#include <admodel.h>

#include <multispecies.htp>

model_data::model_data(void)
{
  nyrs.allocate("nyrs");
  Data.allocate(1,nyrs,1,87,"Data");
  Year.allocate(1,nyrs);
  obs_bio_GB_HAD.allocate(1,nyrs);
  obs_bio_GB_YTL.allocate(1,nyrs);
  obs_bio_GB_WFL.allocate(1,nyrs);
  obs_bio_GB_LSK.allocate(1,nyrs);
  obs_bio_GB_COD.allocate(1,nyrs);
  obs_bio_GB_SFL.allocate(1,nyrs);
  obs_bio_GB_SHK.allocate(1,nyrs);
  obs_bio_GB_SPD.allocate(1,nyrs);
  obs_bio_GB_WSK.allocate(1,nyrs);
  obs_bio_GB_GOS.allocate(1,nyrs);
  obs_bio_GB_POL.allocate(1,nyrs);
  obs_bio_GB_WHK.allocate(1,nyrs);
  obs_bio_GB_HER.allocate(1,nyrs);
  obs_bio_GB_MCK.allocate(1,nyrs);
  obs_bio_GB_SQD.allocate(1,nyrs);
  obs_cat_GB_HAD.allocate(1,nyrs);
  obs_cat_GB_YTL.allocate(1,nyrs);
  obs_cat_GB_WFL.allocate(1,nyrs);
  obs_cat_GB_LSK.allocate(1,nyrs);
  obs_cat_GB_COD.allocate(1,nyrs);
  obs_cat_GB_SFL.allocate(1,nyrs);
  obs_cat_GB_SHK.allocate(1,nyrs);
  obs_cat_GB_SPD.allocate(1,nyrs);
  obs_cat_GB_WSK.allocate(1,nyrs);
  obs_cat_GB_GOS.allocate(1,nyrs);
  obs_cat_GB_POL.allocate(1,nyrs);
  obs_cat_GB_WHK.allocate(1,nyrs);
  obs_cat_GB_HER.allocate(1,nyrs);
  obs_cat_GB_MCK.allocate(1,nyrs);
  obs_cat_GB_SQD.allocate(1,nyrs);
  obs_bio_GOM_HAD.allocate(1,nyrs);
  obs_bio_GOM_YTL.allocate(1,nyrs);
  obs_bio_GOM_WFL.allocate(1,nyrs);
  obs_bio_GOM_LSK.allocate(1,nyrs);
  obs_bio_GOM_COD.allocate(1,nyrs);
  obs_bio_GOM_SFL.allocate(1,nyrs);
  obs_bio_GOM_SHK.allocate(1,nyrs);
  obs_bio_GOM_SPD.allocate(1,nyrs);
  obs_bio_GOM_WSK.allocate(1,nyrs);
  obs_bio_GOM_GOS.allocate(1,nyrs);
  obs_bio_GOM_POL.allocate(1,nyrs);
  obs_bio_GOM_WHK.allocate(1,nyrs);
  obs_bio_GOM_HER.allocate(1,nyrs);
  obs_bio_GOM_MCK.allocate(1,nyrs);
  obs_bio_GOM_SQD.allocate(1,nyrs);
  obs_cat_GOM_HAD.allocate(1,nyrs);
  obs_cat_GOM_YTL.allocate(1,nyrs);
  obs_cat_GOM_WFL.allocate(1,nyrs);
  obs_cat_GOM_LSK.allocate(1,nyrs);
  obs_cat_GOM_COD.allocate(1,nyrs);
  obs_cat_GOM_SFL.allocate(1,nyrs);
  obs_cat_GOM_SHK.allocate(1,nyrs);
  obs_cat_GOM_SPD.allocate(1,nyrs);
  obs_cat_GOM_WSK.allocate(1,nyrs);
  obs_cat_GOM_GOS.allocate(1,nyrs);
  obs_cat_GOM_POL.allocate(1,nyrs);
  obs_cat_GOM_WHK.allocate(1,nyrs);
  obs_cat_GOM_HER.allocate(1,nyrs);
  obs_cat_GOM_MCK.allocate(1,nyrs);
  obs_cat_GOM_SQD.allocate(1,nyrs);
  obs_bio_SNE_YTL.allocate(1,nyrs);
  obs_bio_SNE_WFL.allocate(1,nyrs);
  obs_bio_SNE_LSK.allocate(1,nyrs);
  obs_bio_SNE_SFL.allocate(1,nyrs);
  obs_bio_SNE_SHK.allocate(1,nyrs);
  obs_bio_SNE_SPD.allocate(1,nyrs);
  obs_bio_SNE_WSK.allocate(1,nyrs);
  obs_bio_SNE_GOS.allocate(1,nyrs);
  obs_bio_SNE_POL.allocate(1,nyrs);
  obs_bio_SNE_WHK.allocate(1,nyrs);
  obs_bio_SNE_HER.allocate(1,nyrs);
  obs_bio_SNE_MCK.allocate(1,nyrs);
  obs_bio_SNE_SQD.allocate(1,nyrs);
  obs_cat_SNE_YTL.allocate(1,nyrs);
  obs_cat_SNE_WFL.allocate(1,nyrs);
  obs_cat_SNE_LSK.allocate(1,nyrs);
  obs_cat_SNE_SFL.allocate(1,nyrs);
  obs_cat_SNE_SHK.allocate(1,nyrs);
  obs_cat_SNE_SPD.allocate(1,nyrs);
  obs_cat_SNE_WSK.allocate(1,nyrs);
  obs_cat_SNE_GOS.allocate(1,nyrs);
  obs_cat_SNE_POL.allocate(1,nyrs);
  obs_cat_SNE_WHK.allocate(1,nyrs);
  obs_cat_SNE_HER.allocate(1,nyrs);
  obs_cat_SNE_MCK.allocate(1,nyrs);
  obs_cat_SNE_SQD.allocate(1,nyrs);
  obs_bio_B_GB.allocate(1,nyrs);
  obs_cat_B_GB.allocate(1,nyrs);
  obs_bio_S_GB.allocate(1,nyrs);
  obs_cat_S_GB.allocate(1,nyrs);
  obs_bio_F_GB.allocate(1,nyrs);
  obs_cat_F_GB.allocate(1,nyrs);
  obs_bio_P_GB.allocate(1,nyrs);
  obs_cat_P_GB.allocate(1,nyrs);
  obs_bio_B_GOM.allocate(1,nyrs);
  obs_cat_B_GOM.allocate(1,nyrs);
  obs_bio_S_GOM.allocate(1,nyrs);
  obs_cat_S_GOM.allocate(1,nyrs);
  obs_bio_F_GOM.allocate(1,nyrs);
  obs_cat_F_GOM.allocate(1,nyrs);
  obs_bio_P_GOM.allocate(1,nyrs);
  obs_cat_P_GOM.allocate(1,nyrs);
  obs_bio_B_SNE.allocate(1,nyrs);
  obs_cat_B_SNE.allocate(1,nyrs);
  obs_bio_S_SNE.allocate(1,nyrs);
  obs_cat_S_SNE.allocate(1,nyrs);
  obs_bio_F_SNE.allocate(1,nyrs);
  obs_cat_F_SNE.allocate(1,nyrs);
  obs_bio_P_SNE.allocate(1,nyrs);
  obs_cat_P_SNE.allocate(1,nyrs);
  obs_bio_F_tot.allocate(1,nyrs);
  obs_cat_F_tot.allocate(1,nyrs);
  obs_bio_P_tot.allocate(1,nyrs);
  obs_cat_P_tot.allocate(1,nyrs);
  Year=column(Data,1);
  
  // Georges Bank
  //F = Migrating Piscivores  = Silver hake, spiny dogfish, Winter skate, Goosefish, Pollock, White hake
  obs_bio_F_tot =   column(Data,8) + column(Data,9) + column(Data,10) + column(Data,11) +column(Data,12) + column(Data,13) + 
  column(Data,38) + column(Data,39) + column(Data,40)+ column(Data,41)+ column(Data,42)+ column(Data,43) + 
  column(Data,66) + column(Data,67) + column(Data,68)+ column(Data,69)+ column(Data,70)+ column(Data,71);
  obs_cat_F_tot =  column(Data,23) + column(Data,24) + column(Data,25) + column(Data,26) + column(Data,27) + column(Data,28) +
  column(Data,53) + column(Data,54) + column(Data,55)+ column(Data,56)+ column(Data,57)+ column(Data,58) +
  column(Data,79) + column(Data,80) + column(Data,81)+ column(Data,82)+ column(Data,83)+ column(Data,84);
  //P = Migrating Planktivores = Atlantic herring, Mackerel, Longfin squid
  obs_bio_P_tot = column(Data,14)+column(Data,15)+column(Data,16)+column(Data,44)+column(Data,45)+column(Data,46)+column(Data,72)+column(Data,73)+column(Data,74);
  obs_cat_P_tot = column(Data,59)+column(Data,60)+column(Data,61)+column(Data,29)+column(Data,30)+column(Data,31)+column(Data,85)+column(Data,86)+column(Data,87);
  obs_bio_P_GB  = column(Data,14)+column(Data,15)+column(Data,16);
  obs_cat_P_GB  = column(Data,29)+column(Data,30)+column(Data,31) ;
  obs_bio_P_GOM = column(Data,44)+column(Data,45)+column(Data,46);
  obs_cat_P_GOM = column(Data,59)+column(Data,60)+column(Data,61) ;
  obs_bio_P_SNE = column(Data,72)+column(Data,73)+column(Data,74);
  obs_cat_P_SNE = column(Data,85)+column(Data,86)+column(Data,87) ;
  obs_bio_F_GB  = column(Data,8) + column(Data,9) + column(Data,10) + column(Data,11) +column(Data,12) + column(Data,13);
  obs_cat_F_GB  = column(Data,23) + column(Data,24) + column(Data,25) + column(Data,26) + column(Data,27) + column(Data,28);
  obs_bio_F_GOM = column(Data,38) + column(Data,39) + column(Data,40)+ column(Data,41)+ column(Data,42)+ column(Data,43);
  obs_cat_F_GOM = column(Data,53) + column(Data,54) + column(Data,55)+ column(Data,56)+ column(Data,57)+ column(Data,58);
  obs_bio_F_SNE = column(Data,66) + column(Data,67) + column(Data,68)+ column(Data,69)+ column(Data,70)+ column(Data,71);
  obs_cat_F_SNE = column(Data,79) + column(Data,80) + column(Data,81)+ column(Data,82)+ column(Data,83)+ column(Data,84);
  obs_bio_B_GB  = column(Data,2) + column(Data,3) + column(Data,4) + column(Data,5);
  obs_cat_B_GB  = column(Data,17) + column(Data,18) + column(Data,19) + column(Data,20);
  obs_bio_B_GOM = column(Data,32) + column(Data,33) + column(Data,34) + column(Data,35);
  obs_cat_B_GOM = column(Data,47) + column(Data,48) + column(Data,49) + column(Data,50);
  obs_bio_B_SNE = column(Data,62) + column(Data,63) + column(Data,64);
  obs_cat_B_SNE = column(Data,75) + column(Data,76) + column(Data,77);
  //S =Non-migrating Piscivores  = Atlantic cod, Summer flounder
  obs_bio_S_GB = column(Data,6) + column(Data,7);
  obs_cat_S_GB = column(Data,21)+ column(Data,22);
  obs_bio_S_GOM = column(Data,36) + column(Data,37);
  obs_cat_S_GOM = column(Data,51) + column(Data,52);
  obs_bio_S_SNE = column(Data,65);
  obs_cat_S_SNE = column(Data,78);
k_pseudo_B_GB=max(obs_bio_B_GB)*3;
k_pseudo_B_GOM=max(obs_bio_B_GOM)*2;
k_pseudo_B_SNE=max(obs_bio_B_SNE)*2;
k_pseudo_F_tot=max(obs_bio_F_tot)*1.5;
k_pseudo_P_tot=max(obs_bio_P_tot)*1.5; 
}

model_parameters::model_parameters(int sz,int argc,char * argv[]) : 
 ad_comm(argc,argv), model_data() , function_minimizer(sz)
{
  initializationfunction();
  log_r_P_tot.allocate(-4.6,-0.11,"log_r_P_tot");
  r_P_tot.allocate("r_P_tot");
  #ifndef NO_AD_INITIALIZE
  r_P_tot.initialize();
  #endif
  log_k_P_tot.allocate(1.0,10.0,"log_k_P_tot");
  k_P_tot.allocate("k_P_tot");
  #ifndef NO_AD_INITIALIZE
  k_P_tot.initialize();
  #endif
  log_B0_P_tot.allocate(1.0,10.0,"log_B0_P_tot");
  B0_P_tot.allocate("B0_P_tot");
  #ifndef NO_AD_INITIALIZE
  B0_P_tot.initialize();
  #endif
  log_r_F_tot.allocate(-4.6,-0.11,"log_r_F_tot");
  r_F_tot.allocate("r_F_tot");
  #ifndef NO_AD_INITIALIZE
  r_F_tot.initialize();
  #endif
  log_k_F_tot.allocate(1.0,10.0,"log_k_F_tot");
  k_F_tot.allocate("k_F_tot");
  #ifndef NO_AD_INITIALIZE
  k_F_tot.initialize();
  #endif
  log_B0_F_tot.allocate(1.0,10.0,"log_B0_F_tot");
  B0_F_tot.allocate("B0_F_tot");
  #ifndef NO_AD_INITIALIZE
  B0_F_tot.initialize();
  #endif
  log_r_B_GB.allocate(-4.6,-0.11,"log_r_B_GB");
  r_B_GB.allocate("r_B_GB");
  #ifndef NO_AD_INITIALIZE
  r_B_GB.initialize();
  #endif
  log_k_B_GB.allocate(1.0,10.0,"log_k_B_GB");
  k_B_GB.allocate("k_B_GB");
  #ifndef NO_AD_INITIALIZE
  k_B_GB.initialize();
  #endif
  log_B0_B_GB.allocate(1.0,10.0,"log_B0_B_GB");
  B0_B_GB.allocate("B0_B_GB");
  #ifndef NO_AD_INITIALIZE
  B0_B_GB.initialize();
  #endif
  log_r_B_GOM.allocate(-4.6,-0.11,"log_r_B_GOM");
  r_B_GOM.allocate("r_B_GOM");
  #ifndef NO_AD_INITIALIZE
  r_B_GOM.initialize();
  #endif
  log_k_B_GOM.allocate(1.0,10.0,"log_k_B_GOM");
  k_B_GOM.allocate("k_B_GOM");
  #ifndef NO_AD_INITIALIZE
  k_B_GOM.initialize();
  #endif
  log_B0_B_GOM.allocate(1.0,10.0,"log_B0_B_GOM");
  B0_B_GOM.allocate("B0_B_GOM");
  #ifndef NO_AD_INITIALIZE
  B0_B_GOM.initialize();
  #endif
  log_r_B_SNE.allocate(-4.6,-0.11,"log_r_B_SNE");
  r_B_SNE.allocate("r_B_SNE");
  #ifndef NO_AD_INITIALIZE
  r_B_SNE.initialize();
  #endif
  log_k_B_SNE.allocate(1.0,10.0,"log_k_B_SNE");
  k_B_SNE.allocate("k_B_SNE");
  #ifndef NO_AD_INITIALIZE
  k_B_SNE.initialize();
  #endif
  log_B0_B_SNE.allocate(1.0,10.0,"log_B0_B_SNE");
  B0_B_SNE.allocate("B0_B_SNE");
  #ifndef NO_AD_INITIALIZE
  B0_B_SNE.initialize();
  #endif
  log_r_S_GB.allocate(-4.6,-0.11,"log_r_S_GB");
  r_S_GB.allocate("r_S_GB");
  #ifndef NO_AD_INITIALIZE
  r_S_GB.initialize();
  #endif
  k_S_GB.allocate(-1,"k_S_GB");
  log_B0_S_GB.allocate("log_B0_S_GB");
  B0_S_GB.allocate("B0_S_GB");
  #ifndef NO_AD_INITIALIZE
  B0_S_GB.initialize();
  #endif
  log_r_S_GOM.allocate(-4.6,-0.11,"log_r_S_GOM");
  r_S_GOM.allocate("r_S_GOM");
  #ifndef NO_AD_INITIALIZE
  r_S_GOM.initialize();
  #endif
  k_S_GOM.allocate(-1,"k_S_GOM");
  log_B0_S_GOM.allocate("log_B0_S_GOM");
  B0_S_GOM.allocate("B0_S_GOM");
  #ifndef NO_AD_INITIALIZE
  B0_S_GOM.initialize();
  #endif
  log_r_S_SNE.allocate(-4.6,-0.11,"log_r_S_SNE");
  r_S_SNE.allocate("r_S_SNE");
  #ifndef NO_AD_INITIALIZE
  r_S_SNE.initialize();
  #endif
  k_S_SNE.allocate(-1,"k_S_SNE");
  log_B0_S_SNE.allocate("log_B0_S_SNE");
  B0_S_SNE.allocate("B0_S_SNE");
  #ifndef NO_AD_INITIALIZE
  B0_S_SNE.initialize();
  #endif
  log_n_PB_GB.allocate(-16.0,-2.3,2,"log_n_PB_GB");
  n_PB_GB.allocate("n_PB_GB");
  #ifndef NO_AD_INITIALIZE
  n_PB_GB.initialize();
  #endif
  log_n_BP_SNE.allocate(-16.0,-2.3,2,"log_n_BP_SNE");
  n_BP_SNE.allocate("n_BP_SNE");
  #ifndef NO_AD_INITIALIZE
  n_BP_SNE.initialize();
  #endif
  log_c_fb_GB.allocate(-16.0,-2.3,3,"log_c_fb_GB");
  c_fb_GB.allocate("c_fb_GB");
  #ifndef NO_AD_INITIALIZE
  c_fb_GB.initialize();
  #endif
  log_d_fb_GB.allocate(-16.0,-2.3,3,"log_d_fb_GB");
  d_fb_GB.allocate("d_fb_GB");
  #ifndef NO_AD_INITIALIZE
  d_fb_GB.initialize();
  #endif
  log_alpha_fb_GB.allocate(-16.0,-2.3,3,"log_alpha_fb_GB");
  alpha_fb_GB.allocate("alpha_fb_GB");
  #ifndef NO_AD_INITIALIZE
  alpha_fb_GB.initialize();
  #endif
  log_alpha_fp_GB.allocate(-16.0,-2.3,3,"log_alpha_fp_GB");
  alpha_fp_GB.allocate("alpha_fp_GB");
  #ifndef NO_AD_INITIALIZE
  alpha_fp_GB.initialize();
  #endif
  log_c_fb_GOM.allocate(-16.0,-2.3,3,"log_c_fb_GOM");
  c_fb_GOM.allocate("c_fb_GOM");
  #ifndef NO_AD_INITIALIZE
  c_fb_GOM.initialize();
  #endif
  log_alpha_fb_GOM.allocate(-16.0,-2.3,3,"log_alpha_fb_GOM");
  alpha_fb_GOM.allocate("alpha_fb_GOM");
  #ifndef NO_AD_INITIALIZE
  alpha_fb_GOM.initialize();
  #endif
  log_alpha_fp_GOM.allocate(-16.0,-2.3,3,"log_alpha_fp_GOM");
  alpha_fp_GOM.allocate("alpha_fp_GOM");
  #ifndef NO_AD_INITIALIZE
  alpha_fp_GOM.initialize();
  #endif
  pred_bio_P_tot.allocate(1,nyrs,"pred_bio_P_tot");
  #ifndef NO_AD_INITIALIZE
    pred_bio_P_tot.initialize();
  #endif
  pred_bio_F_tot.allocate(1,nyrs,"pred_bio_F_tot");
  #ifndef NO_AD_INITIALIZE
    pred_bio_F_tot.initialize();
  #endif
  prop_GB_P.allocate(1,nyrs,"prop_GB_P");
  #ifndef NO_AD_INITIALIZE
    prop_GB_P.initialize();
  #endif
  prop_GOM_P.allocate(1,nyrs,"prop_GOM_P");
  #ifndef NO_AD_INITIALIZE
    prop_GOM_P.initialize();
  #endif
  prop_SNE_P.allocate(1,nyrs,"prop_SNE_P");
  #ifndef NO_AD_INITIALIZE
    prop_SNE_P.initialize();
  #endif
  pred_bio_P_GB.allocate(1,nyrs,"pred_bio_P_GB");
  #ifndef NO_AD_INITIALIZE
    pred_bio_P_GB.initialize();
  #endif
  pred_bio_P_GOM.allocate(1,nyrs,"pred_bio_P_GOM");
  #ifndef NO_AD_INITIALIZE
    pred_bio_P_GOM.initialize();
  #endif
  pred_bio_P_SNE.allocate(1,nyrs,"pred_bio_P_SNE");
  #ifndef NO_AD_INITIALIZE
    pred_bio_P_SNE.initialize();
  #endif
  prop_GB_F.allocate(1,nyrs,"prop_GB_F");
  #ifndef NO_AD_INITIALIZE
    prop_GB_F.initialize();
  #endif
  prop_GOM_F.allocate(1,nyrs,"prop_GOM_F");
  #ifndef NO_AD_INITIALIZE
    prop_GOM_F.initialize();
  #endif
  prop_SNE_F.allocate(1,nyrs,"prop_SNE_F");
  #ifndef NO_AD_INITIALIZE
    prop_SNE_F.initialize();
  #endif
  pred_bio_F_GB.allocate(1,nyrs,"pred_bio_F_GB");
  #ifndef NO_AD_INITIALIZE
    pred_bio_F_GB.initialize();
  #endif
  pred_bio_F_GOM.allocate(1,nyrs,"pred_bio_F_GOM");
  #ifndef NO_AD_INITIALIZE
    pred_bio_F_GOM.initialize();
  #endif
  pred_bio_F_SNE.allocate(1,nyrs,"pred_bio_F_SNE");
  #ifndef NO_AD_INITIALIZE
    pred_bio_F_SNE.initialize();
  #endif
  pred_bio_B_GB.allocate(1,nyrs,"pred_bio_B_GB");
  #ifndef NO_AD_INITIALIZE
    pred_bio_B_GB.initialize();
  #endif
  pred_bio_B_GOM.allocate(1,nyrs,"pred_bio_B_GOM");
  #ifndef NO_AD_INITIALIZE
    pred_bio_B_GOM.initialize();
  #endif
  pred_bio_B_SNE.allocate(1,nyrs,"pred_bio_B_SNE");
  #ifndef NO_AD_INITIALIZE
    pred_bio_B_SNE.initialize();
  #endif
  pred_bio_B_tot.allocate(1,nyrs,"pred_bio_B_tot");
  #ifndef NO_AD_INITIALIZE
    pred_bio_B_tot.initialize();
  #endif
  pred_bio_S_SNE.allocate(1,nyrs,"pred_bio_S_SNE");
  #ifndef NO_AD_INITIALIZE
    pred_bio_S_SNE.initialize();
  #endif
  pred_bio_S_GOM.allocate(1,nyrs,"pred_bio_S_GOM");
  #ifndef NO_AD_INITIALIZE
    pred_bio_S_GOM.initialize();
  #endif
  pred_bio_S_GB.allocate(1,nyrs,"pred_bio_S_GB");
  #ifndef NO_AD_INITIALIZE
    pred_bio_S_GB.initialize();
  #endif
  fpenP_tot.allocate("fpenP_tot");
  #ifndef NO_AD_INITIALIZE
  fpenP_tot.initialize();
  #endif
  fpenF_tot.allocate("fpenF_tot");
  #ifndef NO_AD_INITIALIZE
  fpenF_tot.initialize();
  #endif
  fpenB_GB.allocate("fpenB_GB");
  #ifndef NO_AD_INITIALIZE
  fpenB_GB.initialize();
  #endif
  fpenB_GOM.allocate("fpenB_GOM");
  #ifndef NO_AD_INITIALIZE
  fpenB_GOM.initialize();
  #endif
  fpenB_SNE.allocate("fpenB_SNE");
  #ifndef NO_AD_INITIALIZE
  fpenB_SNE.initialize();
  #endif
  fpenS_SNE.allocate("fpenS_SNE");
  #ifndef NO_AD_INITIALIZE
  fpenS_SNE.initialize();
  #endif
  fpenS_GOM.allocate("fpenS_GOM");
  #ifndef NO_AD_INITIALIZE
  fpenS_GOM.initialize();
  #endif
  fpenS_GB.allocate("fpenS_GB");
  #ifndef NO_AD_INITIALIZE
  fpenS_GB.initialize();
  #endif
  p.allocate("p");
  #ifndef NO_AD_INITIALIZE
  p.initialize();
  #endif
  y.allocate("y");
  #ifndef NO_AD_INITIALIZE
  y.initialize();
  #endif
  AIC.allocate("AIC");
  #ifndef NO_AD_INITIALIZE
  AIC.initialize();
  #endif
p = 30; //number of parameters
y = nyrs*8; //number of guilds: 4
  sd_r_P_tot.allocate("sd_r_P_tot");
  sd_k_P_tot.allocate("sd_k_P_tot");
  sd_B0_P_tot.allocate("sd_B0_P_tot");
  sd_r_F_tot.allocate("sd_r_F_tot");
  sd_k_F_tot.allocate("sd_k_F_tot");
  sd_B0_F_tot.allocate("sd_B0_F_tot");
  sd_r_B_GB.allocate("sd_r_B_GB");
  sd_k_B_GB.allocate("sd_k_B_GB");
  sd_B0_B_GB.allocate("sd_B0_B_GB");
  sd_r_B_GOM.allocate("sd_r_B_GOM");
  sd_k_B_GOM.allocate("sd_k_B_GOM");
  sd_B0_B_GOM.allocate("sd_B0_B_GOM");
  sd_r_B_SNE.allocate("sd_r_B_SNE");
  sd_k_B_SNE.allocate("sd_k_B_SNE");
  sd_B0_B_SNE.allocate("sd_B0_B_SNE");
  sd_r_S_GB.allocate("sd_r_S_GB");
  sd_B0_S_GB.allocate("sd_B0_S_GB");
  sd_r_S_GOM.allocate("sd_r_S_GOM");
  sd_B0_S_GOM.allocate("sd_B0_S_GOM");
  sd_r_S_SNE.allocate("sd_r_S_SNE");
  sd_B0_S_SNE.allocate("sd_B0_S_SNE");
  sd_n_PB_GB.allocate("sd_n_PB_GB");
  sd_n_BP_SNE.allocate("sd_n_BP_SNE");
  sd_c_fb_GB.allocate("sd_c_fb_GB");
  sd_d_fb_GB.allocate("sd_d_fb_GB");
  sd_alpha_fb_GB.allocate("sd_alpha_fb_GB");
  sd_alpha_fp_GB.allocate("sd_alpha_fp_GB");
  sd_c_fb_GOM.allocate("sd_c_fb_GOM");
  sd_alpha_fb_GOM.allocate("sd_alpha_fb_GOM");
  sd_alpha_fp_GOM.allocate("sd_alpha_fp_GOM");
  f.allocate("f");
}

void model_parameters::initializationfunction(void)
{
  log_r_P_tot.set_initial_value(-1.33);
  log_k_P_tot.set_initial_value(8.44);
  log_B0_P_tot.set_initial_value(6.88);
  log_r_F_tot.set_initial_value(-1.98);
  log_k_F_tot.set_initial_value(8.29);
  log_B0_F_tot.set_initial_value(7.6);
  log_r_B_GB.set_initial_value(-1.34);
  log_k_B_GB.set_initial_value(6.05);
  log_B0_B_GB.set_initial_value(5.3);
  log_r_B_GOM.set_initial_value(-0.95);
  log_k_B_GOM.set_initial_value(4.39);
  log_B0_B_GOM.set_initial_value(3.95);
  log_r_B_SNE.set_initial_value(-0.62);
  log_k_B_SNE.set_initial_value(5.4);
  log_B0_B_SNE.set_initial_value(4.84);
  log_r_S_GB.set_initial_value(-0.49);
  log_B0_S_GB.set_initial_value(4.87);
  k_S_GB.set_initial_value(300);
  log_r_S_GOM.set_initial_value(-0.246);
  log_B0_S_GOM.set_initial_value(3.42);
  k_S_GOM.set_initial_value(80);
  log_r_S_SNE.set_initial_value(-0.22);
  log_B0_S_SNE.set_initial_value(4.1);
  k_S_SNE.set_initial_value(100);
  log_n_PB_GB.set_initial_value(-6.2);
  log_n_BP_SNE.set_initial_value(-7.9);
  log_c_fb_GB.set_initial_value(-4.7);
  log_d_fb_GB.set_initial_value(-4.8);
  log_alpha_fb_GB.set_initial_value(-4.4);
  log_alpha_fp_GB.set_initial_value(-2.4);
  log_c_fb_GOM.set_initial_value(-4.8);
  log_alpha_fb_GOM.set_initial_value(-3.9);
  log_alpha_fp_GOM.set_initial_value(-3.1);
}

void model_parameters::preliminary_calculations(void)
{
  prop_GB_P  = elem_div(obs_bio_P_GB,obs_bio_P_tot);
  prop_GOM_P = elem_div(obs_bio_P_GOM,obs_bio_P_tot);
  prop_SNE_P = elem_div(obs_bio_P_SNE,obs_bio_P_tot);
  prop_GB_F  = elem_div(obs_bio_F_GB,obs_bio_F_tot);
  prop_GOM_F = elem_div(obs_bio_F_GOM,obs_bio_F_tot);
  prop_SNE_F = elem_div(obs_bio_F_SNE,obs_bio_F_tot);
}

void model_parameters::userfunction(void)
{
  r_P_tot = mfexp(log_r_P_tot);
  k_P_tot = mfexp(log_k_P_tot);
  B0_P_tot = mfexp(log_B0_P_tot);
  r_F_tot = mfexp(log_r_F_tot);
  k_F_tot = mfexp(log_k_F_tot);
  B0_F_tot = mfexp(log_B0_F_tot);
  r_B_GB = mfexp(log_r_B_GB);
  k_B_GB = mfexp(log_k_B_GB);
  B0_B_GB = mfexp(log_B0_B_GB);
  r_B_GOM = mfexp(log_r_B_GOM);
  k_B_GOM = mfexp(log_k_B_GOM);
  B0_B_GOM = mfexp(log_B0_B_GOM);
  r_B_SNE = mfexp(log_r_B_SNE);
  k_B_SNE = mfexp(log_k_B_SNE);
  B0_B_SNE = mfexp(log_B0_B_SNE);
 
  r_S_GB = mfexp(log_r_S_GB);
  B0_S_GB = mfexp(log_B0_S_GB);
  r_S_GOM = mfexp(log_r_S_GOM);
  B0_S_GOM = mfexp(log_B0_S_GOM);
  r_S_SNE = mfexp(log_r_S_SNE);
  B0_S_SNE = mfexp(log_B0_S_SNE);
  n_PB_GB = mfexp(log_n_PB_GB);
  n_BP_SNE = mfexp(log_n_BP_SNE);
  // Type 3 functional response for interaction between B and F in Georges Bank
  c_fb_GB = mfexp(log_c_fb_GB);
  d_fb_GB = mfexp(log_d_fb_GB);
  alpha_fb_GB = mfexp(log_alpha_fb_GB);
  alpha_fp_GB = mfexp(log_alpha_fp_GB); 
  // Type 3 functional response for interaction between B and F in Gulf of Maine
  c_fb_GOM = mfexp(log_c_fb_GOM);
  //d_fb_GOM = mfexp(log_d_fb_GOM);
  alpha_fb_GOM = mfexp(log_alpha_fb_GOM);
  alpha_fp_GOM = mfexp(log_alpha_fp_GOM); 
  //cout statements useful for viewing parameters
  cout << "r_P_tot  " << '\t' << r_P_tot << endl;
  cout << "k_P_tot  " << '\t' << k_P_tot << endl;
  cout << "B0_P_tot" << '\t' << B0_P_tot << endl;
  cout << "r_F_tot " << '\t' << r_F_tot << endl;
  cout << "k_F_tot " << '\t' << k_F_tot << endl;
  cout << "B0_F_tot" << '\t' << B0_F_tot << endl;
  cout << "r_B_GB  " << '\t' << r_B_GB << endl;
  cout << "k_B_GB  " << '\t' << k_B_GB << endl;
  cout << "B0_B_GB  " << '\t' << B0_B_GB << endl;
 
  cout << "r_B_GOM  " << '\t' << r_B_GOM << endl;
  cout << "k_B_GOM  " << '\t' << k_B_GOM << endl;
  cout << "B0_B_GOM " << '\t' << B0_B_GOM << endl;
 
  cout << "r_B_SNE  " << '\t' << r_B_SNE << endl;
  cout << "k_B_SNE  " << '\t' << k_B_SNE << endl;
  cout << "B0_B_SNE " << '\t' << B0_B_SNE << endl;
  cout << "r_S_GB    " << '\t' << r_S_GB << endl;
  cout << "k_S_GB    " << '\t' << k_S_GB << endl;
  cout << "B0_S_GB   " << '\t' << B0_S_GB << endl;
  cout << "r_S_GOM   " << '\t' << r_S_GOM << endl;
  cout << "k_S_GOM   " << '\t' << k_S_GOM << endl;
  cout << "B0_S_GOM  " << '\t' << B0_S_GOM << endl;
  cout << "r_S_SNE   " << '\t' << r_S_SNE << endl;
  cout << "k_S_SNE   " << '\t' << k_S_SNE << endl;
  cout << "B0_S_SNE  " << '\t' << B0_S_SNE << endl;
  cout << "n_PB_GB   " << '\t' << n_PB_GB << endl;
  cout << "n_BP_SNE  " << '\t' << n_BP_SNE << endl;
  // Type 3 functional response for interaction between B and F in Georges Bank
  cout << "c_fb_GB    " << '\t' << c_fb_GB << endl;
  cout << "d_fb_GB    " << '\t' << d_fb_GB << endl;
  cout << "alpha_fb_GB" << '\t' << alpha_fb_GB << endl;
  cout << "alpha_fp_GB" << '\t' << alpha_fp_GB << endl;
  // Type 3 functional response for interaction between B and F in Gulf of Maine
  cout << "c_fb_GOM    " << '\t' << c_fb_GOM << endl;
  //cout << "d_fb_GOM    " << '\t' << d_fb_GOM << endl;
  cout << "alpha_fb_GOM" << '\t' << alpha_fb_GOM << endl;
  cout << "alpha_fp_GOM" << '\t' << alpha_fp_GOM << endl;
  //reset fpens to 0.0
  fpenP_tot = 0.0;
  fpenF_tot = 0.0;
 
  fpenB_GB = 0.0;
  fpenB_GOM = 0.0;
  fpenB_SNE = 0.0;
  fpenS_SNE = 0.0;
  fpenS_GOM = 0.0;
  fpenS_GB = 0.0;
  //define sdreport numbers
  sd_r_P_tot= r_P_tot;
  sd_k_P_tot = k_P_tot;
  sd_B0_P_tot = B0_P_tot;
  sd_r_F_tot  = r_F_tot;
  sd_k_F_tot  = k_F_tot;
  sd_B0_F_tot = B0_F_tot;
  sd_r_B_GB = r_B_GB;
  sd_k_B_GB = k_B_GB;
  sd_B0_B_GB = B0_B_GB;
  sd_r_B_GOM = r_B_GOM;
  sd_k_B_GOM = k_B_GOM;
  sd_B0_B_GOM = B0_B_GOM;
  sd_r_B_SNE = r_B_SNE;
  sd_k_B_SNE = k_B_SNE;
  sd_B0_B_SNE = B0_B_SNE;
  sd_r_S_GB = r_S_GB;
  sd_B0_S_GB = B0_S_GB;
  sd_r_S_GOM = r_S_GOM;
  sd_B0_S_GOM = B0_S_GOM;
  sd_r_S_SNE = r_S_SNE;
  sd_B0_S_SNE = B0_S_SNE;
  sd_n_PB_GB = n_PB_GB;
  sd_n_BP_SNE = n_BP_SNE;
  // Type 3 functional response for interaction between B and F in Georges Bank
  sd_c_fb_GB = c_fb_GB;
  sd_d_fb_GB = d_fb_GB;
  sd_alpha_fb_GB = alpha_fb_GB;
  sd_alpha_fp_GB = alpha_fp_GB;
  // Type 3 functional response for interaction between B and F in Gilf of Maine
  sd_c_fb_GOM = c_fb_GOM;
  //sd_d_fb_GOM = d_fb_GOM;
  sd_alpha_fb_GOM = alpha_fb_GOM;
  sd_alpha_fp_GOM = alpha_fp_GOM;
  //initial biomass
  pred_bio_P_tot(1) = B0_P_tot;
  pred_bio_F_tot(1) = B0_F_tot;
  pred_bio_B_GB(1) = B0_B_GB;
  pred_bio_B_GOM(1) = B0_B_GOM;
  pred_bio_B_SNE(1) = B0_B_SNE;
  pred_bio_S_SNE(1) = B0_S_SNE;
  pred_bio_S_GOM(1) = B0_S_GOM;
  pred_bio_S_GB(1) = B0_S_GB;
  pred_bio_P_GB(1)  = prop_GB_P(1)*pred_bio_P_tot(1);
  pred_bio_P_GOM(1) = prop_GOM_P(1)*pred_bio_P_tot(1);
  pred_bio_P_SNE(1) = prop_SNE_P(1)*pred_bio_P_tot(1);
  pred_bio_F_GB(1)  = prop_GB_F(1)*pred_bio_F_tot(1);
  pred_bio_F_GOM(1) = prop_GOM_F(1)*pred_bio_F_tot(1);
  pred_bio_F_SNE(1) = prop_SNE_F(1)*pred_bio_F_tot(1);
  pred_bio_B_tot(1)=pred_bio_B_GB(1)+pred_bio_B_GOM(1)+pred_bio_B_SNE(1);
  //loop through all years to calculate predicted biomass
  for (i = 1; i<= nyrs-1; i++)
  {
  pred_bio_P_tot(i+1)=posfun(pred_bio_P_tot(i)+r_P_tot*pred_bio_P_tot(i)*(1-pred_bio_P_tot(i)/k_P_tot)-obs_cat_P_tot(i)
  -n_PB_GB*(prop_GB_P(i)*pred_bio_P_tot(i))*pred_bio_B_GB(i)
  ,0.01,fpenP_tot);
  pred_bio_F_tot(i+1)=posfun(pred_bio_F_tot(i)+r_F_tot*pred_bio_F_tot(i)*(1-pred_bio_F_tot(i)/k_F_tot)-obs_cat_F_tot(i)
  + (d_fb_GB*(prop_GB_F(i)*pred_bio_F_tot(i))*(pred_bio_B_GB(i)*pred_bio_B_GB(i)))/
  (1+alpha_fb_GB*(pred_bio_B_GB(i)*pred_bio_B_GB(i))+alpha_fp_GB*((prop_GB_P(i)*pred_bio_P_tot(i))*(prop_GB_P(i)*pred_bio_P_tot(i))))
  //+ (d_fb_GOM*(prop_GOM_F(i)*pred_bio_F_tot(i))*(pred_bio_B_GOM(i)*pred_bio_B_GOM(i)))/
  //(1+alpha_fb_GOM*(pred_bio_B_GOM(i)*pred_bio_B_GOM(i)) + alpha_fp_GOM*( (prop_GOM_P(i)*pred_bio_P_tot(i))*(prop_GOM_P(i)*pred_bio_P_tot(i))))
  ,0.01,fpenF_tot); 
  pred_bio_B_GB(i+1)=posfun(pred_bio_B_GB(i)+r_B_GB*pred_bio_B_GB(i)*(1-pred_bio_B_GB(i)/k_B_GB)-obs_cat_B_GB(i)
  - (c_fb_GB*(prop_GB_F(i)*pred_bio_F_tot(i))*(pred_bio_B_GB(i)*pred_bio_B_GB(i)))/
  (1+alpha_fb_GB*(pred_bio_B_GB(i)*pred_bio_B_GB(i))+alpha_fp_GB*((prop_GB_P(i)*pred_bio_P_tot(i))*(prop_GB_P(i)*pred_bio_P_tot(i))))
  ,0.01,fpenB_GB);
  pred_bio_B_GOM(i+1)=posfun(pred_bio_B_GOM(i)+r_B_GOM*pred_bio_B_GOM(i)*(1-pred_bio_B_GOM(i)/k_B_GOM)-obs_cat_B_GOM(i)
  - (c_fb_GOM*(prop_GOM_F(i)*pred_bio_F_tot(i))*(pred_bio_B_GOM(i)*pred_bio_B_GOM(i)))/
  (1+alpha_fb_GOM*(pred_bio_B_GOM(i)*pred_bio_B_GOM(i)) + alpha_fp_GOM*( (prop_GOM_P(i)*pred_bio_P_tot(i))*(prop_GOM_P(i)*pred_bio_P_tot(i))))
  ,0.01,fpenB_GOM);
  pred_bio_B_SNE(i+1)=posfun(pred_bio_B_SNE(i)+r_B_SNE*pred_bio_B_SNE(i)*(1-pred_bio_B_SNE(i)/k_B_SNE)-obs_cat_B_SNE(i)
  -n_BP_SNE*pred_bio_B_SNE(i)*(prop_SNE_P(i)*pred_bio_P_tot(i))
  ,0.01,fpenB_SNE);
 
  pred_bio_S_GOM(i+1)=posfun(pred_bio_S_GOM(i)+r_S_GOM*pred_bio_S_GOM(i)*(1-pred_bio_S_GOM(i)/k_S_GOM)-obs_cat_S_GOM(i)
  ,0.01,fpenS_GOM);
  pred_bio_S_SNE(i+1)=posfun(pred_bio_S_SNE(i)+r_S_SNE*pred_bio_S_SNE(i)*(1-pred_bio_S_SNE(i)/k_S_SNE)-obs_cat_S_SNE(i)
  ,0.01,fpenS_SNE);
  pred_bio_S_GB(i+1)=posfun(pred_bio_S_GB(i)+r_S_GB*pred_bio_S_GB(i)*(1-pred_bio_S_GB(i)/k_S_GB)-obs_cat_S_GB(i)
  ,0.01,fpenS_GB);
  }
  //tell us about fpens
  if(fpenP_tot>0) cout << "FPEN P_tot="<< endl << fpenP_tot << endl;
  if(fpenF_tot>0) cout << "FPEN F_tot="<< endl << fpenF_tot << endl; 
  if(fpenB_GB>0)  cout << "FPEN B_GB= "<< endl << fpenB_GB  << endl;
  if(fpenB_GOM>0) cout << "FPEN B_GOM="<< endl << fpenB_GOM << endl;
  if(fpenB_SNE>0) cout << "FPEN B_SNE="<< endl << fpenB_SNE << endl;
  if(fpenS_GOM>0) cout << "FPEN S_GOM="<< endl << fpenS_GOM << endl;
  if(fpenS_SNE>0) cout << "FPEN S_SNE="<< endl << fpenS_SNE << endl;
  if(fpenS_GB>0)  cout << "FPEN S_GB= "<< endl << fpenS_GB  << endl;
  //the objective function for total biomass of migrating Planktivores and Piscivores
  dvar_vector resid_P_tot = (log(pred_bio_P_tot(1,nyrs)+1.e-3) - log(obs_bio_P_tot(1,nyrs)+1.e-3));
  dvariable ssq_P_tot = norm2(resid_P_tot) + square(log(k_pseudo_P_tot) - log(k_P_tot));
  dvar_vector resid_F_tot = (log(pred_bio_F_tot(1,nyrs)+1.e-3) - log(obs_bio_F_tot(1,nyrs)+1.e-3));
  dvariable ssq_F_tot = norm2(resid_F_tot)  + square(log(k_pseudo_F_tot) - log(k_F_tot));
  // additional objective function of Benthivores (GB, GoM, SNE)
  dvar_vector resid_B_GB = (log(pred_bio_B_GB(1,nyrs)+1.e-3) - log(obs_bio_B_GB(1,nyrs)+1.e-3));
  dvariable ssq_B_GB = norm2(resid_B_GB) + square(log(k_pseudo_B_GB) - log(k_B_GB));
  dvar_vector resid_B_GOM = (log(pred_bio_B_GOM(1,nyrs)+1.e-3) - log(obs_bio_B_GOM(1,nyrs)+1.e-3)); 
  dvariable ssq_B_GOM = norm2(resid_B_GOM) + square(log(k_pseudo_B_GOM) - log(k_B_GOM));
  dvar_vector resid_B_SNE = (log(pred_bio_B_SNE(1,nyrs)+1.e-3) - log(obs_bio_B_SNE(1,nyrs)+1.e-3));
  dvariable ssq_B_SNE = norm2(resid_B_SNE) +  square(log(k_pseudo_B_SNE) - log(k_B_SNE));
  dvar_vector resid_S_GOM = (log(pred_bio_S_GOM(1,nyrs)+1.e-3) - log(obs_bio_S_GOM(1,nyrs)+1.e-3));
  dvariable ssq_S_GOM = norm2(resid_S_GOM);
  dvar_vector resid_S_SNE = (log(pred_bio_S_SNE(1,nyrs)+1.e-3) - log(obs_bio_S_SNE(1,nyrs)+1.e-3));
  dvariable ssq_S_SNE = norm2(resid_S_SNE);
  dvar_vector resid_S_GB = (log(pred_bio_S_GB(1,nyrs)+1.e-3) - log(obs_bio_S_GB(1,nyrs)+1.e-3));
  dvariable ssq_S_GB = norm2(resid_S_GB) ;
  f = ssq_P_tot + ssq_F_tot + ssq_B_GB + ssq_B_GOM + ssq_B_SNE + ssq_S_GOM +ssq_S_SNE + ssq_S_GB;
  cout << "obj func value - SSR" << '\t' << f << endl;
  cout << "ssqP_tot  " << "\t" << ssq_P_tot << endl;
  cout << "ssqF_tot  " << "\t" << ssq_F_tot << endl;
  cout << "ssqB_GB   " << "\t" << ssq_B_GB << endl;
  cout << "ssqB_GOM  " << "\t" << ssq_B_GOM << endl;
  cout << "ssqB_SNE  " << "\t" << ssq_B_SNE << endl;
  cout << "ssqS_GB   " << "\t" << ssq_S_GB << endl;
  cout << "ssqS_GOM  " << "\t" << ssq_S_GOM << endl;
  cout << "ssqS_SNE  " << "\t" << ssq_S_SNE << endl;
  cout << endl;
  //calculate Nll and AIC
  dvariable nll = 0.5*y*log(f);
  dvariable AIC = 2*nll + 2*p*(y/(y-p-1));
  cout << "Negative Ln Likelihood (-Ln(L))" << "\t" << nll << endl;
  cout << "AIC" << "\t" << AIC << endl << endl;
}

void model_parameters::set_runtime(void)
{
  dvector temp1("{40000;}");
  maximum_function_evaluations.allocate(temp1.indexmin(),temp1.indexmax());
  maximum_function_evaluations=temp1;
}

void model_parameters::report()
{
 adstring ad_tmp=initial_params::get_reportfile_name();
  ofstream report((char*)(adprogram_name + ad_tmp));
  if (!report)
  {
    cerr << "error trying to open report file"  << adprogram_name << ".rep";
    return;
  }
  report<<"observed biomass_P_tot" << obs_bio_P_tot << endl;
  report<<"predicted biomass_P_tot" << pred_bio_P_tot << endl;
  report<<"obs_catch_P_tot" << obs_cat_P_tot << endl;
  report<<""<<endl;
  report<<"observed biomass_F_tot: " << obs_bio_F_tot << endl;
  report<<"predicted biomass_F_tot: " << pred_bio_F_tot << endl;
  report<<"obs_catch_F_tot: " << obs_cat_F_tot << endl;
  report<<""<<endl;
  report<<"observed biomass_B_GB"<<obs_bio_B_GB<<endl;
  report<<"predicted biomass_B_GB"<<pred_bio_B_GB<<endl;
  report<<"obs_catch_B_GB"<<obs_cat_B_GB<<endl;
  report<<""<<endl;
 
  report<<"observed biomass_B_GOM"<<obs_bio_B_GOM<<endl;
  report<<"predicted biomass_B_GOM"<<pred_bio_B_GOM<<endl;
  report<<"obs_catch_B_GOM"<<obs_cat_B_GOM<<endl;
  report<<""<<endl;
  report<<"observed biomass_B_SNE"<<obs_bio_B_SNE<<endl;
  report<<"predicted biomass_B_SNE"<<pred_bio_B_SNE<<endl;
  report<<"obs_catch_B_SNE"<<obs_cat_B_SNE<<endl;
  report<<""<<endl;
  report<<"observed biomass_S_GB"<<obs_bio_S_GB<<endl;
  report<<"predicted biomass_S_GB"<<pred_bio_S_GB<<endl;
  report<<"obs_catch_S_GB"<<obs_cat_S_GB<<endl;
  report<<""<<endl;
  report<<"observed biomass_S_GOM"<<obs_bio_S_GOM<<endl;
  report<<"predicted biomass_S_GOM"<<pred_bio_S_GOM<<endl;
  report<<"obs_catch_S_GOM"<<obs_cat_S_GOM<<endl;
  report<<""<<endl;
  report<<"observed biomass_S_SNE"<<obs_bio_S_SNE<<endl;
  report<<"predicted biomass_S_SNE"<<pred_bio_S_SNE<<endl;
  report<<"obs_catch_S_SNE"<<obs_cat_S_SNE<<endl;
  report<<""<<endl;
  report<<""<<endl;
  report<<" prop_GB_P=   "<< prop_GB_P << endl;
  report<<""<<endl;
  report<<" prop_GOM_P=  "<< prop_GOM_P << endl;
  report<<""<<endl;
  report<<" prop_SNE_P=  "<< prop_SNE_P << endl;
  report<<""<<endl;
  report<<" prop_GB_F=   "<< prop_GB_F << endl;
  report<<""<<endl;
  report<<" prop_GOM_F=  "<< prop_GOM_F << endl;
  report<<""<<endl;
  report<<" prop_SNE_F=  "<< prop_SNE_F << endl;
  report<<""<<endl;
  report<<"observed biomass_P_GB: " << obs_bio_P_GB << endl;
  report<<"predicted biomass_P_GB="<<"prop_GB_P*pred_bio_P_tot"<<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_GB_P(i)*pred_bio_P_tot(i) << endl;
  }
  report<<"obs_catch_P_GB: " << obs_cat_P_GB << endl;
  report<<""<<endl;
  report<<"observed biomass_P_GOM: " << obs_bio_P_GOM << endl;
  report<<"predicted biomass_P_GOM="<<"prop_GOM_P*pred_bio_P_tot" <<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_GOM_P(i)*pred_bio_P_tot(i) << endl;
  }
 
  report<<"obs_catch_P_GOM: " << obs_cat_P_GOM << endl;
  report<<""<<endl;
  report<<"observed biomass_P_SNE: " << obs_bio_P_SNE << endl;
  report<<"predicted biomass_P_SNE="<< "prop_SNE_P*pred_bio_P_tot" <<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_SNE_P(i)*pred_bio_P_tot(i) << endl;
  }
 
  report<<"obs_catch_P_SNE: " << obs_cat_P_SNE << endl;
  report<<""<<endl;
  report<<"observed biomass_F_GB: " << obs_bio_F_GB << endl;
  report<<"predicted biomass_F_GB="<< "prop_GB_F*pred_bio_F_tot" <<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_GB_F(i)*pred_bio_F_tot(i) << endl;
  }
 
  report<<"obs_catch_F_GB: " << obs_cat_F_GB << endl;
  report<<""<<endl;
  report<<"observed biomass_F_GOM: " << obs_bio_F_GOM << endl;
  report<<"predicted biomass_F_GOM="<< "prop_GOM_F*pred_bio_F_tot" <<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_GOM_F(i)*pred_bio_F_tot(i) << endl;
  }
  report<<"obs_catch_F_GOM: " << obs_cat_F_GOM << endl;
  report<<""<<endl;
  report<<"observed biomass_F_SNE: " << obs_bio_F_SNE << endl;
  report<<"predicted biomass_F_SNE="<< "prop_SNE_F*pred_bio_F_tot" <<endl;
  for (i = 1; i<= nyrs; i++)
  {
      report << prop_SNE_F(i)*pred_bio_F_tot(i) << endl;
  }
  report<<"obs_catch_F_SNE: " << obs_cat_F_SNE << endl;
  report<<""<<endl;
 
}

model_data::~model_data()
{}

model_parameters::~model_parameters()
{}

void model_parameters::final_calcs(void){}

#ifdef _BORLANDC_
  extern unsigned _stklen=10000U;
#endif


#ifdef __ZTC__
  extern unsigned int _stack=10000U;
#endif

  long int arrmblsize=0;

int main(int argc,char * argv[])
{
    gradient_structure::set_NO_DERIVATIVES();
    gradient_structure::set_YES_SAVE_VARIABLES_VALUES();
  #if defined(__GNUDOS__) || defined(DOS386) || defined(__DPMI32__)  || \
     defined(__MSVC32__)
      if (!arrmblsize) arrmblsize=150000;
  #else
      if (!arrmblsize) arrmblsize=25000;
  #endif
    model_parameters mp(arrmblsize,argc,argv);
    mp.iprint=10;
    mp.preliminary_calculations();
    mp.computations(argc,argv);
    return 0;
}