BH_steep" = "h",
                       "SR_sigmaR" = "sigma_r",
                       "SR_autocorr" = "rho",
                       "VonBert_K_Fem_GP_1" = "c",
                       in_name)
  }
  return(new_name)
}