SS_readcontrol_330.tpl

// SS_Label_file  #4. **SS_readcontrol.tpl**
// SS_Label_file  # * read *control_file* named in starter.ss
// SS_Label_file  #     * define and read needed parameters from model options selected
// SS_Label_file  #     * creates labels for those parameters
// SS_Label_file  #     * uses a function found in SS_global, <u>create_timevary()</u>, to create, index and label time-varying parameters; including autogeneration option
// SS_Label_file  #     * creates and labels derived quantities
// SS_Label_file  #     * creates covariance matrix
// SS_Label_file  #     * reads *wt_at_age.ss* if requested
// SS_Label_file  # * finish DATA_SECTION

 LOCAL_CALCS
  // clang-format on
  //********CONTROLS********************************
  //  SS_Label_Info_4.0 #Begin Reading from Control File
  // /*  SS_Label_Flow  begin reading from control file */
  ad_comm::change_datafile_name(ctlfilename);
  echoinput << endl
            << " Begin reading control file " << endl;
  cout << " reading from control file" << endl;
  ifstream Control_Stream(ctlfilename); // even if the global_datafile name is used, there still is a different logical device created
  
  //  SS_Label_Info_4.1 #Read and store comments at top of control file
  k = 0;
  N_CC = 0;
  while (k == 0)
  {
    Control_Stream >> readline; // reads the line from input stream
    if (length(readline) > 2)
    {
      checkchar = readline(1);
      k = strcmp(checkchar, "#");
      checkchar = readline(1, 2);
      j = strcmp(checkchar, "#C");
      if (j == 0) {
        N_CC++;
        Control_Comments += readline;
      }
    }
  }
  // clang-format off
 END_CALCS

//  when a parameter is defined and its label (hence usage) is created,
//  the value of its min, max, init, prior have not yet been read
//  so when it gets created, need to pushback a code to indicate what special conditions affect it
//  also may want to save indicator of whether the parameter is multiplier, logit, etc.
//  so push_back a code to the ivector Parm_minmax
//  and add a string to the adstring_array Parm_info
  ivector minmax_types(1,10)  //  set of canned min-max types

!!//  SS_Label_Info_4.2 #Read info for growth patterns, gender, settlement events, platoons
  init_int WTage_rd  // 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters
                     //  future option 2 will suppress reading and use of growth
!!echoinput<<WTage_rd<<" wtatage switch "<<endl;
!!if (WTage_rd > 0) timevary_MG_firstyr = styr;
  init_int N_GP  // number of growth patterns (morphs)
!!echoinput<<N_GP<<" N growth patterns "<<endl;
  init_int N_platoon  //  number of platoons  1, 3, 5 are best values to use
!!echoinput<<N_platoon<<"  N platoons (1, 3 or 5)"<<endl;

  number sd_ratio_rd;  // ratio of stddev within platoon to between morphs from file
  number platoon_sd_ratio;  // ratio of stddev within platoon to between morphs
  number sd_within_platoon;
  number sd_between_platoon;

  ivector ishadow(1,N_platoon);
  vector shadow(1,N_platoon);
  vector platoon_distr(1,N_platoon);

 LOCAL_CALCS
  // clang-format on
  if (WTage_rd > 0)
  {
    // Remove unnecessary or confusing reports (issue #383)
    pick_report_use(8) = "N";
    pick_report_use(27) = "N";
    pick_report_use(31) = "N";
    pick_report_use(38) = "N";
    pick_report_use(42) = "N";
    // Incompatible option, fatal condition 
    if (nobs_mnwt > 0)
    {
	  warnstream << "expected value for mean body-wt will be from the growth curve, not from empirical wtatage.ss";
      write_message (WARN, 1);
    }
  }
  
  if (N_platoon > 1)
  {
    *(ad_comm::global_datafile) >> sd_ratio_rd;
    *(ad_comm::global_datafile) >> platoon_distr;
    echoinput << sd_ratio_rd << "  sd_ratio_rd" << endl;
    echoinput << platoon_distr << "  platoon_distr" << endl;
  }
  else
  {
    sd_ratio_rd = 1.;
    platoon_distr(1) = 1.;
    echoinput << "  do not read sd_ratio or platoon_distr" << endl;
  }
  //  SS_Label_Info_4.2.1 #Assign distribution among growth platoons if needed
  if (platoon_distr(1) < 0.)
  {
    if (N_platoon == 1)
    {
      platoon_distr(1) = 1.;
    }
    else if (N_platoon == 3)
    {
      platoon_distr.fill("{0.15,0.70,0.15}");
    }
    else if (N_platoon == 5)
    {
      platoon_distr.fill("{0.031, 0.237, 0.464, 0.237, 0.031}");
    }
  }
  platoon_distr /= sum(platoon_distr);
  // calculate stdev values
  if (sd_ratio_rd < 0)
  {
    platoon_sd_ratio = -sd_ratio_rd;
    warnstream << "sd_ratio read is < 0, so expecting sd parameter after movement params.";
    write_message (NOTE, 1);
  }
  else
  {
    platoon_sd_ratio = sd_ratio_rd;
  }
  if (N_platoon > 1)
  {
    sd_between_platoon = sqrt(1. / (1. + platoon_sd_ratio * platoon_sd_ratio));
    sd_within_platoon = platoon_sd_ratio * sd_between_platoon;
  }
  else
  {
    sd_between_platoon = 0.000001;
    sd_within_platoon = 1;
  }
  
  if (N_platoon == 1)
  {
    ishadow(1) = 0;
    shadow(1) = 0.;
  }
  else if (N_platoon == 3)
  {
    ishadow.fill_seqadd(-1, 1);
    shadow.fill_seqadd(-1., 1.);
  }
  else if (N_platoon == 5)
  {
    ishadow.fill_seqadd(-2, 1);
    shadow.fill_seqadd(-2., 1.);
  }
  else
  {
    warnstream << "illegal N platoons: " << N_platoon << "; must be 1, 3 or 5 " ;
    write_message (FATAL, 1); // EXIT!
  }
  // clang-format off
          
 END_CALCS

!!//  SS_Label_Info_4.2.2  #Define distribution of recruitment(settlement) among growth patterns, areas, months

  int recr_dist_method  //  1=like 3.24 (not used); 2=main effects for GP, Settle timing, Area; 3=each Settle entity; 4=no parms (only if GPXsettleXarea=1)
  int recr_dist_area  //  1=global SRR; 2=area-specific SRR
  int N_settle_assignments  //  number of assigned settlements for GP, Settle_month, Area (>=0)
  int N_settle_assignments_rd  //  number read, needed to distinguish between ss3.24 and SS3.30 setup
  int N_settle_timings  //  number of recruitment settlement timings per spawning (>=1) - important for number of morphs calculation
                         //  will be calculated from the number of unique settle_months among the settle_assignments
  int settle  //  index to settle_assignments
  int settle_time  //  index to setting timings
  int Comp_Err_Parm_Start
  int recr_dist_inx
 LOCAL_CALCS
  // clang-format on
  * (ad_comm::global_datafile) >> recr_dist_method;
  echoinput << recr_dist_method << "  # Recruitment distribution method; where: 2=parms for main effects for GP, Area, Settle timing; 3=one parm for each Settle event" << endl;
  *(ad_comm::global_datafile) >> recr_dist_area;
  echoinput << recr_dist_area << "  # future option for recr_dist_area: 1 is hardwired to do global SRR; 2 in future will do area-specific SRR" << endl;
  recr_dist_area = 1; //hardwire for testing
  N_settle_assignments_rd = 0;
  N_settle_assignments = 1; // default
  
  switch (recr_dist_method)
  {
    case 1:
    {
      *(ad_comm::global_datafile) >> N_settle_assignments_rd;
      *(ad_comm::global_datafile) >> recr_dist_inx;
      N_settle_assignments = N_settle_assignments_rd;
      break;
    }
    case 2:
    {
      *(ad_comm::global_datafile) >> N_settle_assignments;
      *(ad_comm::global_datafile) >> recr_dist_inx;
      break;
    }
    case 3:
    {
      *(ad_comm::global_datafile) >> N_settle_assignments;
      *(ad_comm::global_datafile) >> recr_dist_inx;
      break;
    }
    case 4:
    {
      *(ad_comm::global_datafile) >> N_settle_assignments;
      *(ad_comm::global_datafile) >> recr_dist_inx;
      if (N_settle_assignments > 1)
      {
        warnstream << "Need to change to recr_dist_method=3 because >1 settle assignments requested";
        write_message (FATAL, 0); // EXIT!
      }
      break;
    }
  }
  echoinput << N_settle_assignments << " Number of settlement events: GP/area/month to read (>=0) " << endl;
  if (recr_dist_method == 1)
  {
    warnstream << "recr_dist_method cannot be 1 in SS3.30 ";
    write_message (FATAL, 0); // EXIT!
  }
  else if (N_settle_assignments == 1 && recr_dist_method != 4)
  {
    warnstream << "This model has just one settlement event. Changing to recr_dist_method 4 and removing the recruitment distribution parameters at the end of the MG parms section (below growth parameters) will produce identical results and simplify the model.";
    write_message (SUGGEST, 0);
  }
  else if (recr_dist_method == 2)
  {
    warnstream << " recr_dist_method 3 is simpler and takes 1 parm for each settlement";
    write_message (SUGGEST, 0);
  }
  echoinput << recr_dist_inx << "  # unused option " << endl;
  // clang-format off
 END_CALCS

  int birthseas;  //  is this still needed??

  matrix settlement_pattern_rd(1,N_settle_assignments,1,4);   //  for each settlement event:  GPat, Month, area, age
  ivector settle_assignments_timing(1,N_settle_assignments);  //  stores the settle_timing index for each assignment
  matrix settle_timings_tempvec(1,N_settle_assignments,1,2)  //  temporary storage for real_month and age of each settlement_timing
                                                        //  dimensioned by assignments, but only uses N_settle_timings of these
 LOCAL_CALCS
          // clang-format on
          *(ad_comm::global_datafile) >>
      settlement_pattern_rd;
  echoinput << " settlement pattern as read " << endl
            << "GPat  Month  Area Age" << endl
            << "*" << settlement_pattern_rd << "*" << endl;
  echoinput << "Now calculate the number of unique settle timings, which will dictate the number of recr_dist_timing parameters " << endl;
  N_settle_timings = 0;
  settle_timings_tempvec.initialize();
  if (N_settle_assignments == 0)
  {
    N_settle_timings = 1;
    settle_timings_tempvec(1, 1) = 1.0;
    settle_timings_tempvec(1, 2) = 0;
  }
  else
  {
    for (settle = 1; settle <= N_settle_assignments; settle++)
    {
      real_month = settlement_pattern_rd(settle, 2);
      int settle_age_here = settlement_pattern_rd(settle, 4);
      if (N_settle_timings == 0)
      {
        N_settle_timings++;
        settle_timings_tempvec(N_settle_timings, 1) = real_month;
        settle_timings_tempvec(N_settle_timings, 2) = settle_age_here;
        settle_assignments_timing(settle) = N_settle_timings;
      }
      else
      {
        k = 0;
        for (j = 1; j <= N_settle_timings; j++)
        {
          if (settle_timings_tempvec(j, 1) == real_month && settle_timings_tempvec(j, 2) == settle_age_here) // found matching settle_time
          {
            settle_assignments_timing(settle) = j;
            k = 1;
          }
        }
        if (k == 0)
        {
          N_settle_timings++;
          settle_timings_tempvec(N_settle_timings, 1) = real_month;
          settle_timings_tempvec(N_settle_timings, 2) = settle_age_here;
          settle_assignments_timing(settle) = N_settle_timings;
        }
      }
    }
  }
  echoinput << "N settle timings: " << N_settle_timings << endl;
  echoinput << "settle events use these settle_times: " << settle_assignments_timing << endl;
  
  if (recr_dist_method == 2)
  {
    echoinput << " Need to read N_GP * Narea * N_settletimings=" << N_GP * pop * N_settle_timings << "  recruitment distribution parameters " << endl;
  }
  else if (recr_dist_method == 3)
  {
    echoinput << " Need to read N_settle_assignments=" << N_settle_assignments << "  recruitment distribution parameters " << endl;
  }
  
  //  SS_Label_Info_4.2.3 #Set-up arrays and indexing for growth patterns, gender, settlements, platoons
  // clang-format off
 END_CALCS
   int g3i;
//  SPAWN-RECR:   define settlement timings
  ivector Settle_seas(1,N_settle_timings)  //  calculated season in which settlement occurs
  ivector Settle_seas_offset(1,N_settle_timings)  //  calculated number of seasons between spawning and the season in which settlement occurs
  vector  Settle_timing_seas(1,N_settle_timings)  //  calculated elapsed time (frac of year) between settlement and the begin of season in which it occurs
  vector  Settle_month(1,N_settle_timings)  //  month (real)in which settlement occurs
  ivector Settle_age(1,N_settle_timings)  //  calculated age at which settlement occurs, with age 0 being the year in which spawning occurs
  3iarray recr_dist_pattern(1,N_GP,1,N_settle_timings,0,pop);  //  has flag to indicate each settlement events

 LOCAL_CALCS
  // clang-format on
  Settle_seas_offset.initialize();
  Settle_timing_seas.initialize();
  Settle_age.initialize();
  Settle_seas.initialize();
  recr_dist_pattern.initialize();
  
  echoinput << "Calculated assignments in which settlement occurs " << endl
            << "Settle_event / Month / Seas / Seas_from_spawn / time_from_seas_start / age_at_settle" << endl;
  if (N_settle_assignments > 0)
  {
    for (settle = 1; settle <= N_settle_assignments; settle++)
    {
      gp = settlement_pattern_rd(settle, 1); //  growth patterns
      p = settlement_pattern_rd(settle, 3); //  settlement area
      settle_time = settle_assignments_timing(settle);
      Settle_age(settle_time) = settlement_pattern_rd(settle, 4); //  settlement age as read
      recr_dist_pattern(gp, settle_time, p) = 1; //  indicates that settlement will occur here
      recr_dist_pattern(gp, settle_time, 0) = 1; //  for growth updating
      Settle_month(settle_time) = settle_timings_tempvec(settle_time, 1);
    }
    for (settle_time = 1; settle_time <= N_settle_timings; settle_time++)
    {
      j = 0; //  temp value for calculated settlement age
      if (Settle_month(settle_time) < spawn_month )  //  settlement month before spawn_month, so settlement will be at least 1 calender year increment after spawning
      {
        k = 1; //  so sets season 1 as earliest possible season for settlement
        j = max( 1, Settle_age(settle_time) );  //  calendar elapsed years at settlement
      }
      else  //  settlement date is at or after spawn_month
      {
        k = spawn_seas; //  earliest possible season for settlement
        j = Settle_age(settle_time);  //  calendar elapsed years at settlement 
     }
      temp = azero_seas(k); //  annual elapsed time fraction at begin of this season
      Settle_timing_seas(settle_time) = (Settle_month(settle_time) - 1.0) / sumseas; //  fraction of year at settlement month
  
      while ((temp + seasdur(k)) <= Settle_timing_seas(settle_time))
      {
        temp += seasdur(k);
        if (k == nseas)
        {
          k = 1;  // got to seas 1 in next year
          j++;  // advance years since spawning
        }
        else
        {
          k++;
        }
      }

      Settle_seas(settle_time) = k;
//       echoinput << "Calendar years since spawning: " << j << endl;
     Settle_seas_offset(settle_time) = Settle_seas(settle_time) - spawn_seas + j * nseas; //  number of seasons between spawning and the season in which settlement occurs
      Settle_timing_seas(settle_time) -= temp; //  timing from beginning of this season; needed for mortality calculation
      echoinput << settle_time << " / " << Settle_month(settle_time);
      echoinput << "  /  " << Settle_seas(settle_time) << " / " << Settle_seas_offset(settle_time) << " / "
                << Settle_timing_seas(settle_time) << "  / " << Settle_age(settle_time) << endl;
      if ( Settle_seas_offset(settle_time) == 0 && spawn_time_seas > 0.0 && Settle_age(settle_time) == 0 )
      {
        warnstream << "Cannot have spawn_time_seas after beginning of a season and settlements in the same season" << endl
                   << "++ put spawning at beginning of the season, or move settlements to next season";
        write_message (FATAL, 0); // EXIT!
      }
    }
  }
  else
  {
    recr_dist_pattern(1, 1, 1) = 1;
    recr_dist_pattern(1, 1, 0) = 1;
    Settle_month(1) = 1.;
    Settle_timing_seas(1) = 0.0;
    Settle_seas(1) = 1;
    Settle_seas_offset(1) = 0;
    Settle_age(1) = 0;
  }
  
  gmorph = gender * N_GP * N_settle_timings * N_platoon; //  total potential number of biological entities, some may not get used so see use_morph(g)
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.2.1.1 #Define indexing vectors to keep track of characteristics of each morph
  ivector sx(1,gmorph) //  define sex for each growth morph
  ivector GP4(1,gmorph)   // index to GPat
  ivector GP(1,gmorph)    //  index for gender*GPat;  note that gp is nested inside gender
  ivector GP3(1,gmorph)   // index for main gender*GPat*settlement
  ivector GP2(1,gmorph)  // reverse pointer for platoon
  imatrix g_finder(1,N_GP,1,gender)  //  reverse pointer to middle "g" for each main morph (used only with Growth_Std
  ivector g_Start(1,N_GP*gender)  //  base "g" for this growth pattern
  ivector Bseas(1,gmorph)  // birth season
//  following two containers are used to track which morphs are being used
  ivector use_morph(1,gmorph)
  imatrix TG_use_morph(1,N_TG2,1,gmorph)
  imatrix ALK_range_g_lo(1,N_subseas*nseas*gmorph,0,nages)
  imatrix ALK_range_g_hi(1,N_subseas*nseas*gmorph,0,nages)

  vector azero_G(1,gmorph);  //  time since Jan 1 at beginning of settlement in which "g" was born
  3darray real_age(1,gmorph,1,nseas*N_subseas,0,nages);  // real age since settlement
  3darray keep_age(1,gmorph,1,nseas*N_subseas,0,nages);  // set to 0.0 if real_age<0.  this allows omitting virtual young fish to be excluded from expected values
  3darray calen_age(1,gmorph,1,nseas*N_subseas,0,nages);  // real age since Jan 1 of spawn year

  3darray lin_grow(1,gmorph,1,nseas*N_subseas,0,nages)  //  during linear phase has fraction of Size at Afix
  ivector settle_g(1,gmorph)   //  settlement pattern for each platoon
  int ALK_count;

 LOCAL_CALCS
  // clang-format on
  ALK_count = 0;
  
  use_morph.initialize();
  TG_use_morph.initialize();
  keep_age.initialize();
  keep_age = 1.0;
  
  for (gp = 1; gp <= N_GP * gender; gp++)
  {
    g_Start(gp) = (gp - 1) * N_settle_timings * N_platoon + int(N_platoon / 2) + 1 - N_platoon; // find the mid-morph being processed
  }
  
  g = 0;
  g3i = 0;
  echoinput << endl
            << "MORPH_INDEXING" << endl;
  echoinput << "g Sex GP Settlement Birth_Seas Platoon Platoon% Sex*GP Sex*GP*settle_time Used(0/1) SettleTime_frac_yr" << endl;
  for (gg = 1; gg <= gender; gg++)
    for (gp = 1; gp <= N_GP; gp++)
      for (settle = 1; settle <= N_settle_timings; settle++)
      {
        g3i++;
        {
          for (gp2 = 1; gp2 <= N_platoon; gp2++)
          {
            g++;
            GP3(g) = g3i; // track counter for main morphs (gender x pattern x settlement)
            Bseas(g) = Settle_seas(settle);
            sx(g) = gg;
            GP(g) = gp + (gg - 1) * N_GP; // counter for pattern x gender so gp is nested inside gender
            GP2(g) = gp2; //   reverse pointer to platoon counter
            GP4(g) = gp; //  counter for growth pattern
            settle_g(g) = settle; //  to find the settlement timing for this platoon
            azero_G(g) = (Settle_month(settle) - 1.0) / sumseas; //  settlement month converted to fraction of year; could be > one year
            for (p = 1; p <= pop; p++)
            {
              if (recr_dist_pattern(gp, settle, p) == 1)
              {
                use_morph(g) = 1;
              }
            }
            if (use_morph(g) == 1)
            {
              if ((N_platoon == 1) || (N_platoon == 3 && gp2 == 2) || (N_platoon == 5 && gp2 == 3)) g_finder(gp, gg) = g; // finds g for a given GP and gender and last birstseason
            }
            echoinput << g << "   " << sx(g) << "  " << GP4(g) << "       " << settle << "       " << Bseas(g) << "       "
                      << GP2(g) << "       " << 100. * platoon_distr(GP2(g)) << "       " << GP(g) << "        " << GP3(g) << "               " << use_morph(g) << "       " << azero_G(g) << endl;
          }
        }
      }
  echoinput << "calen_age is elapsed years since beginning of year in which spawning occurred" << endl;
  echoinput << "real_age is elapsed years since settlement" << endl;
  echoinput << "g  s  subseas  ALK_idx settle_time age@settle age real_age calen_age" << endl;
  calen_age.initialize();
  real_age.initialize();
  keep_age.initialize();
  for (g = 1; g <= gmorph; g++)
    if (use_morph(g) == 1)
      for (s = 1; s <= nseas; s++)
        for (subseas = 1; subseas <= N_subseas; subseas++)
        {
          ALK_idx = (s - 1) * N_subseas + subseas;
          settle_time = settle_g(g);
          //  real_age is real age since settlement and is used in growth calculations
          //  calen_age is real age since the beginning of the year in which spawning occurred
          //  except with seas-as-years, sumseas is < 1.0 so calen_age needs to be in terms of season count, not age
          //  so, divide by sumseas
          for (a = 0; a <= nages; a++)
          {
            calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s) / (sumseas / 12.);
            if (a < Settle_age(settle_time))
            {
              real_age(g, ALK_idx, a) = 0.;
              keep_age(g, ALK_idx, a) = 0.;
            }
            else if (a == Settle_age(settle_time))
            {
              if (calen_age(g, ALK_idx, a) >= (azero_G(g) + Settle_age(settle_time)))
              {
                real_age(g, ALK_idx, a) = calen_age(g, ALK_idx, a) - azero_G(g) - Settle_age(settle_time);
                keep_age(g, ALK_idx, a) = 1.;
              }
              else
              {
                real_age(g, ALK_idx, a) = 0.;
                keep_age(g, ALK_idx, a) = 0.;
              }
            }
            else
            {
              real_age(g, ALK_idx, a) = calen_age(g, ALK_idx, a) - azero_G(g) - Settle_age(settle_time);
              keep_age(g, ALK_idx, a) = 1.;
            }
            if (a < 4) echoinput << g << " " << s << " " << subseas << " " << ALK_idx << " " << settle_time << " " << Settle_age(settle_time)
                                 << " " << a << " " << real_age(g, ALK_idx, a) << " " << calen_age(g, ALK_idx, a) << endl;
          }
        }
  
  if (N_TG > 0)
  {
    for (TG = 1; TG <= N_TG; TG++)
    {
      for (g = 1; g <= gmorph; g++)
      {
        if (TG_release(TG, 6) > 2)
        {
          warnstream << "Gender for tag groups must be 0, 1 or 2 ";
          write_message (WARN, 0);
        }
        if (use_morph(g) > 0 && (TG_release(TG, 6) == 0 || TG_release(TG, 6) == sx(g))) TG_use_morph(TG, g) = 1;
      }
    }
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.3  #Define movement between areas
   int do_migration  //  number of explicit movements to define
   number migr_firstage
   matrix migr_start(1,nseas,1,N_GP)
 LOCAL_CALCS
   // clang-format on
   migr_firstage = 0.0;
  do_migration = 0;
  if (pop > 1)
  {
    *(ad_comm::global_datafile) >> do_migration;
    echoinput << do_migration << " N_migration definitions to read" << endl;
    if (do_migration > 0)
    {
      *(ad_comm::global_datafile) >> migr_firstage;
      echoinput << migr_firstage << " migr_firstage" << endl;
    }
  }
  else
  {
    echoinput << " only 1 area, so no read of do_migration or migr_firstage " << endl;
  }
  // clang-format off
 END_CALCS
  init_matrix move_def(1,do_migration,1,6)   // seas morph source dest minage maxage
//  ivector GP3(1,gmorph)   // index for main gender*GPat*settlement in that order
//  plan to revise such that movement is by GP3, not GP
   4iarray move_pattern(1,nseas,1,N_GP,1,pop,1,pop)
   int do_migr2
   ivector firstBseas(1,N_GP)

 LOCAL_CALCS
      // clang-format on
      move_pattern.initialize();
  do_migr2 = 0;
  if (do_migration > 0)
  {
    echoinput << " migration setup " << endl
              << move_def << endl;
    for (k = 1; k <= do_migration; k++)
    {
      s = move_def(k, 1);
      gp = move_def(k, 2);
      p = move_def(k, 3);
      p2 = move_def(k, 4);
      move_pattern(s, gp, p, p2) = k; // save index for definition of this pattern to find the right parameters
    }
    k = do_migration;
    for (s = 1; s <= nseas; s++)
      for (gp = 1; gp <= N_GP; gp++)
        for (p = 1; p <= pop; p++)
        {
          if (move_pattern(s, gp, p, p) == 0) {
            k++;
            move_pattern(s, gp, p, p) = k;
          } //  no explicit migration for staying in this area, so create implicit
        }
  
    do_migr2 = k; //  number of explicit plus implicit movement rates
    migr_start.initialize();
    // need to modify so it only does the calc for the first settlement used for each GP???
    for (gp = 1; gp <= N_GP; gp++)
    {
      //  use firstBseas so that the start age of migration is calculated only for the first birthseason used for each GP
      firstBseas(gp) = 0;
      for (g = 1; g <= gmorph; g++)
        if (use_morph(g) > 0)
        {
          if (GP4(g) == gp && firstBseas(gp) == 0) firstBseas(gp) = Bseas(g);
        }
    }
    for (g = 1; g <= gmorph; g++)
      if (use_morph(g) > 0 && firstBseas(GP4(g)) == Bseas(g))
      {
        for (s = 1; s <= nseas; s++)
          for (subseas = 1; subseas <= N_subseas; subseas++)
          {
            a = 0;
            ALK_idx = (s - 1) * N_subseas + subseas;
            while (real_age(g, ALK_idx, a) < migr_firstage) {
              a++;
            }
            migr_start(s, GP4(g)) = a;
          }
      }
  }
  // clang-format off
 END_CALCS
   matrix move_def2(1,do_migr2,1,6)    //  movement definitions.  First Do_Migration of these are explicit; rest are implicit

 LOCAL_CALCS
      // clang-format on
      if (do_migration > 0)
  {
    for (k = 1; k <= do_migration; k++) {
      move_def2(k) = move_def(k);
    }
    k = do_migration;
    for (s = 1; s <= nseas; s++)
      for (gp = 1; gp <= N_GP; gp++)
        for (p = 1; p <= pop; p++)
        {
          if (move_pattern(s, gp, p, p) > do_migration)
          {
            k++;
            move_def2(k, 1) = s;
            move_def2(k, 2) = gp;
            move_def2(k, 3) = p;
            move_def2(k, 4) = p;
            move_def2(k, 5) = 0;
            move_def2(k, 6) = nages;
          }
        }
    echoinput << "move_def " << endl
              << move_def2 << endl;
  }
  // clang-format off
 END_CALCS


!!//  SS_Label_Info_4.4 #Define the time blocks for time-varying parameters
  int N_Block_Designs                      // read N block designs
  ivector Nblk(1,1)
  imatrix Block_Design(1,1,1,1)
 LOCAL_CALCS
          // clang-format on
          * (ad_comm::global_datafile) >>
      N_Block_Designs;
  echoinput << N_Block_Designs << " N_Block_Designs" << endl;
  if (N_Block_Designs > 0)
  {
    Nblk.deallocate();
    Nblk.allocate(1, N_Block_Designs);
    *(ad_comm::global_datafile) >> Nblk(1, N_Block_Designs);
    echoinput << Nblk << " N_Blocks_per design" << endl;
  
    ivector Nblk2; //  temporary vector to create ragged array of dimensions for block matrix
    Nblk2.allocate(1, N_Block_Designs);
    Nblk2 = Nblk + Nblk;
    Block_Design.deallocate();
    Block_Design.allocate(1, N_Block_Designs, 1, Nblk2);
    bool endyrChk = false;
    for (j = 1; j <= N_Block_Designs; j++)
    {
      *(ad_comm::global_datafile) >> Block_Design(j)(1, Nblk2(j));
      a = -1;
      for (k = 1; k <= Nblk(j); k++)
      {
        a += 2;
        b = a + 1;
        if (Block_Design(j, b) == -1)
        {
          Block_Design(j, b) = endyr;
        }
        else if (Block_Design(j, b) == -2)
        {
          Block_Design(j, b) = YrMax;
        }
        // check block year values
        if (Block_Design(j, b) > YrMax)
        {
          if (Block_Design(j, b) < 999)  // manual suggests use of 9999, so 999 is safe choice here
          {
            warnstream << "Block_design:" << j << ", block: " << k << ", ends in: " << Block_Design(j, a + 1) << " reset to YrMax:  " << YrMax;
            write_message (ADJUST, 0);
          }
          Block_Design(j, b) = YrMax;
        }
        if (Block_Design(j, a) < styr - 1)
        {
          warnstream << "Block:" << j << " " << k << " starts before styr; resetting";
          write_message (ADJUST, 0);
          Block_Design(j, a) = styr;
        }
        if (Block_Design(j, b) < Block_Design(j, a))
        {
          warnstream << "Block:" << j << " " << k << " ends before it starts; fatal error";
          write_message (FATAL, 0); // EXIT!
        }
        if (Block_Design(j, b) < styr - 1)
        {
          warnstream << "Block:" << j << " " << k << " ends before styr; fatal error";
          write_message (FATAL, 1); // EXIT!
        }
        if (Block_Design(j, a) > retro_yr + 1)
        {
          warnstream << "Block:" << j << " " << k << " starts after retroyr+1; should not estimate ";
          write_message (WARN, 0);
        }
        if (Block_Design(j, b) > retro_yr + 1)
        {
          warnstream << "Block:" << j << " " << k << " ends in: " << Block_Design(j, a + 1) << " after retroyr+1:  " << retro_yr + 1;
          write_message (WARN, 0);
        }
        if (Block_Design(j, a) > YrMax)
        {
          warnstream << "Block:" << j << " " << k << " starts in: " << Block_Design(j, a + 1) << " which is > YrMax:  " << YrMax << " fatal error";
          write_message (FATAL, 0); // EXIT!
        }
        if (Block_Design(j, b) == endyr)
        {
          endyrChk = true;
        }
      }
      echoinput << " block design #: " << j << "  read year pairs: " << Block_Design(j) << endl;
    }
    if (endyrChk == true)
    {
      warnstream << "At least one block pattern ends in endyr. Check the output parameter value time series to see if the values in forecast years are as intended.";
      write_message (WARN, 0);
    }
  }
  else
  {
    Nblk.allocate(1, 1);
    Block_Design.allocate(1, 1, 1, 1);
  }
  // clang-format off
 END_CALCS

  init_int parm_adjust_method
!! echoinput<<parm_adjust_method<<"  timevarying parameter constraint method"<<endl;
  init_ivector autogen_timevary(1,5);  //  0 means to autogenerate time-vary parameters; 1 means to read; (2) read then autogen if parm min==-12345
                                       //  first element for biology, 2nd for SRR; 3rd for Q; 4th for tag; 5th for selex
!! echoinput<<autogen_timevary<<"  timevarying parameter autogenerate (0) or read (1) for each parm type or (2) read then autogen if parm min==-12345"<<endl;
   ivector varparm_estimated(1,5)  // flag to show what types of variance parameters are estimated
   // (1) for growth
   // (2)  for recruitment sigmaR
   // (3)  for survey extraSD
!!  varparm_estimated.initialize();

!!//  SS_Label_Info_4.5 #Read setup and parameters for natmort, growth, biology, recruitment distribution, and migration
// read setup for natmort parameters:  LO, HI, INIT, PRIOR, PR_type, CV, PHASE, use_env, use_dev, dev_minyr, dev_maxyr, dev_phase, Block, Block_type
  int N_MGparm
  int N_natMparms
  int N_predparms
  ivector predparm_pointer(1,Nfleet+1)
  int N_growparms
  int N_M_Grow_parms
  int recr_dist_parms
  int natM_type
  int natM_5_opt  //  option selection for Maunder approach
  imatrix MGparm_point(1,gender,1,N_GP)
  vector NatM_break(1,1);
  matrix Age_NatMort(1,1,1,1);
  number natM_amin;
  number natM_amax;
  number fracfemale;
!!fracfemale=1.00;
  number fracfemale_mult;
!!fracfemale_mult=1.0;  //  multiplier used in female SSB calc; gets changed to femfrac(1) if gender_rd==-1

// read natmort setup
 LOCAL_CALCS
  // clang-format on
  N_natMparms = 0;
  N_predparms = N_pred;
  if (nseas > 1) N_predparms += N_pred * nseas;
  natM_5_opt = 0;
  MGparm_point.initialize();
  //  0=1Parm; 1=segmented; 2=Lorenzen; 3=agespecific; 4=agespec with seas interpolate; 5=Maunder_M; 6=Lorenzen range
  *(ad_comm::global_datafile) >> natM_type;
  echoinput << natM_type << " natM_type" << endl;
  switch (natM_type)
  {
    case 0:
    {
      N_natMparms = 1;
      break;
    }
    case 1:
    {
      *(ad_comm::global_datafile) >> N_natMparms;
      echoinput << N_natMparms << " N breakpoints " << endl;
      NatM_break.deallocate();
      NatM_break.allocate(1, N_natMparms);
      *(ad_comm::global_datafile) >> NatM_break(1, N_natMparms);
      echoinput << NatM_break << " NatM_age_segment_breaks " << endl;
      break;
    }
    case 2:
    {
      N_natMparms = 1;
      *(ad_comm::global_datafile) >> natM_amin;
      echoinput << natM_amin << " natM_A for Lorenzen" << endl;
      break;
    }
    case 3:
    {
      //  same as 4
    }
    case 4:
    {
      N_natMparms = 0;
      Age_NatMort.deallocate();
      Age_NatMort.allocate(1, N_GP * gender, 0, nages);
      for (gp = 1; gp <= N_GP * gender; gp++)
      {
        *(ad_comm::global_datafile) >> Age_NatMort(gp)(0, nages);
      }
      echoinput << " Age_NatMort empirical input: " << endl
                << Age_NatMort << endl;
      break;
    }
    case 5:
    {
      //  Maunder et al. age and sex specific M
      // A) read in an integer for the method to do maturity Maunder_MatType = 1,2,3
      *(ad_comm::global_datafile) >> natM_5_opt;
      echoinput << " Maunder_NatMort option: " << natM_5_opt << endl;
      N_natMparms = 4;
      if (natM_5_opt == 3) N_natMparms = 6;
      //            Maunder_Mjuv = natMparms(1,gp);
      //            Maunder_lambda = natMparms(2,gp);
      //            Maunder_lmat = natMparms(3,gp);
      //            Maunder_Mmat = natMparms(4,gp);
      //            if(natM_5_opt==3){	//use two parameters  mat50% and mat_slope.
      //        		Maunder_L50  = natMparms(5,gp);
      //		        Maunder_beta = natMparms(6,gp);
      break;
    }
    case 6:
    {
      N_natMparms = 1;
      *(ad_comm::global_datafile) >> natM_amin;
      echoinput << natM_amin << " natM_minage for Lorenzen" << endl;
      *(ad_comm::global_datafile) >> natM_amax;
      echoinput << natM_amax << " natM_maxage for Lorenzen" << endl;
      break;
    }
  }
  // clang-format off
 END_CALCS

// read growth setup
  init_int Grow_type  // 1=vonbert; 2=Richards; 3=age-specific K ascend;  4=age-specific K descend; 5=age-specific K; 6=read vector(not implemented); 8=growth cessation
!!echoinput<<Grow_type<<" growth model "<<endl;
!!//  SS_Label_Info_4.5.1 #Create time constants for growth
  number AFIX;
  number AFIX2;
  number AFIX2_forCV;
  number AFIX_delta;
  number AFIX_plus;
  number Linf_decay;  //  decay factor to calculate mean L at maxage from Linf and the decaying abundance above maxage
                      //  forced equal to 0.20 in 3.24 (which also assumed linear, not VBK, growth)
                      //  -999 code uses the 3.24 approach
                      //  -998 code sets no growth within the plus group, even if Linf > Length_at_maxage.  Sets plusgroupsize_update = 0
                      //  -997 code sets no growth within the plus group, but keeps plusgroupsize_update = 1

  int plusgroupsize_update;  // created internally from value of Linf_decay
                      //  = 0 keeps mean size at maxage (i.e. plusgroup) constant during time series, even if there is time-varying growth
                      //  = 1 updates mean size at maxage using weighted average of current mean size and size of incoming cohort, but only in years with timevarying growth
                      //  note that if Linf is > mean size at maxage, then Z during time series logically should cause reduction in mean size at maxage because there are fewer old fish
                      //  SO! there needs to be an additional option to update the plus group mean size even if growth is not time-varying
                      //  but this should be implemented in popdyn, not in biofxn to avoid having to update calculations for all ages
  int do_ageK;
!! k=0;
!! do_ageK=0;
!! if(Grow_type<=2 || Grow_type==8) {k=4;}  //  AFIX and AFIX2
!! if (Grow_type>=3 && Grow_type<=5) {do_ageK=1; k=5;}  //  number of ages for age-specific K
  init_vector tempvec5(1,k)
  int Age_K_count;

 LOCAL_CALCS
  // clang-format on
  Age_K_count = 0;
  if (k > 0) echoinput << tempvec5 << " # growth specifications: AFIX1 AFIX2 LINF_decay placeholder  age-specific_K_ages" << endl;
  k1 = 0;
  AFIX = 0.;
  AFIX2 = 999.; // this value invokes setting Linf equal to the L2 parameter
  Linf_decay = 0.0; //  initialize
  if (Grow_type == 1)
  {
    N_growparms = 5;
    AFIX = tempvec5(1);
    AFIX2 = tempvec5(2);
    Linf_decay = tempvec5(3);
    //  tempvec(4) is a placeholder
  }
  else if (Grow_type == 2 || Grow_type == 8)
  {
    N_growparms = 6;
    AFIX = tempvec5(1);
    AFIX2 = tempvec5(2);
    Linf_decay = tempvec5(3);
    if (Grow_type == 8 && AFIX2 != 999)
    {
      warnstream << "AFIX2 (Age post-settlement for L2, aka Amax) set to 999 for grow_type==8 because only Linfinity allowed for growth cessation ";
      write_message (ADJUST, 0);
      AFIX2 = 999.;
    }
    if (Grow_type == 8 && AFIX != 0.0)
    {
      warnstream << "AFIX (Age post-settlement for L1, aka Amin) set to 0.0 for grow_type==8;  growth cessation ";
      write_message (ADJUST, 0);
      AFIX = 0.0;
    }
    //  tempvec(4) is a placeholder
  }
  else if (do_ageK == 1)
  {
    AFIX = tempvec5(1);
    AFIX2 = tempvec5(2);
    Linf_decay = tempvec5(3);
    //  tempvec(4) is a placeholder
    Age_K_count = tempvec5(5);
    echoinput << " read this number of ages for age-specific K " << Age_K_count << endl;
    N_growparms = 5 + Age_K_count;
  }
  else if (Grow_type == 6) //  not implemented
  {
    N_growparms = 2; // for the two CV parameters
    k1 = N_GP * gender; // for reading empirical length_at_age
  }
  if (AFIX2 != 999 && AFIX2 > nages)
  {
    warnstream << "AFIX2 (Age post-settlement for L2, aka Amax) must be <= nages, entered value = " << AFIX2;
    write_message (FATAL, 0);
    AFIX2 = 999.;
  }

  plusgroupsize_update = 1;  // update mean size in plus group with weighted mean of current size and growth of incoming cohort.  Only implemented beginning in the year for which there is time-varying growth
  if (Linf_decay == -998) plusgroupsize_update = 0;  // option which omits the updating
  echoinput << " N_growparms  " << N_growparms << endl;
  AFIX2_forCV = AFIX2;
  if (AFIX2_forCV > nages) AFIX2_forCV = nages;
  
  AFIX_delta = AFIX2 - AFIX;
  if (AFIX != 0.0)
  {
    AFIX_plus = AFIX;
  }
  else
  {
    AFIX_plus = 1.0e-06;
  }
  N_M_Grow_parms = N_natMparms + N_growparms;
  lin_grow.initialize();
  
  echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow" << endl;
  for (g = 1; g <= gmorph; g++)
    if (use_morph(g) > 0)
    {
      int setfirstgrowage = -1;
      for (a = 0; a <= nages; a++)
      {
        for (s = 1; s <= nseas; s++)
          for (subseas = 1; subseas <= N_subseas; subseas++)
          {
            ALK_idx = (s - 1) * N_subseas + subseas;
            //        if(a==0 && s<Bseas(g))
            //          {lin_grow(g,ALK_idx,a)=0.0;}  //  so fish are not yet born so will get zero length
            if (real_age(g, ALK_idx, a) < AFIX)
            {
              lin_grow(g, ALK_idx, a) = real_age(g, ALK_idx, a) / AFIX_plus;
            } //  on linear portion of the growth
            else if (real_age(g, ALK_idx, a) == AFIX)
            {
              lin_grow(g, ALK_idx, a) = 1.0; //  at the transition from linear to VBK growth
            }
            else if (setfirstgrowage == -1)
            {
              lin_grow(g, ALK_idx, a) = -1.0; //  flag for first age on growth curve beyond AFIX
              if (subseas == N_subseas) {
                setfirstgrowage = a;
              } //  so that lingrow will be -1 for rest of this season
            }
            else
            {
              lin_grow(g, ALK_idx, a) = -2.0;
            } //  flag for being in growth curve
  
            if (a < 4) echoinput << g << " " << a << " " << s << " " << subseas << " " << ALK_idx << " " << real_age(g, ALK_idx, a)
                                 << " " << calen_age(g, ALK_idx, a) << " " << lin_grow(g, ALK_idx, a) << endl;
          }
      }
    }
  // clang-format off
 END_CALCS
  init_ivector Age_K_points(1,Age_K_count);  //  points at which age-specific multipliers to K will be applied
!!if(Age_K_count>0) echoinput<<"Age-specific_K_points"<<Age_K_points<<endl;

  init_matrix Len_At_Age_rd(1,k1,0,nages)
!!if(k1>0) echoinput<<"  Len_At_Age_rd"<<Len_At_Age_rd<<endl;

  init_number SD_add_to_LAA   // constant added to SD length-at-age (set to 0.1 for compatibility with SS2 V1.x
!!echoinput<<SD_add_to_LAA<<"  SD_add_to_LAA"<<endl;
  init_int CV_depvar     //  select CV_growth pattern; 0 CV=f(LAA); 1 CV=F(A); 2 SD=F(LAA); 3 SD=F(A); 4 logSD=f(A)   SS2 V1.x ony had CV=F(LAA)
!!echoinput<<CV_depvar<<"  CV_depvar"<<endl;
  int CV_depvar_a;
  int CV_depvar_b;
  int Grow_logN
 LOCAL_CALCS
      // clang-format on
      if (Age_K_count > 1)
  {
    if (Grow_type == 3)
    {
      for (j = 2; j <= Age_K_count; j++)
      {
        if (Age_K_points(j) <= Age_K_points(j - 1))
        {
          warnstream << "Age K points must be unique and ascending order ";
          write_message (FATAL, 0);  // EXIT!
        }
      }
    }
    else if (Grow_type == 4 || Grow_type == 5)
    {
      for (j = 2; j <= Age_K_count; j++)
      {
        if (Age_K_points(j) >= Age_K_points(j - 1))
        {
          warnstream << "Age K points must be unique and decending order ";
          write_message (FATAL, 0);  // EXIT!
        }
      }
    }
  }
  Grow_logN = 0;
  switch (CV_depvar)
  {
    case 0:
    {
      CV_depvar_a = 0;
      CV_depvar_b = 0;
      break;
    }
    case 1:
    {
      CV_depvar_a = 1;
      CV_depvar_b = 0;
      break;
    }
    case 2:
    {
      CV_depvar_a = 0;
      CV_depvar_b = 1;
      break;
    }
    case 3:
    {
      CV_depvar_a = 1;
      CV_depvar_b = 1;
      break;
    }
    case 4:
    {
      CV_depvar_a = 1;
      CV_depvar_b = 1;
      Grow_logN = 1;
      break;
    }
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.5.2 #Process biology
  int do_fec_len                 //  switch based on maturity option to trigger fecundity calcs
  init_int Maturity_Option       // 1=length logistic; 2=age logistic; 3=read age-maturity
                                  //  4=read age-fecundity;  5=read age-fec from wtatage.ss; 6=read length-maturity
                            // options 1, 2, 3, 6 can be used with fecundity options to create fecundity-at-age: fec(g)
                            // options 4 and 5 read fecundity directly, so the concept of maturity is not defined
 LOCAL_CALCS
      // clang-format on
      echoinput << Maturity_Option << "  Maturity_Option" << endl;
  if (Maturity_Option == 3 || Maturity_Option == 4)
  {
    k1 = N_GP;
  }
  else
  {
    k1 = 0;
  }
  if (Maturity_Option == 6)
  {
    k2 = N_GP;
  }
  else
  {
    k2 = 0;
  }
  if (Maturity_Option == 4 || Maturity_Option == 5) {
    do_fec_len = 0;
  }
  else {
    do_fec_len = 1;
  }
  
  if (Maturity_Option == 5)
  {
    echoinput << " fecundity and weight at age to be read from file:  wtatage.ss" << endl;
    if (WTage_rd == 0)
    {
      warnstream << "Must set WTage_rd to 1 to use wtatage.ss";
      write_message (FATAL, 0); // EXIT!
    }
  }
  // clang-format off
 END_CALCS
  init_matrix Age_Maturity(1,k1,0,nages) // for maturity option 3 or 4
  init_matrix Length_Maturity(1,k2,1,nlength)  //  for maturity option 6
!!if(k1>0) echoinput<<"  read Age_Maturity(3) or Age_Fecundity(4) for each GP"<<Age_Maturity<<endl;
!!if(k2>0) echoinput<<"  read Length_Maturity for each GP"<<Length_Maturity<<endl;

  init_int First_Mature_Age     // first age with non-zero maturity
 LOCAL_CALCS
  echoinput<<First_Mature_Age<<"  First_Mature_Age"<<endl;
  if (First_Mature_Age == 0)
  {
    warnstream<<"First_Mature_Age read as:  " << First_Mature_Age << ", which is unusual. Check logic of spawn_month and settlement time & age";
    write_message(WARN,0);
  }
 END_CALCS

  init_int Fecund_Option
//   Value=1 means interpret the 2 egg parameters as linear eggs/kg on body weight (current SS3 default),
//   so eggs = wt * (a+b*wt), so value of a=1, b=0 causes eggs to be equiv to spawning biomass
//   Value=2 sets eggs=a*L^b   so cannot make equal to biomass
//   Value=3 sets eggs=a*W^b, so values of a=1, b=1 causes eggs to be equiv to spawning biomass
//   Value=4 sets eggs=a+b*L
//   Value=5 sets eggs=a+b*W
!! echoinput<<Fecund_Option<<"  Fecundity option"<<endl;
!! if(Fecund_Option>5) {warnstream<<"Illegal fecundity option:  "<<Fecund_Option;write_message(FATAL,0);} // EXIT!

  int Hermaphro_Option;
  int MGparm_Hermaphro;
  int Hermaphro_seas;
  int Hermaphro_firstage;
  number Hermaphro_seas_rd;
  number Hermaphro_maleSSB;
 LOCAL_CALCS
  // clang-format on
  Hermaphro_seas = 0;
  Hermaphro_maleSSB = 0.0;
  Hermaphro_firstage = 0;
  MGparm_Hermaphro = 0;
  
  *(ad_comm::global_datafile) >> Hermaphro_Option;
  echoinput << Hermaphro_Option << "  Hermaphro_Option: 0 means No; 1 for F to M; -1 for M to F" << endl;
  if (Hermaphro_Option != 0)
  {
    *(ad_comm::global_datafile) >> Hermaphro_seas_rd; //  -1 for all seasons, or integer for particular season <=nseas
    echoinput << Hermaphro_seas_rd << endl;
    Hermaphro_seas = int(Hermaphro_seas_rd);
  
    // fractional part of Hermaphro_seas will be converted to the first age that switches
    if (Hermaphro_seas_rd > 0) {
      Hermaphro_firstage = int((Hermaphro_seas_rd - Hermaphro_seas) * 10.0 + 1.0e-6);
    }
    else
    {
      Hermaphro_firstage = int((abs(Hermaphro_seas_rd) - 1) * 10.0 + 1.0e-6);
    }
    //  so  2.3 will do switch in season 2 beginning with age 3.
    echoinput << Hermaphro_seas << "  Hermaphro_season (-1 means all seasons)" << endl;
    echoinput << Hermaphro_firstage << "  Hermaphro_firstage (from decimal part of seas input; note that firstage can only be a single digit, so 9 is max" << endl;
    *(ad_comm::global_datafile) >> Hermaphro_maleSSB; // read as a fraction (0.0 to 1.0) of the male SSB added into the total SSB
    echoinput << Hermaphro_maleSSB << "  Hermaphro_maleSSB " << endl;
  }
  // clang-format off
 END_CALCS
// if Hermaphro_Option=1, then read 3 parameters for switch from female to male by age
// if Hermaphro_Option=-1, then read 3 parameters for switch from male to female by age
// FUTURE if Hermaphro_Option=2, then read 3 parameters for switch from female to male by age for each GrowPattern
// FUTURE if Hermaphro_Option=3, then read 3 parameters for switch from female to male by length
// FUTURE if Hermaphro_Option=4, then read 3 parameters for switch from female to male by length for each GrowPattern

  init_int MGparm_def       //  offset approach (1=none, 2= M, G, CV_G as offset from female-GP1, 3=like SS2 V1.x)
!! echoinput<<MGparm_def<<"  MGparm_def"<<endl;

  int do_once;
  int doit;

  int MGP_CGD;
  int sd_ratio_param_ptr;
  int CGD_onoff;  //  switch for cohort growth dev

 LOCAL_CALCS
  // clang-format on
  if (parm_adjust_method < 1 || parm_adjust_method > 3)
  {
    warnstream << "Illegal parm_adjust_method; must be 1 or 2 or 3 ";
    write_message (FATAL, 0); // EXIT!
  }
  
  ParCount = 0;
  Parm_minmax.push_back(0); // to start real info at index "1" to align with ParCount
  
  //  retParCount=-1;   // for 3.24 -> 3.30 dome-shaped retention  replace with ivector N_retparm()
  
  //  SS_Label_Info_4.5.3 #Set up indexing and parameter names for MG parameters
  for (gg = 1; gg <= gender; gg++)
  {
    for (gp = 1; gp <= N_GP; gp++)
    {
      MGparm_point(gg, gp) = ParCount + 1; //  starting pointer
      switch (natM_type)
      {
        case 0:
        {
          ParCount++;
          ParmLabel += "NatM_uniform_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          break;
        }
        case 1:
        {
          for (k = 1; k <= N_natMparms; k++)
          {
            ParCount++;
            onenum = "    ";
            sprintf(onenum, "%d", k);
            ParmLabel += "NatM_break_" + onenum + "_" + GenderLbl(gg) + GP_Lbl(gp);
            Parm_info += "val";
            Parm_minmax.push_back(3);
          }
          break;
        }
        case 2:
        {
          ParCount++;
          ParmLabel += "NatM_Lorenzen_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          break;
        }
        case 5: //  new age and maturity specific by Mark Maunder
        {
          ParCount++;
          ParmLabel += "NatM_juv_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          ParCount++;
          ParmLabel += "NatM_power_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          ParCount++;
          ParmLabel += "NatM_infl_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          ParCount++;
          ParmLabel += "NatM_mature_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          if (natM_5_opt == 3)
          {
            ParCount++;
            ParmLabel += "NatM_L50_" + GenderLbl(gg) + GP_Lbl(gp);
            Parm_info += "val";
            Parm_minmax.push_back(3);
            ParCount++;
            ParmLabel += "NatM_slope_" + GenderLbl(gg) + GP_Lbl(gp);
            Parm_info += "val";
            Parm_minmax.push_back(3);
          }
          break;
        }
        case 6:
        {
          ParCount++;
          ParmLabel += "NatM_Lorenzen_average" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          break;
        }
        default:
        {
          break;
        }
      }
  
      switch (Grow_type)
      {
        case 1:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(3);
          ParmLabel += "L_at_Amax_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(2);
          ParmLabel += "VonBert_K_" + GenderLbl(gg) + GP_Lbl(gp);
          Parm_info += "val";
          Parm_minmax.push_back(1);
          ParCount += 3;
          break;
        }
        case 2:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "L_at_Amax_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "VonBert_K_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "Richards_" + GenderLbl(gg) + GP_Lbl(gp);
          ParCount += 4;
          break;
        }
        case 3:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "L_at_Amax_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "VonBert_K_young_" + GenderLbl(gg) + GP_Lbl(gp);
          ParCount += 3;
          for (a = 1; a <= Age_K_count; a++)
          {
            ParmLabel += "Age_K_mult_" + GenderLbl(gg) + GP_Lbl(gp) + "_a_" + NumLbl0(Age_K_points(a) + 1);
            ParCount++;
          }
          break;
        }
        case 4:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "L_at_Amax_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "VonBert_K_old_" + GenderLbl(gg) + GP_Lbl(gp);
          ParCount += 3;
          for (a = 1; a <= Age_K_count; a++)
          {
            ParmLabel += "Age_K_mult_" + GenderLbl(gg) + GP_Lbl(gp) + "_a_" + NumLbl0(Age_K_points(a) + 1);
            ParCount++;
          }
          break;
        }
        case 5:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "L_at_Amax_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "VonBert_K_old_" + GenderLbl(gg) + GP_Lbl(gp);
          ParCount += 3;
          for (a = 1; a <= Age_K_count; a++)
          {
            ParmLabel += "Age_K_each_" + GenderLbl(gg) + GP_Lbl(gp) + "_a_" + NumLbl0(Age_K_points(a) + 1);
            ParCount++;
          }
          break;
        }
        case 8:
        {
          ParmLabel += "L_at_Amin_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "Linf_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "VonBert_K_" + GenderLbl(gg) + GP_Lbl(gp);
          ParmLabel += "Cessation_" + GenderLbl(gg) + GP_Lbl(gp);
          ParCount += 4;
          break;
        }
      }
      //  init_int CV_depvar     //  select CV_growth pattern; 0 CV=f(LAA); 1 CV=F(A); 2 SD=F(LAA); 3 SD=F(A); 4 logSD=f(A)
      if (CV_depvar <= 1)
      {
        ParmLabel += "CV_young_" + GenderLbl(gg) + GP_Lbl(gp);
        ParmLabel += "CV_old_" + GenderLbl(gg) + GP_Lbl(gp);
      }
      else if (CV_depvar <= 3)
      {
        ParmLabel += "SD_young_" + GenderLbl(gg) + GP_Lbl(gp);
        ParmLabel += "SD_old_" + GenderLbl(gg) + GP_Lbl(gp);
      }
      else
      {
        ParmLabel += "lnSD_young_" + GenderLbl(gg) + GP_Lbl(gp);
        ParmLabel += "LnSD_old_" + GenderLbl(gg) + GP_Lbl(gp);
      }
  
      ParCount += 2;
      ParmLabel += "Wtlen_1_" + GenderLbl(gg) + GP_Lbl(gp);
      ParmLabel += "Wtlen_2_" + GenderLbl(gg) + GP_Lbl(gp);
      ParCount += 2;
      if (gg == 1) //  add parms for maturity and fecundity for females only
      {
        ParmLabel += "Mat50%_" + GenderLbl(1) + GP_Lbl(gp);
        ParmLabel += "Mat_slope_" + GenderLbl(1) + GP_Lbl(gp);
        ParCount += 2;
        if (Fecund_Option == 1)
        {
          ParmLabel += "Eggs/kg_inter_" + GenderLbl(1) + GP_Lbl(gp);
          ParmLabel += "Eggs/kg_slope_wt_" + GenderLbl(1) + GP_Lbl(gp);
          ParCount += 2;
        }
        else if (Fecund_Option == 2)
        {
          ParmLabel += "Eggs_scalar_" + GenderLbl(1) + GP_Lbl(gp);
          ParmLabel += "Eggs_exp_len_" + GenderLbl(1) + GP_Lbl(gp);
          ParCount += 2;
        }
        else if (Fecund_Option == 3)
        {
          ParmLabel += "Eggs_scalar_" + GenderLbl(1) + GP_Lbl(gp);
          ParmLabel += "Eggs_exp_wt_" + GenderLbl(1) + GP_Lbl(gp);
          ParCount += 2;
        }
        else if (Fecund_Option == 4)
        {
          ParmLabel += "Eggs_intercept_" + GenderLbl(1) + GP_Lbl(gp);
          ParmLabel += "Eggs_slope_len_" + GenderLbl(1) + GP_Lbl(gp);
          ParCount += 2;
        }
        else if (Fecund_Option == 5)
        {
          ParmLabel += "Eggs_intercept_" + GenderLbl(1) + GP_Lbl(gp);
          ParmLabel += "Eggs_slope_Wt_" + GenderLbl(1) + GP_Lbl(gp);
          ParCount += 2;
        }
      }
    }
  }
  
  if (Hermaphro_Option == 1 || Hermaphro_Option == -1)
  {
    MGparm_Hermaphro = ParCount + 1; // pointer to first hermaphroditism parameter
    ParmLabel += "Herm_Infl_age";
    ParmLabel += "Herm_stdev";
    ParmLabel += "Herm_asymptote";
    ParCount += 3;
  }
  recr_dist_parms = ParCount + 1; // pointer to first recruitment distribution  parameter
  switch (recr_dist_method)
  {
    case 2: //  new method with main effects only
    {
      for (k = 1; k <= N_GP; k++) {
        ParCount++;
        ParmLabel += "RecrDist_GP_" + NumLbl(k);
      }
      for (k = 1; k <= pop; k++) {
        ParCount++;
        ParmLabel += "RecrDist_Area_" + NumLbl(k);
      }
      for (k = 1; k <= N_settle_timings; k++) {
        ParCount++;
        ParmLabel += "RecrDist_month_" + NumLbl(Settle_month(k));
      }
      break;
    }
    case 3: //  new method with parm for each settlement
    {
      for (s = 1; s <= N_settle_assignments; s++)
      {
        ParCount++;
        gp = settlement_pattern_rd(s, 1); //  growth patterns
        p = settlement_pattern_rd(s, 3); //  settlement area
        settle_time = settle_assignments_timing(s);
        ParmLabel += "RecrDist_GP_" + NumLbl(gp) + "_area_" + NumLbl(p) + "_month_" + NumLbl(Settle_month(settle_time));
      }
      break;
    }
    case 4: //  no distribution of recruitments
    {
      break;
    }
  }
  
  MGP_CGD = ParCount + 1; // pointer to cohort growth deviation base parameter
  ParCount++;
  ParmLabel += "CohortGrowDev";
  
  if (do_migration > 0)
  {
    for (k = 1; k <= do_migration; k++)
    {
      s = move_def(k, 1);
      gp = move_def(k, 2);
      p = move_def(k, 3);
      p2 = move_def(k, 4);
      ParCount++;
      ParmLabel += "MoveParm_A_seas_" + NumLbl(s) + GP_Lbl(gp) + "from_" + NumLbl(p) + "to_" + NumLbl(p2);
      ParCount++;
      ParmLabel += "MoveParm_B_seas_" + NumLbl(s) + GP_Lbl(gp) + "from_" + NumLbl(p) + "to_" + NumLbl(p2);
    }
  }
  
  if (N_platoon > 1 && sd_ratio_rd < 0)
  {
    ParCount ++;
    sd_ratio_param_ptr = ParCount;
    ParmLabel += "Platoon_SD_Ratio";
  }
  
  if (Use_AgeKeyZero > 0)
  {
    AgeKeyParm = ParCount + 1;
    for (k = 1; k <= 7; k++)
    {
      ParCount++;
      ParmLabel += "AgeKeyParm" + NumLbl(k);
    }
  }
  
  catch_mult_pointer = -1;
  j = sum(need_catch_mult); //  number of fleets needing a catch multiplier parameter
  if (j > 0) {
    catch_mult_pointer = ParCount + 1;
  }
  for (int ff = 1; ff <= N_catchfleets(0); ff++)
  {
    j = fish_fleet_area(0, ff);
    if (need_catch_mult(j) == 1)
    {
      ParCount++;
      ParmLabel += "Catch_Mult:_" + NumLbl(j) + "_" + fleetname(j);
    }
  }
  
  frac_female_pointer = ParCount + 1;
  for (gp = 1; gp <= N_GP; gp++)
  {
    ParCount++;
    ParmLabel += "FracFemale_GP_" + NumLbl(gp);
  }
  predparm_pointer = -1;
  for (int pc = 1; pc <= N_pred; pc++)
  {
    ParCount++;
    predparm_pointer(pc) = ParCount; //  first parm for this predator
    onenum = "    ";
    sprintf(onenum, "%d", pc);
    ParmLabel += "M2_pred" + onenum;
    Parm_info += "val";
    Parm_minmax.push_back(3);
    if (nseas > 1)
    {
      for (s = 1; s <= nseas; s++)
      {
        ParCount++;
        onenum2 = "    ";
        sprintf(onenum2, "%d", s);
        ParmLabel += "M2_pred" + onenum + "_s" + onenum2;
        Parm_info += "val";
        Parm_minmax.push_back(3);
      }
    }
  }
  predparm_pointer(Nfleet + 1) = ParCount;
  echoinput << " predparm pointer" << predparm_pointer << endl;
  N_MGparm = ParCount;
  // clang-format off
 END_CALCS

  init_matrix MGparm_1(1,N_MGparm,1,14)   // matrix with natmort and growth parms controls
  ivector MGparm_offset(1,N_MGparm)

 LOCAL_CALCS
      // clang-format on
      //set base parm for cohort growth dev to permissable values
      if (MGparm_1(MGP_CGD, 3) == 0 || (MGparm_1(MGP_CGD, 1) == MGparm_1(MGP_CGD, 2)))
  {
    MGparm_1(MGP_CGD, 1) = 0.1; //min
    MGparm_1(MGP_CGD, 2) = 10.; //max
    MGparm_1(MGP_CGD, 3) = 1.; //init
    MGparm_1(MGP_CGD, 4) = 1.; //prior
    MGparm_1(MGP_CGD, 5) = 1.; //  prior_sd
    MGparm_1(MGP_CGD, 6) = 0.; //  prior type
    MGparm_1(MGP_CGD, 7) = -1.; // phase
  }
  
  echoinput << " Biology base parameter setup " << N_MGparm << endl;
  for (i = 1; i <= N_MGparm; i++)
    echoinput << i << " " << MGparm_1(i) << " " << ParmLabel(ParCount - N_MGparm + i) << endl;
  
  //  find MGparms for which the male parameter value is set equal to the female value
  //  only applies for MGparm_def==1 which is direct estimation (no offsets)
  //  only for the natmort and growth parameters (not wtlen, fecundity, movement, recr distribution)
  MGparm_offset.initialize();
  if (MGparm_def == 1 && gender == 2)
  {
    gg = 2; // males
    for (gp = 1; gp <= N_GP; gp++)
    {
      Ip = MGparm_point(gg, gp) - 1;
      for (j = 1; j <= N_M_Grow_parms; j++)
      {
        if (MGparm_1(Ip + j, 3) == 0.0 && MGparm_1(Ip + j, 7) < 0) MGparm_offset(Ip + j) = MGparm_point(1, gp) - 1 + j; // save reference to female parm if male value is zero and not estimated
      }
    }
  }
  // clang-format off
 END_CALCS

  ivector mgp_type(1,N_MGparm)  //  contains category to parameter (1=natmort; 2=growth; 3=wtlen & fec; 4=recr_dist&femfrac; 5=movement; 6=ageerrorkey; 7=catchmult)
  //  labels for the types are found in:  MGtype_Lbl
 LOCAL_CALCS
      // clang-format on
      echoinput<<"start assigning MGparm_type"<<endl;
      gp = 0;
  for (gg = 1; gg <= gender; gg++)
    for (GPat = 1; GPat <= N_GP; GPat++)
    {
      gp++;
      Ip = MGparm_point(gg, GPat);
      mgp_type(Ip, Ip + N_natMparms - 1) = 1; // natmort parms
      Ip += N_natMparms;
      mgp_type(Ip, Ip + N_growparms - 1) = 2; // growth parms

      // check on out of bound Lmin values.  Only check females because male parameter can be offset from females
      // bypass for AFIX <= 0 because those models are inputting the age at L=0, commonly termed t0
      // note that AFIX is age post-settlement
      // if AFIX is > 0, then fish settle at age 0.0 at length = len_bins(1), then grow linearly until reaching Lmin at age (post-settlement) = AFIX
      // keeping Lmin >= len_bins(1) prevents shrinkage during that linear growth stanza
      // additional checks occur in preliminary calcs regarding generating L@age < 0, or generating a decreasing trend in L@age due to linear growth below AFIX

     if ( gp == 1 && WTage_rd == 0 && AFIX >= 0.0)  // apply test
      {
        if (MGparm_1(Ip,1) < len_bins(1))
        {
          warnstream << "parm min for Lmin: " << MGparm_1(Ip,1) << " should not be less than population min length bin " << len_bins(1);
          write_message (WARN, 0); // EXIT!
        }
        if (MGparm_1(Ip,3) < len_bins(1) && MGparm_1(Ip,7) >= 0)
        {
          warnstream << "parm init value for Lmin: " << MGparm_1(Ip,3) << " should not be less than population min length bin if Lmin estimated" << len_bins(1);
          write_message (WARN, 0); // EXIT!
        }
      }
      //  check on estimation of variance parameters for CV_young and CV_old
      for (int kk = Ip + N_growparms - 2; kk <= Ip + N_growparms - 1; kk++)
      {
        if (MGparm_1(kk, 7) > 0) varparm_estimated(1) = 1;
        if (MGparm_1(kk, 8) != 0 || MGparm_1(kk, 9) != 0 || MGparm_1(kk, 13) != 0)
        {
          warnstream << "CV of growth parameters cannot be time-varying";
          write_message (FATAL, 0); // EXIT!
        }
      }
      //     if(MGparm_1(Ip+N_growparms-2,7)>0) varparm_estimated(1)=1;  //  for CV_young
      //     if(MGparm_1(Ip+N_growparms-1,7)>0) varparm_estimated(1)=1;  //  for CV_old
  
      Ip = Ip + N_growparms;
      mgp_type(Ip, Ip + 1) = 3; // wtlen
      Ip += 2;
      if (gg == 1) {
        mgp_type(Ip, Ip + 3) = 3;
        Ip += 4;
      } // maturity and fecundity
    }
  if (Hermaphro_Option != 0) {
    mgp_type(MGparm_Hermaphro, MGparm_Hermaphro + 2) = 3;
  } //   herma parameters done with wtlen and fecundity
  if (recr_dist_method < 4) mgp_type(Ip, MGP_CGD - 1) = 4; // recruit apportionments
  mgp_type(MGP_CGD) = 2; // cohort growth dev
  if (do_migration > 0) mgp_type(MGP_CGD + 1, N_MGparm) = 5; // note that it fills until end of MGparm list, but some get overwritten
  if (N_platoon > 1 && sd_ratio_rd < 0) mgp_type(sd_ratio_param_ptr) = 2;
  if (Use_AgeKeyZero > 0) mgp_type(AgeKeyParm, N_MGparm) = 6;
  if (catch_mult_pointer > 0) mgp_type(catch_mult_pointer, N_MGparm) = 7;
  for (f = frac_female_pointer; f <= frac_female_pointer + N_GP - 1; f++) mgp_type(f) = 4;
  if (N_pred > 0) mgp_type(predparm_pointer(1), predparm_pointer(1) + N_predparms - 1) = 1;
  echoinput << "mgparm_type for each parm:"<<endl;
  for (f = 1; f<= N_MGparm; f++) echoinput << f << " " << MGtype_Lbl(mgp_type(f)) << endl;
  // clang-format off
 END_CALCS

!!// SS_Label_Info_4... //  quantities used to track all time-varying parameters
  int timevary_cnt   //  cumulative count of timevarying parameters across MG, SRR, Q, Selex, Tag
                     //  it counts the number of times timevary_setup is created
                     //  by the function  "create_timevary"
                     //  and is pushed to the vector_vector  timevary_def
  int N_parm_dev     //  number of  all parms that use annual deviations

!!//  SS_Label_Info_4.5.4 #Set up time-varying parameters for MG parms
  int timevary_used;
  int timevary_MG_firstyr;
  int timevary_parm_cnt_MG;
  int timevary_parm_start_MG;

  ivector MGparm_timevary(1,N_MGparm)  //  holds index in timevary_def used by this base parameter
  imatrix timevary_MG(styr-3,YrMax+1,0,7)  // goes to yrmax+1 to allow referencing in forecast, but only endyr+1 is checked
                                            // stores years to calc non-constant MG parms (1=natmort; 2=growth; 3=wtlen & fec; 4=recr_dist&femfrac; 5=movement; 6=ageerrorkey; 7=catchmult)
  ivector timevary_pass(styr-3,YrMax+1)    //  extracted column
  ivector MG_active(0,7)  // 0=all, 1=M, 2=growth 3=wtlen, 4=recr_dist&femfrac, 5=migration, 6=ageerror, 7=catchmult
  ivector MG_active_firstyr(0,7)  //  first year in which a MGparm is timevarying
  vector env_data_pass(1,2)  //  holds min-max year with env data
  int  do_densitydependent;

//  timevary_setup(1)=baseparm type;
//  timevary_setup(2)=baseparm index;
//  timevary_setup(3)=first timevary parm
//  timevary_setup(4)=block or trend type
//  timevary_setup(5)=block pattern
//  timevary_setup(6)=env link type
//  timevary_setup(7)=env variable
//  timevary_setup(8)=dev vector used
//  timevary_setup(9)=dev link type  used in SS_timevarmparm
//  timevary_setup(10)=dev min year
//  timevary_setup(11)=dev maxyear
//  timevary_setup(12)=dev phase
//  timevary_setup(13)=all parm index of baseparm
//  timevary_setup(14)=continue_last dev

 LOCAL_CALCS
  // clang-format on
  do_densitydependent = 0;
  timevary_cnt = 0;
  N_parm_dev = 0;
  timevary_parm_cnt = 0;
  
  //  push once so 0'th row is not used
  ivector timevary_setup(1, 14);
  timevary_setup.initialize();
  timevary_def.push_back(timevary_setup(1, 14));
  dvector tempvec(1, 7); //  temporary vector for a time-vary parameter  LO HI INIT PRIOR PR_type SD PHASE
  timevary_parm_rd.push_back(tempvec);
  
  echoinput << "Now read env, block/trend, and dev adjustments to MGparms " << endl;
  timevary_MG.initialize(); // stores years to calc non-constant MG parms (1=natmort; 2=growth; 3=wtlen & fec; 4=recr_dist; 5=movement)
  MG_active.initialize();
  MG_active_firstyr.initialize();
  CGD_onoff = 0;
  
  timevary_parm_start_MG = 0;
  timevary_parm_cnt_MG = 0;
  timevary_used = 0;
  timevary_MG_firstyr = YrMax;
  MGparm_timevary.initialize();
  ivector block_design_null(1, 1);
  block_design_null.initialize();
  
  for (j = 1; j <= N_MGparm; j++)
  {
    k = mgp_type(j);
    timevary_pass = column(timevary_MG, k); // year vector for this type of MGparm
  
    if (MGparm_1(j, 13) == 0 && MGparm_1(j, 8) == 0 && MGparm_1(j, 9) == 0)
    {
      //  no time-vary parameter effects
    }
    else
    {
      ivector timevary_setup(1, 14); //  temporary vector for timevary specs
      timevary_setup.initialize();
      timevary_parm_start_MG = 1; //  at least one MG parm is time varying
      timevary_used = 1;
      echoinput << endl
                << " timevary for MG parameter: " << j << endl;
      timevary_cnt++; //  count parameters with time-vary effect
      MGparm_timevary(j) = timevary_cnt; //  base parameter will use this timevary specification
      timevary_setup(1) = 1; //  indicates a MG parm
      timevary_setup(2) = j; //  index of base parm within that type of parameter
      timevary_setup(13) = j; //  index of base parm relative to ParCount which is continuous across all types of parameters
      timevary_setup(3) = timevary_parm_cnt + 1; //  first parameter within total list of all timevary parms
      z = MGparm_1(j, 13); // specified block or trend definition
  
      k = int(abs(MGparm_1(j, 8)) / 100); //  find the env link code
      timevary_setup(6) = k; //  link code for env
      if (MGparm_1(j, 8) > 0) //  env variable used
      {
        timevary_setup(7) = int(abs(MGparm_1(j, 8))) - k * 100;
        k = timevary_setup(7);
        //         for(y=styr-1;y<=YrMax;y++) env_data_pass(y)=env_data_RD(y,k);
        env_data_pass(1) = env_data_minyr(k);
        env_data_pass(2) = env_data_maxyr(k);
      }
      else if (abs(MGparm_1(j, 8) > 0)) //  density-dependence
      {
        timevary_setup(7) = -int(abs(MGparm_1(j, 8)) - k * 100);
        do_densitydependent = 1;
  echoinput << "Density-dependent flag for MGparms " << do_densitydependent << " MGparm: " << j << endl;
        k = 0;
        env_data_pass.initialize();
      }
  
      if (z > 0) //  doing blocks
      {
        if (z > N_Block_Designs)
        {
          warnstream << "MG block request exceeds N_block patterns";
          write_message (FATAL, 0); // EXIT!
        }
        create_timevary(MGparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), mgp_type(j), Block_Design(z), env_data_pass, N_parm_dev, finish_starter);
      }
      else
      {
        create_timevary(MGparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), mgp_type(j), block_design_null, env_data_pass, N_parm_dev, finish_starter);
      }
      timevary_def.push_back(timevary_setup(1, 14));
      for (y = styr - 3; y <= YrMax + 1; y++) {
        timevary_MG(y, mgp_type(j)) = timevary_pass(y);
      } // year vector for this category of MGparm
      if (j == MGP_CGD) CGD_onoff = 1;
      if (mgp_type(j) == 6) //  doing time-vary age-age' key;  can only use blocks
      {
        store_agekey_add = Nblk(z) + 2; //  additional storage space for block-based Age error keys
      }
    }
  }
  if (timevary_used == 1) autogen_timevary(1) = 1; //  indicate that some parameter is time-varying
  timevary_parm_cnt_MG = timevary_parm_cnt;
  
  //  SS_Label_Info_4.5.9 #Set up random deviations for MG parms
  //  NOTE:  the parms for the se of the devs are part of the MGparm2 list above, not the dev list below
  
  //  SS_Label_Info_4.5.95 #Populate time_bio_category array defining when biology changes
  k = YrMax + 1;
  echoinput << "Display timevary_MG flag" << endl;
  for (y = styr + 1; y <= YrMax; y++)
  {
    if (timevary_MG(y, 2) > 0 && y < k) k = y;
  }
  if (k < YrMax + 1)
  {
    for (y = k; y <= YrMax + 1; y++)
    {
      timevary_MG(y, 2) = 1;
    }
  }
  for (y = styr - 1; y <= YrMax; y++)
  {
    for (f = 1; f <= 7; f++)
    {
      if (timevary_MG(y, f) > 0)
      {
        MG_active(f) = 1;
        if (MG_active_firstyr(2) == 0 ) MG_active_firstyr(f) = y;
        timevary_MG(y, 0) = 1; // tracks active status for all MG types
        if(timevary_MG_firstyr == YrMax) timevary_MG_firstyr = y;  // save for reporting in MSY and spawn_recruit output
      }
    }

    //  timevary growth or maturity and Maunder M refers to that maturity
    if ((timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0) && natM_type == 5 && natM_5_opt < 3) timevary_MG(y, 1) = 1;
  
    echoinput << y << " timevary_MG: " << timevary_MG(y) << endl;
  }

  if( timevary_MG_firstyr < YrMax || WTage_rd == 1)  //  time-varying biology
  {
    if( timevary_bio_4SRR == 0)  // legacy approach;  this switch is read from starter.ss
    {
      warnstream << "There is timevary biology and the legacy approach to benchmark calculations is being used; user should be aware of possible impacts to benchmark results";
      write_message(WARN, 0);
        if( timevary_bio_4SRR_rd == -1)  // older starter file did not contain necessary flag
        {
          warnstream << "There is timevary biology, so the flag for timevary_bio_4SRR must be set to 0 (old default) or 1 (new improved) in starter.ss";
// make this a WARN while testing, then change to FATAL for operational code
          write_message(WARN, 0);
        }
    }
  }

  for (y = endyr + 1; y <= YrMax; y++)
  {
    for (f = 1; f <= 7; f++)
    {
      if (timevary_MG(y, f) > 0 && Fcast_MGparm_ave(f,2) > 0)
      {
          warnstream << "mean MGparm for forecast is incompatible with timevary parm in forecast yr: " << y << "; for type: " << f << " " << MGtype_Lbl(f) << "; SS3 will disable time-vary";
          write_message(WARN, 0);
          timevary_MG(y, f) = 0;
      }
    }
  }

  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.5.7 #Set up seasonal effects for MG parms
  init_ivector MGparm_seas_effects(1,10)  // femwtlen1, femwtlen2, mat1, mat2, fec1 fec2 Malewtlen1, malewtlen2 L1 K
  int MGparm_doseas
  int N_MGparm_seas                            // number of MGparms that use seasonal effects
 LOCAL_CALCS
      // clang-format on
      echoinput
      << "seasonal effects as read: " << MGparm_seas_effects << endl;
  adstring_array MGseasLbl;
  MGseasLbl += "F-WL1" + CRLF(1);
  MGseasLbl += "F-WL2" + CRLF(1);
  MGseasLbl += "F-Mat1" + CRLF(1);
  MGseasLbl += "F-Mat1" + CRLF(1);
  MGseasLbl += "F-Fec1" + CRLF(1);
  MGseasLbl += "F-Fec1" + CRLF(1);
  MGseasLbl += "M-WL1" + CRLF(1);
  MGseasLbl += "M-WL2" + CRLF(1);
  MGseasLbl += "L1" + CRLF(1);
  MGseasLbl += "VBK" + CRLF(1);
  MGparm_doseas = sum(MGparm_seas_effects);
  N_MGparm_seas = 0; // counter for assigned parms
  if (MGparm_doseas > 0)
  {
    for (j = 1; j <= 10; j++)
    {
      if (MGparm_seas_effects(j) > 0)
      {
        MGparm_seas_effects(j) = N_MGparm + timevary_parm_cnt_MG + N_MGparm_seas; // store base parameter count
        for (s = 1; s <= nseas; s++)
        {
          N_MGparm_seas++;
          ParCount++;
          ParmLabel += MGseasLbl(j) + "_seas_" + NumLbl(s);
        }
      }
    }
    echoinput << MGparm_seas_effects << " MGparm_seas_effects" << endl;
  }
  // clang-format off
 END_CALCS
  init_matrix MGparm_seas_1(1,N_MGparm_seas,1,7)  // read matrix that defines the seasonal parms
!!if(N_MGparm_seas>0) echoinput<<" MGparm_seas"<<endl<<MGparm_seas_1<<endl;

!!//  SS_Label_Info_4.5.9 #Create vectors (e.g. MGparm_PH) to be used to define the actual estimated parameter array
  int N_MGparm2
!! N_MGparm2=N_MGparm+timevary_parm_cnt_MG+N_MGparm_seas;
  vector MGparm_LO(1,N_MGparm2)
  vector MGparm_HI(1,N_MGparm2)
  vector MGparm_RD(1,N_MGparm2)
  vector MGparm_PR(1,N_MGparm2)
  ivector MGparm_PRtype(1,N_MGparm2)
  vector MGparm_CV(1,N_MGparm2)
  ivector MGparm_PH(1,N_MGparm2)

 LOCAL_CALCS
      // clang-format on
      for (f = 1; f <= N_MGparm; f++) //  loop mgparm and map setup to _LO , _HI etc.
  {
    MGparm_LO(f) = MGparm_1(f, 1);
    MGparm_HI(f) = MGparm_1(f, 2);
    MGparm_RD(f) = MGparm_1(f, 3);
    MGparm_PR(f) = MGparm_1(f, 4);
    MGparm_CV(f) = MGparm_1(f, 5);
    MGparm_PRtype(f) = MGparm_1(f, 6);
    MGparm_PH(f) = MGparm_1(f, 7);
    if (MGparm_PH(f) > 0)
    {
      MG_active(mgp_type(f)) = 1;
    }
  }
  if ((natM_type == 2 || natM_type == 6) && MG_active(2) > 0)
  {
    MG_active(1) = 1; // lorenzen M depends on growth
  }
  
  j = N_MGparm;
  if (timevary_parm_cnt_MG > 0)
    for (f = timevary_parm_start_MG; f <= timevary_parm_cnt_MG; f++)
    {
      j++;
      MGparm_LO(j) = timevary_parm_rd[f](1);
      MGparm_HI(j) = timevary_parm_rd[f](2);
      MGparm_RD(j) = timevary_parm_rd[f](3);
      MGparm_PR(j) = timevary_parm_rd[f](4);
      MGparm_CV(j) = timevary_parm_rd[f](5);
      MGparm_PRtype(j) = timevary_parm_rd[f](6);
      MGparm_PH(j) = timevary_parm_rd[f](7);
    }
  
  if (N_MGparm_seas > 0)
    for (f = 1; f <= N_MGparm_seas; f++)
    {
      j++;
      MGparm_LO(j) = MGparm_seas_1(f, 1);
      MGparm_HI(j) = MGparm_seas_1(f, 2);
      MGparm_RD(j) = MGparm_seas_1(f, 3);
      MGparm_PR(j) = MGparm_seas_1(f, 4);
      MGparm_CV(j) = MGparm_seas_1(f, 5);
      MGparm_PRtype(j) = MGparm_seas_1(f, 6);
      MGparm_PH(j) = MGparm_seas_1(f, 7);
    }
  MG_active(0) = sum(MG_active(1, 7));
  echoinput << "MG_active " << MG_active << endl;
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.6 #Read setup for Spawner-Recruitment parameters
  //  SPAWN-RECR: read setup for SR parameters:  LO, HI, INIT, PRIOR, PRtype, CV, PHASE
  init_int SR_fxn
!!echoinput<<SR_fxn<<" #_SR_function: 1=NA; 2=Ricker(2 parms); 3=BevHolt(2); 4=SCAA(2); 5=Hockey(3); 6=B-H_flattop(2); 7=Survival(3); 8=Shepherd(3); 9=Ricker_Power(3); 10=B-H_a,b(4)"<<endl;
  init_int init_equ_steepness;
!!echoinput<<init_equ_steepness<<"  # 0/1 to use steepness in initial equ recruitment calculation"<<endl;
  init_int itemp;

//   echoinput<<sigmaR_dendep<<"  #  future feature:  0/1 to make realized sigmaR a function of SR curvature"<<endl;

  ivector N_SRparm(1,10)
!!N_SRparm.fill("{0,2,2,2,3,2,3,3,3,4}");
  int N_SRparm2
  int N_SRparm3  //  with timevary links included
!!N_SRparm2=N_SRparm(SR_fxn)+3;
  init_matrix SRparm_1(1,N_SRparm2,1,14)
!!echoinput<<" SR parms "<<endl<<SRparm_1<<endl;
   int SR_env_link
//  !!echoinput<<SR_env_link<<" SR_env_link "<<endl;
    int SR_env_target_RD   // 0=none; 1=devs; 2=R0; 3=steepness
//  !!echoinput<<SR_env_target_RD<<" SR_env_target_RD "<<endl;
  int SR_env_target
  int SR_autocorr;  // will be calculated later

  int timevary_SRparm_first;  //   == 0 means that no relevant parms are timevarying
  int firstSRparm;
  int timevary_SRparm_first_yr;  //   year
  int timevary_parm_SR_last;
  ivector timevary_SRparm(styr-3,YrMax+1);
  ivector SRparm_timevary(1,N_SRparm2);

 LOCAL_CALCS
  // clang-format on
  //  SS_Label_Info_4.6.1 #Create S-R parameter labels
  firstSRparm = ParCount;
  timevary_parm_SR_last = 0;
  timevary_SRparm_first = 0;
  timevary_SRparm_first_yr = 0;
  timevary_SRparm.initialize();
  SRparm_timevary.initialize();
  SR_env_link = 0;
  SR_env_target = 0;

  //#_SR_function: 1=null; 2=Ricker; 3=std_B-H; 4=SCAA; 5=Hockey; 6=B-H_flattop; 7=Survival_3Parm; 10=B-H with a,b "<<endl;
  if (SR_fxn == 10)
  {ParmLabel += "SR_LN(R0)_derived";}
  else
  {ParmLabel += "SR_LN(R0)";}
  
  switch (SR_fxn)
  {
    case 1: // previous placement for B-H constrained
    {
      warnstream << "B-H constrained curve is now Spawn-Recr option #6";
      write_message (FATAL, 0); // EXIT!
      break;
    }
    case 2: // Ricker
    {
      ParmLabel += "SR_Ricker_beta";
      break;
    }
    case 3: // Bev-Holt
    {
      ParmLabel += "SR_BH_steep";
      break;
    }
    case 4: // SCAA
    {
      ParmLabel += "SR_SCAA_null";
      break;
    }
    case 5: // Hockey
    {
      ParmLabel += "SR_hockey_infl";
      ParmLabel += "SR_hockey_min_R";
      break;
    }
    case 6: // Bev-Holt flattop
    {
      ParmLabel += "SR_BH_flat_steep";
      break;
    }
    case 7: // survival
    {
      ParmLabel += "SR_surv_zfrac";
      ParmLabel += "SR_surv_Beta";
      break;
    }
    case 8: // Shepherd
    {
      ParmLabel += "SR_steepness";
      ParmLabel += "SR_Shepherd_c";
      break;
    }
    case 9: //  Ricker Power parameters
    {
      ParmLabel += "SR_RkrPower_steep";
      ParmLabel += "SR_RkrPower_gamma";
      break;
    }
    case 10: // Bev-Holt a,b
    {
      ParmLabel += "SR_BH_steep_derived";
      ParmLabel += "SR_BH_ln(alpha)";
      ParmLabel += "SR_BH_ln(beta)";
      break;
    }
  }
  ParmLabel += "SR_sigmaR";
  ParmLabel += "SR_regime";
  ParmLabel += "SR_autocorr";
  ParCount += N_SRparm2;
  
  if (SRparm_1(N_SRparm2 - 2, 7) > 0) varparm_estimated(2) = 1; //  sigmaR is estimated so need sd_offset=1
  
  if (SRparm_1(N_SRparm2, 3) != 0.0 || SRparm_1(N_SRparm2, 7) > 0)
  {
    SR_autocorr = 1;
  }
  else
  {
    SR_autocorr = 0;
  }
  // flag for recruitment autocorrelation
  echoinput << " Do recruitment_autocorr: " << SR_autocorr << endl;

  // note that the regime parameter seems to bypass use of timevary_SRparm, but timevary_SRparm is used for R0, h beginning 3.30.24
  timevary_used = 0;
  for (j = 1; j <= N_SRparm2 - 1; j++)  // so omits autocorr
    if (j != N_SRparm2 - 2) //  because sigmaR cannot be time-varying
    {
      if (SRparm_1(j, 13) == 0 && SRparm_1(j, 8) == 0 && SRparm_1(j, 9) == 0)
      {
        //  no time-vary parameter effects
      }
      else //  set up a timevary parameter definition
      {
        timevary_used = 1;
        ivector timevary_setup(1, 14); //  temporary vector for timevary specs
        timevary_setup.initialize();
        if (timevary_SRparm_first == 0) timevary_SRparm_first = timevary_parm_cnt + 1;  // cumulative index for first timevary SRparm
        echoinput << " timevary for SR parm: " << j << endl;
        timevary_cnt++; //  count parameters with time-vary effect
        SRparm_timevary(j) = timevary_cnt; //  base SR parameter will use this timevary specification
        timevary_setup(1) = 2; //  indicates a SR parm
        if (autogen_timevary(2) == 0)
        {
          echoinput << " timevary SR parms will be autogenerated " << endl;
        }
        else
        {
          echoinput << " timevary SR parms will be read, not autogenerated " << endl;
        }
        timevary_setup(2) = j; //  index of base parm within that type of parameter
        timevary_setup(13) = firstSRparm + j; //  index of base parm relative to ParCount which is continuous across all types of parameters
        timevary_setup(3) = timevary_parm_cnt + 1; //  first parameter within total list of all timevary parms
        timevary_pass = 0; // placeholder; not used for SR parms
        //  set up env link info
        echoinput << " check for env " << SRparm_1(j, 8) << endl;
        k = int(abs(SRparm_1(j, 8)) / 100); //  find the env link code
        timevary_setup(6) = k; //  link code for env
        if (SRparm_1(j, 8) > 0) //  env variable used
        {
          timevary_setup(7) = int(abs(SRparm_1(j, 8))) - k * 100;
          k = timevary_setup(7);
          //         for(y=styr-1;y<=YrMax;y++) env_data_pass(y)=env_data_RD(y,k);
          env_data_pass(1) = env_data_minyr(k);
          env_data_pass(2) = env_data_maxyr(k);
        }
        else if (abs(SRparm_1(j, 8) > 0)) //  density-dependence
        {
          timevary_setup(7) = -int(abs(SRparm_1(j, 8)) - k * 100);
          do_densitydependent = 1;
          k = 0;
          env_data_pass.initialize();
        }
  
        if (SRparm_1(j, 13) > 0) //  doing blocks
        {
          if (SRparm_1(j, 13) > N_Block_Designs)
          {
            warnstream << "SR block request exceeds N_block patterns";
            write_message (FATAL, 0); // EXIT!
          }
          create_timevary(SRparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, Block_Design(SRparm_1(j, 13)), env_data_pass, N_parm_dev, finish_starter);
        }
        else
        {
          create_timevary(SRparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
        }
        timevary_def.push_back(timevary_setup(1, 14));
        int SRflag;
        SRflag = 0;
        for (y = styr - 3; y <= YrMax + 1; y++)
        {
          if (timevary_pass(y) > 0 && j != N_SRparm2 - 1)
          {
            timevary_SRparm(y) = timevary_pass(y);  //  set timevary flag, except for regime parameter
            timevary_SRparm_first_yr = y;
            SRflag = 1; //  first change point
          }
          else if(SRflag == 1)
          {
            if (y > styr)
            {timevary_SRparm(y) = 2;}  //  flag to carry forward current SRR info
            else
            {timevary_SRparm(y) = 1;}  //  keep at 1
          }
        }
      }
    }
  
  N_SRparm3 = N_SRparm2;
  if (timevary_SRparm_first > 0)
  {
    timevary_parm_SR_last = timevary_parm_cnt;
    if (timevary_used == 1) autogen_timevary(2) = 1; //  indicate that some parameter is time-varying
    N_SRparm3 += (timevary_parm_SR_last - timevary_SRparm_first + 1);
    echoinput << " SR timevary_parm_cnt start and end " << timevary_SRparm_first << " " << timevary_parm_SR_last << endl;
    echoinput << "link to timevary parms:  " << SRparm_timevary << endl;
    echoinput << "timevary SRparms:  " << timevary_SRparm << endl;
  }
  echoinput << "SR_Npar and N_SRparm2 and N_SRparm3:  " << N_SRparm(SR_fxn) << " " << N_SRparm2 << " " << N_SRparm3 << endl;
  // clang-format off
 END_CALCS

  vector SRparm_LO(1,N_SRparm3)
  vector SRparm_HI(1,N_SRparm3)
  vector SRparm_RD(1,N_SRparm3)
  vector SRparm_PR(1,N_SRparm3)
  ivector SRparm_PRtype(1,N_SRparm3)
  vector SRparm_CV(1,N_SRparm3)
  ivector SRparm_PH(1,N_SRparm3)
  int use_steepness  //  0/1 to do full steepness calculations with Beverton-Holt; set to 0 if h = 1 and not estimated

 LOCAL_CALCS
      // clang-format on
      for (i = 1; i <= N_SRparm2; i++)
  {
    SRparm_LO(i) = SRparm_1(i, 1);
    SRparm_HI(i) = SRparm_1(i, 2);
    SRparm_RD(i) = SRparm_1(i, 3);
    SRparm_PR(i) = SRparm_1(i, 4);
    SRparm_CV(i) = SRparm_1(i, 5);
    SRparm_PRtype(i) = SRparm_1(i, 6);
    SRparm_PH(i) = SRparm_1(i, 7);
  }
  if (timevary_SRparm_first > 0)
  {
    j = N_SRparm2;
    for (f = timevary_SRparm_first; f <= timevary_parm_SR_last; f++)
    {
      j++;
      echoinput << f << " " << j << " " << timevary_parm_rd[f] << endl;
      SRparm_LO(j) = timevary_parm_rd[f](1);
      SRparm_HI(j) = timevary_parm_rd[f](2);
      SRparm_RD(j) = timevary_parm_rd[f](3);
      SRparm_PR(j) = timevary_parm_rd[f](4);
      SRparm_PRtype(j) = timevary_parm_rd[f](6);
      SRparm_CV(j) = timevary_parm_rd[f](5);
      SRparm_PH(j) = timevary_parm_rd[f](7);
    }
  }
  echoinput << "SRparm_RD: " << SRparm_RD << endl;
  // clang-format off
 END_CALCS

  init_int do_recdev  //  0=none; 1=devvector; 2=simple deviations; 3=dev from R0
!!echoinput<<do_recdev<<" do_recdev"<<endl;
  // check for use of devvector with MCMC
 LOCAL_CALCS
  // clang-format on
  if (do_recdev == 1 && mcmcFlag == 1)
  {
    warnstream << "do_recdev option 1=devvector should not be used with MCMC, recommend option 2=simple deviations. For more detail see https://github.com/admb-project/admb/issues/107.";
    write_message (FATAL, 0);
  }
  // clang-format off
 END_CALCS

  init_int recdev_start;
!!echoinput<<recdev_start<<" recdev_start"<<endl;
  init_int recdev_end;
!!echoinput<<recdev_end<<" recdev_end"<<endl;
  init_int recdev_PH_rd;
!!echoinput<<recdev_PH_rd<<" recdev_PH"<<endl;
  int recdev_PH;
!! recdev_PH=recdev_PH_rd;
  init_int recdev_adv
!!echoinput<<recdev_adv<<" recdev_adv"<<endl;

  init_vector recdev_options_rd(1,13*recdev_adv)
  vector recdev_options(1,13)
  int recdev_early_start_rd
  int recdev_early_start
  int recdev_early_end
  int recdev_first
  int recdev_early_PH_rd
  int Fcast_recr_PH_rd
  int recdev_early_PH
  int Fcast_recr_PH
  int Fcast_recr_PH2
  number Fcast_recr_lambda
  vector recdev_adj(1,5)
  int recdev_cycle
  int recdev_do_early
  int recdev_read
  number recdev_LO;
  number recdev_HI;
  ivector recdev_doit(styr-nages,YrMax)
  vector biasadj(styr-nages,YrMax)  // biasadj as used; depends on whether a recdev is estimated or not
  vector biasadj_full(styr-nages,YrMax)  //  full time series of biasadj values, only used in defined conditions

 LOCAL_CALCS
      // clang-format on
      //  SS_Label_Info_4.6.2 #Setup advanced recruitment options
      recdev_doit = 0;
  if (recdev_adv > 0)
  {
    recdev_options(1, 13) = recdev_options_rd(1, 13);
    recdev_early_start_rd = recdev_options(1);
    recdev_early_PH_rd = recdev_options(2);
    Fcast_recr_PH_rd = recdev_options(3);
    Fcast_recr_lambda = recdev_options(4);
    recdev_adj(1) = recdev_options(5);
    recdev_adj(2) = recdev_options(6);
    recdev_adj(3) = recdev_options(7);
    recdev_adj(4) = recdev_options(8);
    if (recdev_adj(4) > endyr + 1 && do_recdev > 0)
    {
      warnstream << "bias adjustment ramp extends into forecast; biasadj set to 0.0 internally for forecast years";
      write_message (WARN, 0);
    }
    recdev_adj(5) = recdev_options(9); // maxbias adj
  
    recdev_cycle = recdev_options(10);
    recdev_LO = recdev_options(11);
    recdev_HI = recdev_options(12);
    recdev_read = recdev_options(13);
  }
  else
  {
    recdev_early_start_rd = 0; // 0 means no early
    recdev_early_end = -1;
    recdev_early_PH_rd = -4;
    recdev_options(2) = recdev_early_PH_rd;
    Fcast_recr_PH_rd = 0; // so will be reset to maxphase+1
    recdev_options(3) = Fcast_recr_PH_rd;
    Fcast_recr_lambda = 1.;
    recdev_adj(1) = double(styr) - 1000.;
    recdev_adj(2) = styr - nages;
    recdev_adj(3) = recdev_end;
    recdev_adj(4) = double(endyr) + 1.;
    recdev_adj(5) = 1.0;
    recdev_cycle = 0;
    recdev_LO = -5;
    recdev_HI = 5;
    recdev_read = 0;
  }
  
  recdev_early_start = recdev_early_start_rd;
  
  if (do_recdev == 0)
  {
    recdev_PH_rd = -3;
    recdev_early_PH_rd = -4;
    Fcast_recr_PH_rd = -4;
  }
  if (recdev_adv > 0)
  {
    echoinput << "#_start of advanced SR options" << endl;
  }
  else
  {
    echoinput << "# advanced options not read;  defaults displayed below" << endl;
  }
  
  echoinput << recdev_early_start_rd << " #_recdev_early_start (0=none; neg value makes relative to recdev_start)" << endl;
  echoinput << recdev_early_PH_rd << " #_recdev_early_phase" << endl;
  echoinput << Fcast_recr_PH_rd << " #_forecast_recruitment phase (incl. late recr) (0 value resets to maxphase+1)" << endl;
  echoinput << Fcast_recr_lambda << " #_lambda for Fcast_recr_like occurring before endyr+1" << endl;
  if (Fcast_Loop_Control(3) >= 3 && Fcast_recr_PH_rd >= 0)
  {
    warnstream << "Forecast devs will be applied to mean base recruitment over range of historical years in forecast.ss";
    write_message (NOTE, 0);
  }
  if (Do_Impl_Error > 0 && Fcast_recr_PH_rd < 0)
  {
    warnstream << "Implementation error has null effect unless Fcast_recr_PH is >=0";
    write_message (WARN, 0);
  }
  echoinput << recdev_adj(1) << " #_last_early_yr_nobias_adj_in_MPD" << endl;
  echoinput << recdev_adj(2) << " #_first_yr_fullbias_adj_in_MPD" << endl;
  echoinput << recdev_adj(3) << " #_last_yr_fullbias_adj_in_MPD" << endl;
  echoinput << recdev_adj(4) << " #_first_recent_yr_nobias_adj_in_MPD" << endl;
  echoinput << recdev_adj(5) << " #_max_bias_adj_in_MPD" << endl;
  echoinput << " #_NOTE: biasadjustment forced to 0.0 after year recdev_end" << endl;
  echoinput << recdev_cycle << " # period of cycle in recruitment " << endl;
  echoinput << recdev_LO << " #min rec_dev" << endl;
  echoinput << recdev_HI << " #max rec_dev" << endl;
  echoinput << recdev_read << " #_read_recdevs" << endl;
  echoinput << "#_end of advanced SR options" << endl;
  
  //  SS_Label_Info_4.6.3 #Create parm labels for recruitment cycle parameters
  if (recdev_cycle > 0)
  {
    for (y = 1; y <= recdev_cycle; y++)
    {
      ParCount++;
      sprintf(onenum, "%d", y);
      ParmLabel += "RecrDev_Cycle_" + onenum + CRLF(1);
    }
  }
  
  //  SS_Label_Info_4.6.4 #Setup recruitment deviations and create parm labels for each year
  if (recdev_end > retro_yr)
  {
    warnstream << " last main recdev: " << recdev_end << " to retro_yr: " << retro_yr << " reset ";
    write_message (ADJUST, 0);
    recdev_end = retro_yr;
  }
//  if (recdev_end < endyr && (Fcast_Loop_Control(3) == 3 || Fcast_Loop_Control(3) == 4))
//  {
//    warnstream << "Fcast recr option is 3 or 4 and recdev_end: " << recdev_end << " < endyr: " << endyr << " reset ";
//    write_message (ADJUST, 0);
//    recdev_end = endyr;
//  }
  if (recdev_start < (styr - nages))
  {
    warnstream << " recdev_start: " << recdev_start << " < styr-nages: " << styr - nages << " reset ";
    write_message (ADJUST, 0);
    recdev_start = styr - nages;
  }
  recdev_first = recdev_start; // stores first recdev, whether from the early period or the standard dev period
  
  if (recdev_early_start >= recdev_start)
  {
    warnstream << "Cannot set recdev_early_start: " << recdev_early_start << " after main recdev start: " << recdev_start;
    write_message (FATAL, 0); // EXIT!
  }
  else if (recdev_early_start == 0) // do not do early rec devs
  {
    recdev_do_early = 0;
    recdev_early_end = -1;
    if (recdev_early_PH_rd > 0) recdev_early_PH_rd = -recdev_early_PH_rd;
  }
  else
  {
    if (recdev_early_start < 0) recdev_early_start += recdev_start; // do relative to start of recdevs
    recdev_do_early = 1;
    if (recdev_early_start < (styr - nages))
    {
      recdev_early_start = styr - nages;
      warnstream << "Adjusting recdev_early to: " << recdev_early_start;
      write_message (ADJUST, 0);
    }
    if (recdev_start - recdev_early_start < 6)
    {
      warnstream << "Are you sure you want so few early recrdevs? Better to include in range of main recdevs " << recdev_start - recdev_early_start;
      write_message (SUGGEST, 0);
    }
  
    recdev_first = recdev_early_start; // because this is before recdev_start
    recdev_early_end = recdev_start - 1;
    for (y = recdev_early_start; y <= recdev_early_end; y++)
    {
      ParCount++;
      recdev_doit(y) = 1;
      if (y >= styr)
      {
        sprintf(onenum, "%d", y);
        ParmLabel += "Early_RecrDev_" + onenum + CRLF(1);
      }
      else
      {
        onenum = "    ";
        sprintf(onenum, "%d", styr - y);
        ParmLabel += "Early_InitAge_" + onenum + CRLF(1);
      }
    }
  }
  
  if (do_recdev > 0)
  {
    for (y = recdev_start; y <= recdev_end; y++)
    {
      ParCount++;
      recdev_doit(y) = 1;
  
      if (y >= styr)
      {
        sprintf(onenum, "%d", y);
        ParmLabel += "Main_RecrDev_" + onenum + CRLF(1);
      }
      else
      {
        onenum = "    ";
        sprintf(onenum, "%d", styr - y);
        ParmLabel += "Main_InitAge_" + onenum + CRLF(1);
      }
    }
  }

    if (int(Fcast_Loop_Control(3)) >= 4 && Fcast_Rec_yr2 > recdev_end)
  {
    warnstream << " last year of averaging for mean forecast recr must be <= last main recdev" << Fcast_Rec_yr2 << " > " << recdev_end;
    write_message(FATAL, 1);
  }

  if (Do_Forecast > 0)
  {
    if (do_recdev != 0) {
      for (y = recdev_end + 1; y <= YrMax; y++)
      {
        recdev_doit(y) = 1;
        sprintf(onenum, "%d", y);
        ParCount++;
        if (y > endyr)
        {
          ParmLabel += "ForeRecr_" + onenum + CRLF(1);
        }
        else
        {
          ParmLabel += "Late_RecrDev_" + onenum + CRLF(1);
        }
      }
    }
  
    if (Do_Impl_Error > 0) {
      for (y = endyr + 1; y <= YrMax; y++)
      {
        sprintf(onenum, "%d", y);
        ParCount++;
        ParmLabel += "Impl_err_" + onenum + CRLF(1);
      }
    }

    // check recdev start and end against survey year start and end
    for (f = 1; f <=Nfleet; f++) {
      if (Svy_units(f) == 31 || Svy_units(f) == 32 || Svy_units(f) == 33 || Svy_units(f) == 36) { //  select just recruitment surveys
        if (Svy_styr(f) < recdev_first) {
          warnstream << "Recruitment survey: " << f << " has data in: " << Svy_styr(f) << ", which is before first early recdev: " << recdev_first << ". Suggest start recdevs earlier";
          write_message (SUGGEST, 0);
        }
        if (Svy_endyr(f) > recdev_end && Fcast_recr_PH_rd <=0 ) {
          warnstream << "Recruitment survey: " << f << " has data in: " << Svy_endyr(f) << ", which is after last main recdev: " << recdev_end << ". Suggest extend recdev_end, or use pos. phase for fore_recruitments: " << Fcast_recr_PH_rd;
          write_message (SUGGEST, 0);
        }
      }
    }

  }
  
  biasadj_full.initialize();
  if (recdev_adj(5) == -1) //  all years with estimated recruitments
  {
    biasadj_full = recdev_doit;
  }
  else if (recdev_adj(5) == -2) //  no ramp
  {
    biasadj_full(recdev_first, endyr) = recdev_doit(recdev_first, endyr);
  }
  else if (recdev_adj(5) == -3) //  all to 0.0
  {
    biasadj_full = 0.0;
  }
  else
  { //  do ramp
    for (y = styr - nages; y <= YrMax; y++)
    {
      if (y < recdev_first) // before start of recrdevs
      {
        biasadj_full(y) = 0.;
      }
      else if (y <= recdev_adj(1))
      {
        biasadj_full(y) = 0.;
      }
      else if (y <= recdev_adj(2))
      {
        biasadj_full(y) = (y - recdev_adj(1)) / (recdev_adj(2) - recdev_adj(1)) * recdev_adj(5);
      }
      else if (y <= recdev_adj(3))
      {
        biasadj_full(y) = recdev_adj(5);
      } // max bias adjustment
      else if (y <= recdev_adj(4))
      {
        biasadj_full(y) = recdev_adj(5) - (y - recdev_adj(3)) / (recdev_adj(4) - recdev_adj(3)) * recdev_adj(5);
      }
      else
      {
        biasadj_full(y) = 0.;
      }
      if (y > endyr) {
        biasadj_full(y) = 0.0;
      }
    }
  }
  echoinput << "#_recruitment bias adjustment" << endl
            << biasadj_full << endl;
  ;
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.6.5 #Read recdev_cycle parameters and input recruitment deviations if needed
  init_matrix recdev_cycle_parm_RD(1,recdev_cycle,1,14);
!!k=1;
!!if(recdev_cycle>0) k=recdev_cycle;
  vector recdev_cycle_LO(1,k);
  vector recdev_cycle_HI(1,k);
  ivector recdev_cycle_PH(1,k);
!!if(recdev_cycle>0) echoinput<<"recruitment cycle input "<<endl<<recdev_cycle_parm_RD<<endl;

  init_matrix recdev_input(1,recdev_read,1,2);
!!if(recdev_read>0) echoinput<<"recruitment deviation input "<<endl<<recdev_input<<endl;

!!//  SS_Label_Info_4.7 #Input F_method setup
  init_number F_ballpark
!! echoinput<<F_ballpark<<" F ballpark is annual F, as specified in F_reporting, for a specified year"<<endl;
  init_int F_ballpark_yr
!! echoinput<<F_ballpark_yr<<" F_ballpark_yr (<0 to ignore)  "<<endl;

  int y1;
// array definitions related to F;  F_rate; Fparm; Hrate
  vector F_parm_intval(1,Nfleet);  //  initial value for F_parm when not using hybrid for early phases
  matrix F_setup2(1,1,1,1)  // later redimensioned to contain the F_detailed setup
  int F_detail;  // number of specific initial values and phases to read
  ivector F_Method_PH(1,Nfleet);  // phase to transition from hybrid to parameter, then used to setup F_PH_time
  imatrix F_PH_time(0,Nfleet,styr,TimeMax+nseas);  // stores Phase to transition from hybrid to parameters; -1 means keep input parameter; 99 means stay as hybrid
  int F_Tune;
  int F_Method;           // 1=Pope's; 2=continuous F; 3=hybrid; 4=fleet-specific
  number max_harvest_rate
  number Equ_F_joiner

  int N_Fparm
  int Fparm_start  //  location in parameter list for first Fparm
  imatrix do_Fparm_loc(1,Nfleet,styr-nseas,TimeMax+nseas);  // location in F_rate vector of this fleet x time F; location defined even for hybrid
//  vector<ivector>Fparm_loc[]  in global: holds f,t for each element of F_rate vector
  ivector Fparm_PH_dim(1,1);  //  will be redimensioned in param section to (1,N_Fparm)
  // the ivector Fparm_PH_dim is populated from the std::vector<int> Fparm_PH defined in global;
  //  then used to set phase to each F_rate in the parameter vector
  //  defining F_rate as number_vector allows for phase of elements in F_rate parameter vector to be element specific
  // in ss_param:  init_bounded_number_vector F_rate(1,k,0.,max_harvest_rate,Fparm_PH_dim)


 LOCAL_CALCS
  // clang-format on
  Equ_F_joiner = 10; //  defaults
  F_detail = -1;
  F_Tune = 3;
  F_parm_intval = 0.05; //  fill vector

  F_Method_PH = 99; //  default is to stay in hybrid
  F_PH_time.initialize();
  F_PH_time = 99; // so hybrid unless changed
  
  *(ad_comm::global_datafile) >> F_Method;
  echoinput << F_Method << " F_Method as read" << endl;
  if (F_Method < 1 || F_Method > 5)
  {
    warnstream << "F_Method must be 1 or 2 or 3 or 4, value is: " << F_Method;
    write_message (FATAL, 0); // EXIT!
  }
  
  *(ad_comm::global_datafile) >> max_harvest_rate;
  echoinput << max_harvest_rate << " max_harvest_rate " << endl;
  if (F_Method == 1)  //  Pope's
  {
    if (max_harvest_rate > 0.999)
    {
      warnstream << "Max harvest rate must  be <1.0 for F_method 1 " << max_harvest_rate;
      write_message (FATAL, 0); // EXIT!
    }
    if (max_harvest_rate <= 0.30)
    {
      warnstream << "Unexpectedly small value for max harvest rate for F_method 1:  " << max_harvest_rate;
      write_message (NOTE, 0);
    }
    Equ_F_joiner = (log(1. / max_harvest_rate - 1.)) / (max_harvest_rate - 0.2); //  used to spline the harvest rate
  }
  else  // exponential F
  {
    if (max_harvest_rate < 1.0)
    {

      warnstream << "Max harvest rate typically is >1.0 for F_method 2, 3 or 4 " << max_harvest_rate;
      write_message (NOTE, 0);
    }
    switch (F_Method)
    {
      case 2: //  F as parameter for all fleets
      {
        *(ad_comm::global_datafile) >> F_parm_intval(1);
        *(ad_comm ::global_datafile) >> F_Method_PH(1);  // phase to switch from hybrid to parameters
        *(ad_comm::global_datafile) >> F_detail;
        F_parm_intval = F_parm_intval(1); //  copy to rest of fleets
        F_Method_PH = F_Method_PH(1); //  copy to rest of fleets
        F_Tune = 4;
        echoinput << F_parm_intval << " starting F value when not starting from hybrid " << endl;
        echoinput << F_Method_PH(1) << " Phase to switch from hybrid to parameter " << endl;
        echoinput << F_detail << " N_detailed Fsetups to read (later -1 in yr field fills remaining years for that fleet)" << endl;
        if (F_detail > 0) {
          F_setup2.deallocate();
          F_setup2.allocate(1, F_detail, 1, 6); // fleet, yr, seas, Fvalue, se, phase
          *(ad_comm::global_datafile) >> F_setup2;  // reads whole table; will be processed later
          echoinput << " detailed F_setups " << endl
                    << F_setup2 << endl;
          //  add some checks to be sure that a -year record has been read for each fleet with fleet_type<=2
        }
        break;
      }
      case 3: //  hybrid for all fleets
      {
        F_Method_PH = 99;  // never switch to parameters
        *(ad_comm::global_datafile) >> F_Tune;
        echoinput << F_Tune << " N iterations for tuning hybrid F (typically 3-5)" << endl;
        break;
      }
      case 4: //  fleet-specific choice for hybrid vs parameters
      {
        echoinput << "read list of fleet ID, starting F, and phase to transition to parameters" << endl;
        //  each fleet starts with hybrid then switches to parameter in specified phase
        //  enter PH = 99 to not create any F parms for the listed fleet (stays in hybrid)
        //  fishing fleets not listed will use hybrid for all phases
        //  except bycatch fleets always start with parm in phase 1
        //  PH = -1 will keep starting parameter value throughout run
        F_Method_PH = 99;  // default is to stay in hybrid
        ender = 0.;
        F_detail = 0;
        int byc_count;
        byc_count = 0;
        dvector tempvec(1, 3);
        tempvec.initialize();
        F_Method_4_input.push_back(tempvec(1, 3));
        while (ender >= 0.)
        {
          dvector tempvec(1, 3);
          *(ad_comm::global_datafile) >> tempvec(1, 3);
          echoinput << tempvec << endl;
          F_Method_4_input.push_back(tempvec(1, 3));
          ender = tempvec(1);
          f = int(tempvec(1)); // fleet ID
          if (f <= Nfleet && ender > 0)
          {
            if (fleet_type(f) <= 2)
            {
              F_parm_intval(f) = tempvec(2);
              F_Method_PH(f) = tempvec(3);
              if (fleet_type(f) == 2) {
                byc_count++;
              } //  count bycatch fleets listed here to check against number in data file
            }
            else
            {
              warnstream << "cannot set FMethod for survey or predator fleet: " << f << " " << fleetname(f);
              write_message (FATAL, 0); // EXIT!
            }
          }
        }
        if (byc_count != N_bycatch)
        {
          warnstream << "Not all bycatch fleets have been included in Fparm list";
          write_message (FATAL, 0); // EXIT!
        }
        echoinput << "now read N tuning loops while in hybrid phases (2 is OK if switching to parm later, 3 OK, 4 more precise with many fleets)" << endl;
        *(ad_comm::global_datafile) >> F_Tune;
        echoinput << "hybrid tuning loops as read: " << F_Tune << endl;
        if (ender == -9998)  // flag to trigger reading F_detail for f x t specific F values
        {
          echoinput << "# now read List of fleet-time specific F related values to read; enter -Yr to fill remaining years&seasons; -999 for phase or catch_se keeps base value for the run; end that list with -1 for fleet" << endl;
          echoinput << "#Fleet Yr Seas F_value catch_se phase" << endl;

          dvector tempvec(1, 6);
          tempvec.initialize();
          F_detail_input.push_back(tempvec(1, 6));  //  fill the nasty zero row
          ender = 0.;
          F_detail = -1;
          while (ender >= 0.)
          {
            dvector tempvec(1, 6);
            *(ad_comm::global_datafile) >> tempvec(1, 6);
            echoinput << tempvec << endl;
            F_detail_input.push_back(tempvec(1, 6));
            ender = tempvec(1);
            F_detail++;
          }
          F_setup2.deallocate();
          F_setup2.allocate(1, F_detail, 1, 6); // fleet, yr, seas, Fvalue, se, phase
          for (j = 1; j <= F_detail; j++)
          {
            F_setup2(j) = F_detail_input[j];
          }
          echoinput << " detailed F_setups " << endl << F_setup2 << endl;
        }
        break;
      }
    }
  }
  // note that the F_setup2 table will be processed to fill F_PH_time after reading init_F inputs
  // code flow would be cleaner if F_setup was processed before reading and processing the init_F
  // however, for backward compatibility it is necessary to create the init_F parameters before the F parameters
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.7.1 #Read setup for init_F parameters and create init_F parameter labels
//  NEW  only read for catch fleets with positive initial equ catch
  imatrix init_F_loc(1,nseas,1,Nfleet);  // pointer to init_F parameter for each fleet
  int N_init_F;
  int N_init_F2;  //  for conversion of 3.24 to 3.30
 LOCAL_CALCS
  {
  // clang-format on
  init_F_loc.initialize();
  N_init_F = 0;
  N_init_F2 = 0;
  
    for (s = 1; s <= nseas; s++)
      for (int ff = 1; ff <= N_catchfleets(0); ff++)
      {
        f = fish_fleet_area(0, ff);
        if (obs_equ_catch(s, f) != 0.0)
        {
          N_init_F++;
          init_F_loc(s, f) = N_init_F;
        }
        N_init_F2 = N_init_F;
      }
  }
  // clang-format off
 END_CALCS
!! echoinput<<" ready to read init_F setup for: "<<N_init_F<<" fleet x season with initial equilibrium catch"<<endl;
  init_matrix init_F_parm_1(1,N_init_F,1,7)
!! echoinput<<" initial equil F parameter setup"<<endl<<init_F_parm_1<<endl;
  vector init_F_LO(1,N_init_F)
  vector init_F_HI(1,N_init_F)
  vector init_F_RD(1,N_init_F)
  vector init_F_PR(1,N_init_F)
  vector init_F_PRtype(1,N_init_F)
  vector init_F_CV(1,N_init_F)
  ivector init_F_PH(1,N_init_F)

 LOCAL_CALCS
  // clang-format on
  if (N_init_F > 0)
  {
    init_F_LO = column(init_F_parm_1, 1);
    init_F_HI = column(init_F_parm_1, 2);
    init_F_RD = column(init_F_parm_1, 3);
    init_F_PR = column(init_F_parm_1, 4);
    init_F_CV = column(init_F_parm_1, 5);
    init_F_PRtype = column(init_F_parm_1, 6);
    init_F_PH = ivector(column(init_F_parm_1, 7));
  
    k = nseas;
  
    for (s = 1; s <= k; s++)
      for (int ff = 1; ff <= N_catchfleets(0); ff++)
      {
        f = fish_fleet_area(0, ff);
        if (init_F_loc(s, f) > 0)
        {
          ParCount++;
          ParmLabel += "InitF_seas_" + NumLbl(s) + "_flt_" + NumLbl(f) + fleetname(f);
          j = init_F_loc(s, f);
          if (obs_equ_catch(s, f) <= 0.0)
          {
            if (init_F_RD(j) > 0.0)
            {
              warnstream << f << " catch: " << obs_equ_catch(s, f) << " initF: " << init_F_RD(j) << " initF is reset to be 0.0";
              write_message (ADJUST, 0);
            }
            init_F_RD(j) = 0.0;
            init_F_PH(j) = -1;
          }
          if (obs_equ_catch(s, f) > 0.0 && init_F_RD(j) <= 0.0)
          {
            warnstream << f << " catch: " << obs_equ_catch(s, f) << " initF: " << init_F_RD(j) << " initF must be >0";
            write_message (FATAL, 0); // EXIT!
          }
        }
      }
  }  //  end processing init_F parameters

  {  //  begin processing F_setup to create the F parameters
    do_Fparm_loc.initialize();    // location in Fparm vector of this fleet x time F; location defined even for hybrid
  
    Fparm_start = ParCount;  //  beginning of Fparms in total parameter list for tracking of parameter labels
    N_Fparm = 0;
  
    ivector tempin(1, 2);
    tempin.initialize();
    Fparm_loc.push_back(tempin(1, 2));
    Fparm_PH.push_back(0);
  
    if (F_Method == 1 || F_Method == 3) //  no F parameters
    {
      for (int ff = 1; ff <= N_catchfleets(0); ff++)
      {
        f = fish_fleet_area(0, ff);
        if (fleet_type(f) == 2)  //  bycatch
        {
          warnstream << " cannot use Fmethod 1 or 3 for bycatch fleet: " << f << " " << fleetname(f);
          write_message (FATAL, 0); // EXIT!
        }
        else if (fleet_type(f) >= 3) //  survey fleet or predator
        {
          // F_PH_time(f) not used;
        }
        else //  fleet_type = 1
        {
          for(t = styr; t<= TimeMax+nseas; t++)
          {
            if(catch_ret_obs(f,t) > 0) 
            {
              F_PH_time(f,t) = 99;  //  so never (e.g. PH 99) switch to parameters because Fmethod == 3
            }
            else
            {
              F_PH_time(f,t) = -1;  //  no catch, so no F needed
            }
          }
        }
      }
    }
    else //  need F parameters for Fmethod 2 and 4
    {
      for (int ff = 1; ff <= N_catchfleets(0); ff++)
      {
        f = fish_fleet_area(0, ff);
        if (fleet_type(f) >= 3) //  survey fleet or predator
        {
          //  bypass because F not used for survey or predators 
        }
        else  // fleet_type is 1 or 2
        {
          echoinput << " creating parms for fleet " << f << " "<<F_Method_PH(f)<<endl;
          for (y = styr; y <= endyr; y++)
          for (s = 1; s <= nseas; s++)
          {
            t = styr + (y - styr) * nseas + s - 1;
            if (catch_ret_obs(f, t) > 0.)
            {
              if (F_Method_PH(f) < 0) F_PH_time(f, t) = -1; //  parameter will be fixed F
              if (fleet_type(f) == 2)
              {
                F_PH_time(f, t) = 1;  //  begin in phase 1 for a bycatch fleet
                // note:  catch_ret_obs for bycatch fleet is needed as a trigger to create an F, it is not used as an observation
              }
              else
              {
                if (F_Method_PH(f) > 0 && F_Method_PH(f) <= 99) F_PH_time(f, t) = F_Method_PH(f); //  for later phases
              }
              N_Fparm++;
              ivector tempin(1, 2);
              tempin(1) = f;
              tempin(2) = t;
              Fparm_loc.push_back(tempin(1, 2));  //  stores the f, t for each Fparm
              Fparm_PH.push_back(F_PH_time(f, t));  //  stores PH in vector for dimensioning Fparm later
              do_Fparm_loc(f, t) = N_Fparm;  // stores parameter count for this f, t location
              sprintf(onenum, "%d", y);
              ParCount++;
              ParmLabel += "F_fleet_" + NumLbl(f) + "_YR_" + onenum + "_s_" + NumLbl(s) + CRLF(1);
            }
            else
            {
              F_PH_time(f, t) = -1;
            }
            
          }
        }
      }
      echoinput << "N F parameters " << N_Fparm << endl;
      echoinput << "Phase for each f, t: " << endl << F_PH_time << endl;
    }
  
    if (F_detail > 0)
    {
      for (k = 1; k <= F_detail; k++)
      {
        f = F_setup2(k, 1);
        y = F_setup2(k, 2);
        s = F_setup2(k, 3);
        if (y > 0)
        {
          y1 = y;
          y2 = y;
        }
        else
        {
          y1 = -y;
          y2 = endyr;
        }
        echoinput << "detailed F setup #: " << k << ":  " << F_setup2(k) << endl;
        for (y = y1; y <= y2; y++)
        for (s = 1; s <= nseas; s++)
        {
          t = styr + (y - styr) * nseas + s - 1;
          j = do_Fparm_loc(f, t);  //  get index in the Fparm vector
          if (j > 0 && F_setup2(k, 6) != -999) {
            Fparm_PH[j] = F_setup2(k,6);    // phase for each F_rate parameter
            F_PH_time(f,t) = F_setup2(k,6);
          }
          if (j > 0 && F_setup2(k, 5) != -999) catch_se(t, f) = F_setup2(k, 5); //    reset the se for this observation
        }
        //  setup of F_rate values occurs later in the prelim calc section
      }
      echoinput << "After F_detail:  Phase for each f, t: " << endl << F_PH_time << endl;
    }
  
    //  all fleets that use parm approach will do so in PH=1
    // find whether any fleet is hybrid for each phases
    for (y = styr; y <= endyr; y++)
    for (s = 1; s <= nseas; s++)
    {
      t = styr + (y - styr) * nseas + s - 1;
      for (int ff = 1; ff <= N_catchfleets(0); ff++)
      {
        f = fish_fleet_area(0, ff);
        if (F_PH_time(f, t) < 99 && readparfile == 1) //  fleet ends up using parm approach
        {
          F_PH_time(f,t) = 1; //  so start with parm in phase 1 because using parm
        }
        if (F_PH_time(f, t) == 99) F_PH_time(0, t) = 99;  //  if one fleet is hybrid in phase, then set flag for hybrid
      }
    }
    echoinput << f << "  Overall F_PH_time:  " << F_PH_time(0) << endl;
  }
  // clang-format off
 END_CALCS

//  SS_Label_Info_4.8 #Read catchability (Q) setup
  imatrix Q_setup(1,Nfleet,1,5)
  ivector Q_setup_check(1,Nfleet)
  imatrix Q_setup_parms(1,Nfleet,1,5)  //  index of first parameter for:  1=base q with link;  2=extrastd; 3=env; 4=block/trend; 5=dev;
  int parm330_cnt
  int Q_Npar2
  int Q_Npar
  int firstQparm;
  int timevary_parm_cnt_Q;
  int timevary_parm_start_Q;
  int depletion_fleet;  //  stores fleet(survey) number for the fleet that is defined as "depletion" by survey type=34
  int depletion_type;  //  entered by Q_setup(f,2) and stores additional controls for depletion fleet

 LOCAL_CALCS
  // clang-format on
  firstQparm = 0;
  timevary_parm_cnt_Q = 0;
  timevary_parm_start_Q = 0;

  depletion_fleet = 0;
  depletion_type = 0;
  
  //Q_setup for 3.30
  // 1:  link type
  // 2:  extra input for link, i.e. mirror fleet or dev_vector index associated with survey
  // 3:  0/1 to select extra sd parameter
  // 4:  0/1 for biasadj or not
  // 5:  0/1 to float
  
  //  read setup and get the parameter count
  echoinput << "# read Q setup only for fleets with survey/CPUE/effort observations, end with fleet_ID<0 " << endl
            << "#  fleet_ID link_type link_info  extra_se(0/1)   biasadj(0/1)  float(0/1)" << endl;
  firstQparm = ParCount; //  base index before adding Q parms
  Q_setup.initialize();
  Q_setup_parms.initialize();
  Q_Npar = 0;
  Q_setup_check.initialize();
  j = 1;
  do
  {
    *(ad_comm::global_datafile) >> j;
    if (j > 0)
    {
      *(ad_comm::global_datafile) >> Q_setup(j);
      Q_setup_check(j) = 1;
    }
    else
    {
      *(ad_comm::global_datafile) >> tempvec(1, 5);
    }
  } while (j > 0);
  echoinput << "Q setup " << endl
            << "Note: control file should only contain rows for fleets with index observations" << endl
            << "      but setup is reported here as one row for each fleet (with no fleet column)" << endl
            << Q_setup << endl;
  
  //  get base parameter count
  for (f = 1; f <= Nfleet; f++)
  {
    if (Svy_N_fleet(f) > 0)
    {
      if (Q_setup_check(f) == 0)
      {
        warnstream << "Q setup;  survey obs exist for fleet " << f << " but no Q setup was read ";
        write_message (FATAL, 0); // EXIT!
      }
      Q_Npar++;
      ParCount++;
      Q_setup_parms(f, 1) = Q_Npar; //  first parameter index for this fleet that has obs so needs a Q
      if (Svy_errtype(f) == -1)
      {
        ParmLabel += "Q_base_" + fleetname(f) + "(" + NumLbl(f) + ")";
        if (Q_setup(f, 5) == 1) //  float
        {
          warnstream << "Q setup:  can't use float option with normal error distribution, fleet: " << f;
          write_message (FATAL, 0); // EXIT!
        }
      }
      else if (Svy_errtype(f) >= 0)  // lognormal or T-dist
      {
        ParmLabel += "LnQ_base_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
      if (Svy_units(f) == 35)
      {
        echoinput << "fleet: " << f << "  is a survey of dev vector:  " << Q_setup(f, 2) << endl;
        if (Q_setup(f, 2) == 0)
        {
          warnstream << "Q setup:  must enter index of dev_vector surveyed by fleet:  " << f;
          write_message (FATAL, 0); // EXIT!
        }
      }

      switch (Q_setup(f, 1))
      {
        case 1: //  simple Q
        {
          break;
        }
        case 2: //  mirror
        {
          int fmirror;
          fmirror = Q_setup(f, 2);
          if (fmirror == 0 || fmirror >= f)
          {
            warnstream << "Illegal mirror for q for fleet: " << f << " trying to mirror fleet: " << Q_setup(f, 2);
            write_message (FATAL, 0); // EXIT!
          }
          if (Q_setup(fmirror, 5) == 1)
          {
            warnstream << "Fleet: " << f << "  cannot mirror fleet that has float q: " << fmirror;
            write_message (FATAL, 0); // EXIT!
          }
          break;
        }
        case 3: //  add power
        {
          Q_Npar++;
          ParCount++;
          ParmLabel += "Q_power_" + fleetname(f) + "(" + NumLbl(f) + ")";
          break;
        }
        case 4: //  mirror with offset, where offset typically is ln(area_base/area_dependent)  ln(Q2) = ln(Q1) + ln (area1 / area2)
        {
          if (Q_setup(f, 2) == 0 || Q_setup(f, 2) >= f)
          {
            warnstream << "Illegal mirror for q for fleet: " << f << " trying to mirror fleet: " << Q_setup(f, 2);
            write_message (FATAL, 0); // EXIT!
          }
          Q_Npar++;
          ParCount++;
          ParmLabel += "Q_mirror_scale_" + fleetname(f) + "(" + NumLbl(f) + ")";
          break;
        }
        case 5: //  add offset
        {
          Q_Npar++;
          ParCount++;
          ParmLabel += "Q_offset_" + fleetname(f) + "(" + NumLbl(f) + ")";
          break;
        }
        case 6: //  add offset and power
        {
          Q_Npar++;
          ParCount++;
          ParmLabel += "Q_offset_" + fleetname(f) + "(" + NumLbl(f) + ")";
          Q_Npar++;
          ParCount++;
          ParmLabel += "Q_power_" + fleetname(f) + "(" + NumLbl(f) + ")";
          break;
        }
      }
      if (Q_setup(f, 3) > 0)
      {
        Q_Npar++;
        ParCount++;
        Q_setup_parms(f, 2) = Q_Npar;
        ParmLabel += "Q_extraSD_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
      if (Svy_units(f) == 35 || Svy_units(f) == 36)  // env index of recdev or parm dev vector
      {
        if (Q_setup(f, 1) < 5)  //  so OK for 5 and 6
        {
          warnstream << "Suggest using Q option 5 to include offset parameter for an index of deviations (type 35 or 36)";
          write_message (WARN, 0);
        }
        if (Q_setup(f, 1) == 3 || Q_setup(f,1) == 6)         
        {
          warnstream << "Power function cannot be used for an index of deviations (type 35 or 36) because of negative values";
          write_message (FATAL, 0);
        }
      }
      if (Svy_units(f) == 34) //  special code for depletion, so prepare to adjust phases and lambdas
      {
        echoinput << "# survey: " << f << " " << fleetname(f) << " is a depletion fleet" << endl;
        depletion_fleet = f;
        depletion_type = Q_setup(f, 2);
        if (depletion_type == 0)
          echoinput << "link_info=0; add 1 to phases of all parms; only R0 active in new phase 1 (same as 3.24 logic)" << endl;
        if (depletion_type == 1)
          echoinput << "link_info=1  only R0 active in phase 1; then exit;  useful for data-limited draws of other fixed parameter" << endl;
        if (depletion_type == 2)
          echoinput << "link_info=2  no phase adjustments, can be used when profiling on fixed R0" << endl;
        if (Q_setup(f, 5) == 1)
        {
          warnstream << "Change to no_float for depletion fleet # " << f << endl;
          warnstream << "++ and you must set phase to negative so not estimated";
          write_message (ADJUST, 1);
          Q_setup(f, 5) = 0;
        }
      }
    }
    else
    {
      if (Q_setup_check(f) > 0)
      {
        warnstream << " Q setup error; no survey obs for fleet " << f << " but Q setup was read ";
        write_message (FATAL, 0); // EXIT!
      }
    }
  }

  echoinput << "Q_Npar (number of long parameter lines): " << Q_Npar << endl
            << endl << "Q setup parameter index " << endl
            << "column have index of first parameter for:  1=base q with link;  2=extrastd; 3=env; 4=block/trend; 5=dev;"
            << Q_setup_parms << endl;
  // clang-format off
 END_CALCS

  init_matrix Q_parm_1(1,Q_Npar,1,14)
  ivector Qparm_timevary(1,Q_Npar) //  holds index in timevary_def used by each base parameter
  //  dimensioned to hold the extra_sd parms, but these cannot be time-varying
  imatrix timevary_Qparm(styr-3,YrMax+1,0,Nfleet) // goes to yrmax+1 to allow referencing in forecast, but only endyr+1 is checked
  // stores years to calc non-constant sel parms by fleet

 LOCAL_CALCS
      // clang-format on
      //  now create time_vary parameters
      parm330_cnt = 0; //  restart the index
  Qparm_timevary.initialize();
  timevary_Qparm.initialize();
  timevary_parm_start_Q = 0;
  timevary_parm_cnt_Q = 0;
  timevary_used = 0;
  for (f = 1; f <= Nfleet; f++)
    if (Svy_N_fleet(f) > 0)
    {
      j = Q_setup_parms(f, 1);
      echoinput << "fleet " << f << " base index " << j << endl;
      if (Q_setup(f, 5) == 1) //  float
      {
        if (Q_parm_1(j, 7) >= 0)
        {
          warnstream << "Fleet: " << f << "  SS3 changed Q to not estimate because it is set to float";
          write_message (ADJUST, 0);
          Q_parm_1(j, 7) = -1;
        }
      }
  
      //  depletion fleet check
      if (Svy_units(f) == 34) //  special code for depletion
      {
        if (Q_parm_1(j, 7) >= 0)
        {
          warnstream << "Fleet: " << f << " SS3 changed Q to not estimate because it is depletion fleet";
          write_message (ADJUST, 0);
          Q_parm_1(j, 7) = -1;
        }
      }
  
      //  check for extraSD estimation
      if (Q_setup(f, 3) > 0)
      {
        if (Q_parm_1(Q_setup_parms(f, 2), 7) > 0) varparm_estimated(3) = 1; // extraSD is estimated, so need sd_offset=1
      }
  
      if (Q_parm_1(j, 13) == 0 && Q_parm_1(j, 8) == 0 && Q_parm_1(j, 9) == 0)
      {
        //  no time-vary parameter effects
      }
      else //  set up a timevary parameter definition
      {
        timevary_used = 1;
        ivector timevary_setup(1, 14); //  temporary vector for timevary specs
        timevary_setup.initialize();
        if (timevary_parm_start_Q == 0) timevary_parm_start_Q = timevary_parm_cnt + 1;
        echoinput << endl
                  << " timevary Q for fleet: " << f << endl;
        timevary_cnt++; //  count parameters with time-vary effect
        Qparm_timevary(j) = timevary_cnt; //  base Q parameter will use this timevary specification
        timevary_setup(1) = 3; //  indicates a Q parm
        timevary_setup(2) = j; //  index of base parm within that type of parameter
        timevary_setup(13) = firstQparm + j; //  index of base parm relative to ParCount which is continuous across all types of parameters
        timevary_setup(3) = timevary_parm_cnt + 1; //  first parameter within total list of all timevary parms
        timevary_pass = column(timevary_Qparm, f); // year vector for this fleet
        //  set up env link info
        echoinput << " check for env " << Q_parm_1(j, 8) << endl;
  
        k = int(abs(Q_parm_1(j, 8)) / 100); //  find the env link code
        timevary_setup(6) = k; //  link code for env
        if (Q_parm_1(j, 8) > 0) //  env variable used
        {
          timevary_setup(7) = int(abs(Q_parm_1(j, 8))) - k * 100;
          k = timevary_setup(7);
          //         for(y=styr-1;y<=YrMax;y++) env_data_pass(y)=env_data_RD(y,k);
          env_data_pass(1) = env_data_minyr(k);
          env_data_pass(2) = env_data_maxyr(k);
        }
        else if (abs(Q_parm_1(j, 8) > 0)) //  density-dependence
        {
          timevary_setup(7) = -int(abs(Q_parm_1(j, 8)) - k * 100);
          do_densitydependent = 1;
          k = 0;
          env_data_pass.initialize();
        }
  
        if (Q_parm_1(j, 13) > 0) //  doing blocks
        {
          if (Q_parm_1(j, 13) > N_Block_Designs)
          {
            warnstream << "Q block request exceeds N_block patterns" ;
            write_message (FATAL, 0); // EXIT!
          }
          create_timevary(Q_parm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, Block_Design(Q_parm_1(j, 13)), env_data_pass, N_parm_dev, finish_starter);
        }
        else
        {
          create_timevary(Q_parm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), f, block_design_null, env_data_pass, N_parm_dev, finish_starter);
        }
        timevary_def.push_back(timevary_setup(1, 14));
        for (y = styr - 3; y <= YrMax + 1; y++) {
          timevary_Qparm(y, f) = timevary_pass(y);
        } // year vector for this category og MGparm
      }
    }
  
  Q_Npar2 = Q_Npar;
  if (timevary_parm_start_Q > 0)
  {
    if (timevary_used == 1) autogen_timevary(3) = 1; //  indicate that some parameter is time-varying
    timevary_parm_cnt_Q = timevary_parm_cnt;
    Q_Npar2 += (timevary_parm_cnt_Q - timevary_parm_start_Q + 1);
    echoinput << "Q  uses timevary parms:  " << Qparm_timevary << endl;
    echoinput << " Q  timevary_parm_cnt start and end " << timevary_parm_start_Q << " " << timevary_parm_cnt_Q << endl;
  }
  echoinput << "Q_Npar (long lines) and Q_Npar2 (long + short lines):  " << Q_Npar << " " << Q_Npar2 << endl;
  // clang-format off
 END_CALCS

  vector Q_parm_LO(1,Q_Npar2)
  vector Q_parm_HI(1,Q_Npar2)
  vector Q_parm_RD(1,Q_Npar2)
  vector Q_parm_PR(1,Q_Npar2)
  ivector Q_parm_PRtype(1,Q_Npar2)
  vector Q_parm_CV(1,Q_Npar2)
  ivector Q_parm_PH(1,Q_Npar2)

 LOCAL_CALCS
      // clang-format on
      if (Q_Npar2 == 0)
  {
    Q_parm_LO = -1.;
    Q_parm_HI = 1.;
    Q_parm_PH = -4;
  }
  else
  {
    for (i = 1; i <= Q_Npar; i++)
    {
      Q_parm_LO(i) = Q_parm_1(i, 1);
      Q_parm_HI(i) = Q_parm_1(i, 2);
      Q_parm_RD(i) = Q_parm_1(i, 3);
      Q_parm_PR(i) = Q_parm_1(i, 4);
      Q_parm_CV(i) = Q_parm_1(i, 5);
      Q_parm_PRtype(i) = Q_parm_1(i, 6);
      Q_parm_PH(i) = Q_parm_1(i, 7);
    }
    if (timevary_parm_start_Q > 0)
    {
      j = Q_Npar;
      for (f = timevary_parm_start_Q; f <= timevary_parm_cnt_Q; f++)
      {
        j++;
        echoinput << f << " " << j << " " << timevary_parm_rd[f] << endl;
        Q_parm_LO(j) = timevary_parm_rd[f](1);
        Q_parm_HI(j) = timevary_parm_rd[f](2);
        Q_parm_RD(j) = timevary_parm_rd[f](3);
        Q_parm_PR(j) = timevary_parm_rd[f](4);
        Q_parm_PRtype(j) = timevary_parm_rd[f](6);
        Q_parm_CV(j) = timevary_parm_rd[f](5);
        Q_parm_PH(j) = timevary_parm_rd[f](7);
      }
    }
  }
  echoinput << "Q_parm_RD: " << endl;
  for (z = 1; z <= Q_Npar2; z++)
    echoinput << z << " " << Q_parm_RD(z) << " " << ParmLabel(ParCount - Q_Npar2 + z) << endl;
  echoinput << "#" << endl;
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.9 #Define Selectivity patterns and N parameters needed per pattern
  ivector seltype_Nparam(0,50)
 LOCAL_CALCS
   // clang-format on
   seltype_Nparam(0) = 0; // selex=1.0 for all sizes
  seltype_Nparam(1) = 2; // logistic; with 95% width specification
  seltype_Nparam(2) = 6; // test version of double normal (24)
  seltype_Nparam(3) = 6; // flat middle, power up, power down
  seltype_Nparam(4) = 0; // set size selex=female maturity
  seltype_Nparam(5) = 2; // mirror another selex; PARMS pick the min-max bin to mirror
  seltype_Nparam(6) = 2; // non-parm len selex, additional parm count is in seltype(f,4)
  seltype_Nparam(7) = 8; // New doublelogistic with smooth transitions and constant above Linf option
  seltype_Nparam(8) = 8; // New doublelogistic with smooth transitions and constant above Linf option
  seltype_Nparam(9) = 6; // simple 4-parm double logistic with starting length; parm 5 is first length; parm 6=1 does desc as offset
  
  seltype_Nparam(10) = 0; //  First age-selex  selex=1.0 for all ages
  seltype_Nparam(11) = 2; //  pick min-max age
  seltype_Nparam(12) = 2; //   logistic
  seltype_Nparam(13) = 8; //   double logistic
  seltype_Nparam(14) = nages + 1; //   empirical
  seltype_Nparam(15) = 0; //   mirror another selex
  seltype_Nparam(16) = 2; //   Coleraine - Gaussian
  seltype_Nparam(17) = nages + 1; //   empirical as random walk  N parameters to read can be overridden by setting special to non-zero
  seltype_Nparam(18) = 8; //   double logistic - smooth transition
  seltype_Nparam(19) = 6; //   simple 4-parm double logistic with starting age
  seltype_Nparam(20) = 6; //   double_normal,using joiners
  
  seltype_Nparam(21) = 2; // non-parm len selex, additional parm count is in seltype(f,4), read as pairs of size, then selex
  seltype_Nparam(22) = 4; //   double_normal as in CASAL
  seltype_Nparam(23) = 6; //   double_normal where final value is directly equal to sp(6) so can be >1.0
  seltype_Nparam(24) = 6; //   double_normal with sel(minL) and sel(maxL), using joiners
  seltype_Nparam(25) = 3; //   exponential-logistic in size
  seltype_Nparam(26) = 3; //   exponential-logistic in age
  seltype_Nparam(27) = 3; // cubic spline for selex at length, additional parm count is in seltype(f,4)
  //   seltype_Nparam(28)=3;   // cubic spline for selex at age, additional parm count is in seltype(f,4)
  seltype_Nparam(29) = 0; //   undefined
  
  seltype_Nparam(41) = 2 + seltype_Nparam(17); // like 17, with 2 additional parameters for scaling (average over bin range)
  seltype_Nparam(42) = 2 + seltype_Nparam(27); // like 27, with 2 additional parameters for scaling (average over bin range)
  seltype_Nparam(43) = seltype_Nparam(6); // like 6, with 2 additional parameters for scaling (average over bin range)
  seltype_Nparam(44) = 4; // like 17 for two sexes with male selectivity as separate parameters
  seltype_Nparam(45) = 4; // like 14 for two sexes with male selectivity as separate parameters
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.9.1 #Read selectivity definitions
//  do 2*Nfleet to create options for size-selex (first), then age-selex
  init_imatrix seltype_rd(1,2*Nfleet,1,4)    // read selex type for each fleet/survey, retention option, male_offset_option, special
  imatrix seltype(1,2*Nfleet,1,4)    // read selex type for each fleet/survey, retention option, male_offset_option, special

  int N_selparm   // figure out the Total number of selex parameters
  int N_selparm3                 // N selparms plus timevary parms
  int N_selparm2                 // N selparms plus timevary parms and 2D_AR1 parms
  ivector N_selparmvec(1,2*Nfleet)  //  N selparms by type, including extra parms for male selex, retention, etc.
  ivector Maleselparm(1,2*Nfleet)
  ivector RetainParm(1,Nfleet)  //  can only have length or age retention, not both for a fleet
  ivector dolen(1,Nfleet)
  int blkparm
  int firstselparm
  ivector N_ret_parm(0,6)  //  6 possible retention functions allowed
  ivector N_disc_mort_parm(0,6)  //  6 possible discard mortality functions allowed
  ivector Do_Retain(1,Nfleet)  // indicates 0=none, 1=length based, 2=age based
  ivector Min_selage(1,Nfleet) //  minimum selected age
  imatrix Comp_Err_parmloc(1,Comp_Err_ParmCount,1,2);  //  for each comp_err_index, locate starting parameter in parcount (2) and in Selparm (1).

 LOCAL_CALCS
      // clang-format on
      echoinput
      << " selex types " << endl
      << seltype_rd << endl;
  
  //  identify fleets with adjusted first_selected age
  seltype = seltype_rd; //  set matrices to be same
  Min_selage.initialize();
  for (f = 1; f <= 2 * Nfleet; f++)
  {
    echoinput << f << " " << seltype_rd(f, 1) << endl;
    if (seltype_rd(f, 1) >= 100)
    {
      if (f <= Nfleet)
      {
        warnstream << "Fleet: " << f << "  cannot use >100 code for length selectivity; SS3 will correct";
        write_message (ADJUST, 0);
        j = int(seltype(f, 1) / 100);
        k = seltype(f, 1) - 100 * j;
        seltype_rd(f, 1) = k; //  change input value so will be written correctly in ss_new
        seltype(f, 1) = seltype_rd(f, 1);
      }
      else
      {
        Min_selage(f - Nfleet) = int(seltype(f, 1) / 100);
        k = seltype(f, 1) - 100 * Min_selage(f - Nfleet);
        echoinput << seltype(f, 1) << " " << k << " " << Min_selage(f - Nfleet) << endl;
        if (k == 12 || k == 13 || k == 14 || k == 16 || k == 18 || k == 26 || k == 27)
        {
          echoinput << "OK to use min_selage for selex pattern: " << k << " for fleet: " << f - Nfleet << endl;
        }
        else if (k == 17 || k == 44 || k == 45)
        {
          warnstream << "Don't use min_selage for age selectivity: " << k << " for fleet: " << f - Nfleet << " because separate control exists; SS3 will correct";
          write_message (ADJUST, 0);
          seltype_rd(f, 1) = k;
        } //  change input value so will be written correctly in ss_new
        else if (k == 19)
        {
          warnstream << "Can't use min_selage for age selectivity: " << k << " for fleet: " << f - Nfleet << " because separate control sets sel = 1.0e-06 below a specified age SS3 will correct";
          write_message (ADJUST, 0);
          seltype_rd(f, 1) = k;
        }
        else if (k == 20)
        {
          warnstream << "OK to use min_selage for age selectivity: " << k << " for fleet: " << f - Nfleet << " but be aware that a separate control for parm 5 can set sel = 1.0e-06 below a specified age";
          write_message (WARN, 0);
        }
        else
        {
          echoinput << "Min_selage not implemented and not relevant for selex pattern: " << k << " for fleet: " << f - Nfleet << endl;
          seltype_rd(f, 1) = k;
        }
        seltype(f, 1) = k;
      }
    }
  }
  
  RetainParm.initialize();
  //  define number of parameters for each retention type
  N_ret_parm(0) = 0;
  N_ret_parm(1) = 4; // for asymptotic retention
  N_ret_parm(2) = 4; // for asymptotic retention and 4 param discard mort
  N_ret_parm(3) = 0; // all dead
  N_ret_parm(4) = 7; // for dome-shaped retention and 4 param discard mort
  
  //  define number of discard mortality parameters for each retention type
  N_disc_mort_parm(0) = 0;
  N_disc_mort_parm(1) = 0; // for asymptotic retention
  N_disc_mort_parm(2) = 4; // for asymptotic retention and 4 param discard mort
  N_disc_mort_parm(3) = 0; // all dead
  N_disc_mort_parm(4) = 4; // for dome-shaped retention and 4 param discard mort
  
  //  SS_Label_Info_4.9.2 #Process selectivity parameter count and create parameter labels
  firstselparm = ParCount;
  N_selparm = 0;
  //   N_ret_parm=7;    // to allow for dome-shaped retention
  Do_Retain.initialize();
  for (f = 1; f <= Nfleet; f++)
  {
    if (WTage_rd > 0 && seltype(f, 1) > 0)
    {
      warnstream << "Use of size selectivity not advised when reading empirical wt-at-age ";
      write_message (WARN, 0);
    }
    N_selparmvec(f) = seltype_Nparam(seltype(f, 1)); // N Length selex parms
    if (seltype(f, 1) == 6 || seltype(f, 1) == 43) N_selparmvec(f) += seltype(f, 4); // special setup of N parms
    if (seltype(f, 1) == 21) N_selparmvec(f) += 2 * (seltype(f, 4) - 1); // special setup of N parms
    if (seltype(f, 1) == 27) N_selparmvec(f) += 2 * seltype(f, 4); // special setup of N parms for cubic spline
    if (seltype(f, 1) == 42) N_selparmvec(f) += 2 * seltype(f, 4); // special setup of N parms for cubic spline
    if (seltype(f, 1) > 0 && Svy_units(f) < 30) {
      dolen(f) = 1;
    }
    else
    {
      dolen(f) = 0;
    }
    if (seltype(f, 1) == 15 || seltype(f, 1) == 5) // mirror
    {
      if (seltype(f, 4) == 0 || seltype(f, 4) >= f)
      {
        warnstream << "Illegal mirror for len selex fleet " << f << "trying to mirror fleet: " << seltype(f, 4);
        write_message (FATAL, 1); // EXIT!
      }
    }
    if (seltype(f, 1) == 43)
    {
      ParCount++;
      ParmLabel += "SizeSel_ScaleBinLo_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "SizeSel_ScaleBinHi_" + fleetname(f) + "(" + NumLbl(f) + ")";
      echoinput << "N parm " << N_selparmvec(f) << endl;
    }
  
    if (seltype(f, 1) == 27 || seltype(f, 1) == 42)
    {
      if (seltype(f, 1) == 42)
      {
        ParCount++;
        ParmLabel += "SizeSpline_ScaleBinLo_" + fleetname(f) + "(" + NumLbl(f) + ")";
        ParCount++;
        ParmLabel += "SizeSpline_ScaleBinHi_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
      ParCount++;
      ParmLabel += "SizeSpline_Code_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "SizeSpline_GradLo_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "SizeSpline_GradHi_" + fleetname(f) + "(" + NumLbl(f) + ")";
      for (s = 1; s <= seltype(f, 4); s++)
      {
        ParCount++;
        ParmLabel += "SizeSpline_Knot_" + NumLbl(s) + "_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
      for (s = 1; s <= seltype(f, 4); s++)
      {
        ParCount++;
        ParmLabel += "SizeSpline_Val_" + NumLbl(s) + "_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
    }
    else if (seltype(f, 1) == 24 || seltype(f, 1) == 2) //  double_normal
    {
      ParCount++;
      ParmLabel += "Size_DblN_peak_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_DblN_top_logit_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_DblN_ascend_se_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_DblN_descend_se_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_DblN_start_logit_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_DblN_end_logit_" + fleetname(f) + "(" + NumLbl(f) + ")";
    }
    else if (seltype(f, 1) == 1) //  logistic
    {
      ParCount++;
      ParmLabel += "Size_inflection_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "Size_95%width_" + fleetname(f) + "(" + NumLbl(f) + ")";
    }
    else if (seltype(f, 1) == 11)
    {
      ParCount++;
      ParmLabel += "SizeSel=1_BinLo_" + fleetname(f) + "(" + NumLbl(f) + ")";
      ParCount++;
      ParmLabel += "SizeSel=1_BinHi_" + fleetname(f) + "(" + NumLbl(f) + ")";
    }
  
    else
    {
      for (j = 1; j <= N_selparmvec(f); j++)
      {
        ParCount++;
        ParmLabel += "SizeSel_P" + NumLbl(j) + "_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
    }
  
    // account for the low and high bin parameters
    if (seltype(f, 1) == 43) N_selparmvec(f) += 2;
  
    if (seltype(f, 2) >= 1)
    {
      if (WTage_rd > 0)
      {
        warnstream << "Length-based retention will use the same empirical wtatage for discard and retained fish for fleet: " << f;
        write_message (NOTE, 0);
      }
      Do_Retain(f) = 1;
      if (fleet_type(f) == 2 && seltype(f, 2) != 3)
      {
        warnstream << "Fleet: " << f << " is a bycatch fleet, so consider using retention option =3 so no parameters needed";
        write_message (SUGGEST, 0);
      }
      if (seltype(f, 2) == 3)
      {
        RetainParm(f) = 0;
      } //  no parameters needed
      else
      {
        RetainParm(f) = N_selparmvec(f) + 1;
        //       N_selparmvec(f) +=N_ret_parm*seltype(f,2);          // N retention parms first [N_ret_parm] for retention; next [N_ret_parm] for discard mortality
        if (N_ret_parm(seltype(f, 2)) > 0)
        {
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_L_infl_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_L_width_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_L_asymptote_logit_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_L_maleoffset_" + fleetname(f) + "(" + NumLbl(f) + ")";
          if (N_ret_parm(seltype(f, 2)) == 7) //  doing dome
          {
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_L_dome_infl_" + fleetname(f) + "(" + NumLbl(f) + ")";
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_L_dome_width_" + fleetname(f) + "(" + NumLbl(f) + ")";
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_L_dome_maleoffset_" + fleetname(f) + "(" + NumLbl(f) + ")";
          }
        }
        if (seltype(f, 2) == 2 || seltype(f, 2) == 4)
        {
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_L_infl_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_L_width_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_L_level_old_" + fleetname(f) + "(" + NumLbl(f) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_L_male_offset_" + fleetname(f) + "(" + NumLbl(f) + ")";
        }
      }
    }
    else if (seltype(f, 2) < 0) //  mirror retention
    {
      Do_Retain(f) = 1;
      RetainParm(f) = 0;
    }
    if (seltype(f, 3) >= 1)
    {
      if (gender == 1)
      {
        warnstream << "Male selex cannot be used in one sex model; fleet: " << f ;
        write_message (FATAL, 1); // EXIT!
      }
      Maleselparm(f) = N_selparmvec(f) + 1;
      if (seltype(f, 3) == 1 || seltype(f, 3) == 2)
      {
        N_selparmvec(f) += 4; // add male parms
        ParCount += 4;
        ParmLabel += "SzSel_MaleDogleg_" + fleetname(f) + "(" + NumLbl(f) + ")";
        ParmLabel += "SzSel_MaleatZero_" + fleetname(f) + "(" + NumLbl(f) + ")";
        ParmLabel += "SzSel_MaleatDogleg_" + fleetname(f) + "(" + NumLbl(f) + ")";
        ParmLabel += "SzSel_MaleatMaxage_" + fleetname(f) + "(" + NumLbl(f) + ")";
      }
      else if (seltype(f, 3) >= 3)
      {
        if (seltype(f, 3) == 3) {
          anystring = "Male_";
        }
        else
        {
          anystring = "Fem_";
        }
        if (seltype(f, 1) == 1)
        {
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Infl_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Slope_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Scale_" + fleetname(f) + "(" + NumLbl(f) + ")";
        }
        else if (seltype(f, 1) == 24 || seltype(f, 1) == 2)
        {
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Peak_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Ascend_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Descend_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Final_" + fleetname(f) + "(" + NumLbl(f) + ")";
          N_selparmvec(f)++;
          ParCount++;
          ParmLabel += "SzSel_" + anystring + "Scale_" + fleetname(f) + "(" + NumLbl(f) + ")";
        }
        else
        {
          warnstream << "Illegal male selex option selected for fleet " << f ;
          write_message (FATAL, 1); // EXIT!
        }
      }
    }
  
    if (seltype(f, 1) == 7)
    {
      warnstream << "Selectivity pattern #7 is no longer supported ";
      write_message (WARN, 0);
    }
    if (seltype(f, 1) == 23 && F_Method == 1)
    {
      warnstream << "Do not use F_Method = Pope's with selex pattern #23 ";
      write_message (WARN, 0);
    }
    N_selparm += N_selparmvec(f);
  }
  for (f = Nfleet + 1; f <= 2 * Nfleet; f++)
  {
    int f1 = f - Nfleet; // actual fleet number
    if (seltype(f, 1) == 15) // mirror
    {
      if (seltype(f, 4) == 0 || seltype(f, 4) >= f1)
      {
        warnstream << "Illegal mirror for age selex fleet " << f - Nfleet;
        write_message (FATAL, 0); // EXIT!
      }
      N_selparmvec(f) = 0; // Nunber of Age selex parms
    }
    else if (seltype(f, 1) != 17 && seltype(f, 1) != 41)
    {
      N_selparmvec(f) = seltype_Nparam(seltype(f, 1)); // Nunber of Age selex parms
    }
    else if (seltype(f, 4) == 0)
    {
      N_selparmvec(f) = seltype_Nparam(seltype(f, 1)); // this is nages+1
    }
    else
    {
      N_selparmvec(f) = abs(seltype(f, 4)) + 1; // so reads value for age 0 through this age
      if (seltype(f, 1) == 41) N_selparmvec(f) +=2;  //  for the scaling parameters
    }
  
    if (seltype(f, 1) == 41)
    {
      ParCount++;
      ParmLabel += "AgeSel_ScaleAgeLo_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "AgeSel_ScaleAgeHi_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
    }
  
    if (seltype(f, 1) == 27 || seltype(f, 1) == 42)
    {
      if (seltype(f, 1) == 42)
      {
        ParCount++;
        ParmLabel += "AgeSpline_ScaleAgeLo_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        ParCount++;
        ParmLabel += "AgeSpline_ScaleAgeHi_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      }
      N_selparmvec(f) += 2 * seltype(f, 4); // special setup of N parms for cubic spline
      ParCount++;
      ParmLabel += "AgeSpline_Code_" + fleetname(f1) + "_" + NumLbl(f1);
      ParCount++;
      ParmLabel += "AgeSpline_GradLo_" + fleetname(f1) + "_" + NumLbl(f1);
      ParCount++;
      ParmLabel += "AgeSpline_GradHi_" + fleetname(f1) + "_" + NumLbl(f1);
      for (s = 1; s <= seltype(f, 4); s++)
      {
        ParCount++;
        ParmLabel += "AgeSpline_Knot_" + NumLbl(s) + "_" + fleetname(f1) + "_" + NumLbl(f1);
      }
      for (s = 1; s <= seltype(f, 4); s++)
      {
        ParCount++;
        ParmLabel += "AgeSpline_Val_" + NumLbl(s) + "_" + fleetname(f1) + "_" + NumLbl(f1);
      }
    }
    else if (seltype(f, 1) == 44)
    {
      N_selparmvec(f) = 2 + gender + gender * seltype(f, 4);
      ParCount++;
      ParmLabel += "first_selage_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "first_age_mean_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "last_age_mean_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      if (gender == 2)
      {
        ParCount++;
        ParmLabel += "Male_ln(ratio)_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "female_ln(selchange)_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "male_ln(selchange)_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
      }
      else
      {
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "ln(selchange)_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
      }
    }
    else if (seltype(f, 1) == 45)
    {
      N_selparmvec(f) = 2 + gender + gender * seltype(f, 4);
      ParCount++;
      ParmLabel += "first_selage_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "first_age_mean_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "last_age_mean_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      if (gender == 2)
      {
        ParCount++;
        ParmLabel += "Male_ln(ratio)_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "female_sel_logit_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "male_sel_logit_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
      }
      else
      {
        for (int gg = 1; gg <= seltype(f, 4); gg++)
        {
          ParCount++;
          ParmLabel += "ln(selchange)_" + NumLbl(gg) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
      }
    }
  
    else if (seltype(f, 1) == 20)
    {
      ParCount++;
      ParmLabel += "Age_DblN_peak_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_DblN_top_logit_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_DblN_ascend_se_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_DblN_descend_se_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_DblN_start_logit_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_DblN_end_logit_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
    }
    else if (seltype(f, 1) == 12)
    {
      ParCount++;
      ParmLabel += "Age_inflection_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "Age_95%width_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
    }
    else if (seltype(f, 1) == 11)
    {
      ParCount++;
      ParmLabel += "minage@sel=1_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      ParCount++;
      ParmLabel += "maxage@sel=1_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
    }
    else
    {
      
      k = 0;
      if (seltype(f, 1) == 41) k = 2;  // reduce count for the scaling parameters
      for (j = 1; j <= N_selparmvec(f) - k; j++)
      {
        ParCount++;
        ParmLabel += "AgeSel_P" + NumLbl(j) + "_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
      }
    }
  
    //  age-specific retention function
    if (seltype(f, 2) >= 1)
    {
      Do_Retain(f1) = 2;
      if (WTage_rd > 0)
      {
        warnstream << "Age-based retention will use the same empirical wtatage for discarded and retained fish for fleet: " << f;
        write_message (NOTE, 0);
      }
      if (seltype(f1, 2) > 0)
      {
        warnstream << "cannot have both age and size retention functions " << f << "  but retention parms not setup ";
        write_message (FATAL, 0); // EXIT!
      }
      if (seltype(f, 2) == 3)
      {
        RetainParm(f1) = 0;
      } //  no parameters needed
      else
      {
        RetainParm(f1) = N_selparmvec(f) + 1;
        //         N_selparmvec(f) +=N_ret_parm*seltype(f,2);          // N retention parms first [N_ret_parm] for retention; next [N_ret_parm] for discard mortality
        //         for (j=1;j<=N_ret_parm(seltype(f,2));j++)
        //         {
        //           ParCount++; N_selparmvec(f)++; ParmLabel+="Retain_age_P"+NumLbl(j)+"_"+fleetname(f1)+"("+NumLbl(f1)+")";
        //         }
        if (N_ret_parm(seltype(f, 2)) > 0)
        {
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_A_infl_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_A_width_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_A_asymptote_logit_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "Retain_A_maleoffset_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          if (N_ret_parm(seltype(f, 2)) == 7) //  doing dome
          {
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_A_dome_infl_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_A_dome_width_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
            ParCount++;
            N_selparmvec(f)++;
            ParmLabel += "Retain_A_dome_maleoffset_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          }
        }
  
        if (seltype(f, 2) == 2 || seltype(f, 2) == 4)
        {
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_A_infl_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_A_width_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_A_level_old_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
          ParCount++;
          N_selparmvec(f)++;
          ParmLabel += "DiscMort_A_male_offset_" + fleetname(f1) + "(" + NumLbl(f1) + ")";
        }
      }
    }
    else if (seltype(f, 2) < 0) //  mirror retention
    {
      Do_Retain(f1) = 2;
      RetainParm(f1) = 0;
    }
  
    if (seltype(f, 3) >= 1)
    {
      if (gender == 1)
      {
        warnstream << "Male selex cannot be used in one sex model; fleet: " << f;
        write_message (FATAL, 0); // EXIT!
      }
      Maleselparm(f) = N_selparmvec(f) + 1;
      if (seltype(f, 3) == 1 || seltype(f, 3) == 2)
      {
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + "MaleDogleg_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + "MaleatZero_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + "MaleatDogleg_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + "MaleatMaxage_" + fleetname(f1);
      }
      else if (seltype(f, 3) >= 3 && seltype(f, 1) == 20)
      {
        if (seltype(f, 3) == 3) {
          anystring = "Male_";
        }
        else
        {
          anystring = "Fem_";
        }
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + anystring + "Peak_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + anystring + "Ascend_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + anystring + "Descend_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + anystring + "Final_" + fleetname(f1);
        N_selparmvec(f)++;
        ParCount++;
        ParmLabel += "AgeSel_" + NumLbl(f1) + anystring + "Scale_" + fleetname(f1);
      }
      else
      {
        warnstream << "Illegal male selex option selected for fleet " << f;
        write_message (FATAL, 1); // EXIT!
      }
    }
    N_selparm += N_selparmvec(f);
  }
  
  //  create index to fleets with discard
  disc_fleet_list.initialize();
  N_retain_fleets = 0;
  for (f = 1; f <= Nfleet; f++)
  {
    if (Do_Retain(f) > 0)
    {
      N_retain_fleets++;
      disc_fleet_list(f) = N_retain_fleets; //  for compact storage of disc_age(t,f,g)
    }
  }
  
  //  SS_Label_Info_4.097 #Read parameters needed for estimating variance of composition data
  {
    echoinput << "#Now create parameters for D-M variance of composition data; CANNOT be time-varying" << endl;
    Comp_Err_Parm_Start = 0;
    if (Comp_Err_ParmCount > 0)
    {
      echoinput << Comp_Err_ParmCount << "  #_definitions are needed: " << endl;
      Comp_Err_Parm_Start = N_selparm;
      //  create a D-M parameter or tweedie parameter pair only for the first fleet that references that parm number
      for (f = 1; f <= Nfleet; f++)
      for (int parti = 0; parti <= 2; parti++)
      {
        if (DM_parmlist(parti, f) > 0)  //  create DM parameter labels for definitions first referenced for lencomp
        {
          N_selparm ++;
          ParCount ++;
          Comp_Err_parmloc(Comp_Err_L2(parti, f),1) = N_selparm;  //  first parameter used by this method
          Comp_Err_parmloc(Comp_Err_L2(parti, f),2) = ParCount;  //  use this index in write_report to display the correct parameter label
          switch (Comp_Err_L(parti, f))
          {
            case 1:
            {
              ParmLabel += "ln(DM_theta)_Len_P" + NumLbl(Comp_Err_L2(parti, f));
              break;
            }
            case 2:
            {
              ParmLabel += "ln(DM_beta)_Len_P" + NumLbl(Comp_Err_L2(parti, f));
              break;
            }
            case 3:
            {
              ParmLabel += "ln(tweedie_Phi)_Len_P" + NumLbl(Comp_Err_L2(parti, f));
              N_selparm ++;
              ParCount ++;
              ParmLabel += "ln(tweedie_Power)_Len_P" + NumLbl(Comp_Err_L2(parti, f));
              break;
            }
          }
        }
      }

      for (f = 1; f <= Nfleet; f++) 
      {
        if (DM_parmlist(0, f + Nfleet) > 0) //  create DM parameter labels for definitions first referenced for agecomp
        {
          N_selparm ++;
          ParCount ++;
          Comp_Err_parmloc(Comp_Err_A2(f),1) = N_selparm;  //  first parameter used by this method
          Comp_Err_parmloc(Comp_Err_A2(f),2) = ParCount;  //  use this index in write_report to display the correct parameter label
          switch (Comp_Err_A(f))
          {
            case 1:
            {
              ParmLabel += "ln(DM_theta)_Age_P" + NumLbl(Comp_Err_A2(f));
              break;
            }
            case 2:
            {
              ParmLabel += "ln(DM_beta)_Age_P" + NumLbl(Comp_Err_A2(f));
              break;
            }
            case 3:
            {
              ParmLabel += "ln(tweedie_Phi)_Age_P" + NumLbl(Comp_Err_A2(f));
              N_selparm ++;
              ParCount ++;
              ParmLabel += "ln(tweedie_Power)_Age_P" + NumLbl(Comp_Err_A2(f));
              break;
            }
          }
        }
      }

      for (int f = 1; f <= SzFreq_Nmeth; f++) 
      {
        if (DM_parmlist(0, f + 2 * Nfleet) > 0) //  create DM parameter labels for definitions first referenced for sizefreq.  note that sizefreq comps are by method, not fleet
        {
          N_selparm ++;
          ParCount ++;
          Comp_Err_parmloc(Comp_Err_Sz2(f),1) = N_selparm;  //  first parameter used by this method
          Comp_Err_parmloc(Comp_Err_Sz2(f),2) = ParCount;  //  use this index in write_report to display the correct parameter label
          switch (Comp_Err_Sz(f))
          {
            case 1:
            {
              ParmLabel += "ln(DM_theta)_Sz_P" + NumLbl(Comp_Err_Sz2(f));
              break;
            }
            case 2:
            {
              ParmLabel += "ln(DM_Beta)_Sz_P" + NumLbl(Comp_Err_Sz2(f));
              break;
            }
            case 3:
            {
              ParmLabel += "ln(tweedie_Phi)_Sz_P" + NumLbl(Comp_Err_Sz2(f));
              N_selparm ++;
              ParCount ++;
              ParmLabel += "ln(tweedie_Power)_Sz_P" + NumLbl(Comp_Err_Sz2(f));
              break;
            }
          }
        }
      }
   //  note that it would take a lot more code to append labels for parameters that are used by more than one fleet or type
    }
  }

  for (f = 1; f <= Nfleet; f++)
  {
    if (disc_N_fleet(f) > 0 && seltype(f, 2) == 0 && seltype(f + Nfleet, 2) == 0)
    {
      warnstream << "discard data exists for fleet " << f << "  but retention parms not setup " ;
      write_message (FATAL, 0); // EXIT!
    }
    else if (disc_N_fleet(f) == 0 && seltype(f, 2) > 0)
    {
      warnstream << "no discard amount data for fleet " << f << "  but retention parms have been defined ";
      write_message (WARN, 0);
    }
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.9.3 #Read selex parameters
  init_matrix selparm_1(1,N_selparm,1,14)
  ivector selparm_fleet(1,N_selparm) // holds the fleet ID for each selparm
                                  //  equivalent to the mgp_type() for MGparms
  matrix mirror_mask(1,Nfleet,1,nlength)
  matrix mirror_mask_a(1,Nfleet,0,nages)
 LOCAL_CALCS
   // clang-format on
   mirror_mask.initialize();
  mirror_mask_a.initialize();
  selparm_fleet.initialize();
  echoinput << " selex and composition base parameters " << endl;
  for (g = 1; g <= N_selparm; g++)
  {
    echoinput << g << " ## " << selparm_1(g) << " ## " << ParmLabel(ParCount - N_selparm + g) << endl;
  }
  
  //  now identify the fleet associated with each parameter
  echoinput << "identify the fleet associated with each parameter" << endl;
  j = 0;
  for (f = 1; f <= 2 * Nfleet; f++)
  {
    if (N_selparmvec(f) > 0)
    {
      for (g = 1; g <= N_selparmvec(f); g++)
      {
        j++;
        selparm_fleet(j) = f;
      }
    }
  }
  if (Comp_Err_ParmCount > 0)
  {
    echoinput << "comp_error parameter selection by partition (row) and fleet" << endl
              << "L_type: " << Comp_Err_L << endl
              << "L_parm: " << Comp_Err_L2 << endl
              << "A_type: " << Comp_Err_A << endl
              << "A_parm: " << Comp_Err_A2 << endl
              << "Sz_type: " << Comp_Err_Sz << endl
              << "Sz_parm: " << Comp_Err_Sz2 << endl;
              
    for (f = 1; f <= Nfleet; f++)
    for (int parti = 0; parti <= 2; parti++)
    {
      // if Dirichlet was indicated, set fleet for this parameter
      if (Comp_Err_L2(parti, f) > 0)
      {
        j = Comp_Err_parmloc(Comp_Err_L2(parti, f),1);
        selparm_fleet(j) = f;
      }
      if (Comp_Err_A2(f) > 0)
      {
        j = Comp_Err_parmloc(Comp_Err_A2(f),1);
        selparm_fleet(j) = f;
      }
    }
  }
  echoinput<<"selparm_fleet:"<<endl<<selparm_fleet<<endl;
  //  check on conversion of retention parameter
  echoinput << "check on conversion of retention parameter" << endl;
  int parmcount;
  int new_lower_bound;
  int new_upper_bound;
  parmcount = 0;
  for (f = 1; f <= Nfleet; f++)
  {
    if (RetainParm(f) > 0) //  could point to length or age retention
    {
      k = parmcount + RetainParm(f) + 2;
      if (selparm_1(k, 1) >= 0.0) // check to see if user has bounds relevant for 3.24 format
      {
        warnstream << "Converting asymptotic retention parameter to 1/(1+e(-x)) format for fleet: " << f << " parm: " << k << endl;
        warnstream << "++      because parm min was >=0.0" << endl;
        warnstream << "++      old min, max, init, prior: " << selparm_1(k)(1, 4);
        write_message (WARN, 1);
        new_lower_bound = -10.;
        new_upper_bound = 10.;
  
        // check initial value against lower and upper bounds first
        if (selparm_1(k, 3) <= selparm_1(k, 1))
        {
          selparm_1(k, 3) = new_lower_bound;
        }
        else if (selparm_1(k, 3) >= selparm_1(k, 2))
        {
          selparm_1(k, 3) = new_upper_bound;
        }
        else if (selparm_1(k, 3) > 0.)
        {
          if (selparm_1(k, 3) < 1.0)
          {
            selparm_1(k, 3) = -log(1.0 / selparm_1(k, 3) - 1.0);
          }
          else
          {
            selparm_1(k, 3) = 999.;
          } //  hardwire to force to be 1.0
        }
        else
        {
          selparm_1(k, 3) = -999.;
        } //  hardwire to force to 0.0
  
        // check prior value against lower and upper bounds first
        if (selparm_1(k, 4) <= selparm_1(k, 1))
        {
          selparm_1(k, 4) = new_lower_bound;
        }
        else if (selparm_1(k, 4) >= selparm_1(k, 2))
        {
          selparm_1(k, 4) = new_upper_bound;
        }
        else if (selparm_1(k, 4) > 0.)
        {
          if (selparm_1(k, 4) < 1.0)
          {
            selparm_1(k, 4) = -log(1.0 / selparm_1(k, 4) - 1.0);
          }
          else
          {
            selparm_1(k, 4) = 999.;
          } //  hardwire to force to be 1.0
        }
        else
        {
          selparm_1(k, 4) = -999.;
        } //  hardwire to force to 0.0
  
        selparm_1(k, 1) = new_lower_bound;
        selparm_1(k, 2) = new_upper_bound;
  
        warnstream << "new min, max, init, prior: " << selparm_1(k)(1, 4);
        write_message (WARN, 0);
      }
    }
    parmcount += N_selparmvec(f);
  }
  
  echoinput << "check on mirror bounds" << endl;
  parmcount = 0;
  for (f = 1; f <= Nfleet; f++)
  {
    if (seltype(f, 1) == 5) //  uses mirror
    {
      i = int(selparm_1(parmcount + 1, 3));
      j = int(selparm_1(parmcount + 2, 3));
      echoinput << "check on size selex mirror bounds for fleet: " << f << " " << endl;
      if (i <= -1) {
        i = 1;
      } // legit input, use to set mirror_mask
      else if (i == 0)
      {
        echoinput << " size selex mirror, length range min bin read is (" << i << ") reset to 1 for fleet: " << f << endl;
        selparm_1(parmcount + 1, 3) = 1;
        i = 1;
      }
      if (j <= -1) {
        j = nlength;
      } // legit input, use to set mirror_mask
      else if (j == 0)
      {
        warnstream << "size selex mirror, length range max bin read is (" << j << ") reset to nlength for fleet: " << f;
        write_message (ADJUST, 1);
        selparm_1(parmcount + 2, 3) = -1;
        j = nlength;
      }
      if (j > nlength)
      {
        warnstream << "size selex mirror length is > nlength for fleet: " << f << " reset to nlength";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = -1;
        j = nlength;
      }
      if (i > j)
      {
        warnstream << "size selex mirror length range min (" << i << ") greater than max (" << j << ") for fleet: " << f;
        write_message (FATAL, 0); // EXIT!
      }
      if (j > nlength)
      {
        warnstream << "size selex mirror length is > nlength for fleet: " << f << " reset to nlength";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = nlength;
        j = nlength;
      }
      if (i > j)
      {
        warnstream << "size selex mirror length range min (" << i << ") greater than max (" << j << ") for fleet: " << f;
        write_message (FATAL, 0); // EXIT!
      }
      mirror_mask(f) = 1.0e-10;
      mirror_mask(f)(i, j) = 1.;
      echoinput << "fleet: " << f << "  set mirror for bins: " << i << " through " << j << endl;
      echoinput << "set to no prior and not estimated, just in case " << endl;
      selparm_1(parmcount + 1, 6) = 0;
      selparm_1(parmcount + 2, 6) = 0;
      selparm_1(parmcount + 1, 7) = -99;
      selparm_1(parmcount + 2, 7) = -99;
      echoinput << "end check on mirror mask:  " << endl;
    }
    else if (seltype(f, 1) == 11) // setting min-max len range
    {
      echoinput << "check on size selex min-max for fleet: " << f << " " << selparm_1(parmcount + 1, 3) << " " << selparm_1(parmcount + 2, 3) << " nsize bins: " << nlength << endl;
      i = int(selparm_1(parmcount + 1, 3));
      j = int(selparm_1(parmcount + 2, 3));
      if ((selparm_1(parmcount + 1, 3) - i) > 0.)
      {
        warnstream << "fleet: " << f << " age selex range min read is: " << selparm_1(parmcount + 1, 3) << "; SS3 expected an integer and will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 1, 3) = i;
      }
      if ((selparm_1(parmcount + 2, 3) - j) > 0.)
      {
        warnstream << "fleet: " << f << " age selex range max read is: " << selparm_1(parmcount + 2, 3) << "; SS3 expected an integer and will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = j;
      }
      if (selparm_1(parmcount + 2, 3) > nlength)
      {
        warnstream << "fleet: " << f << " age selex range max read is: " << selparm_1(parmcount + 2, 3) << "; is >nsizes; SS3 will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = nlength;
      }
      echoinput << " accepted range: " << selparm_1(parmcount + 1, 3) << " " << selparm_1(parmcount + 2, 3) << endl;
      echoinput << "set to no prior and not estimated, just in case " << endl;
      selparm_1(parmcount + 1, 6) = 0;
      selparm_1(parmcount + 2, 6) = 0;
      selparm_1(parmcount + 1, 7) = -99;
      selparm_1(parmcount + 2, 7) = -99;
      mirror_mask(f) = 1.0e-10;
      mirror_mask(f)(selparm_1(parmcount + 1, 3), selparm_1(parmcount + 2, 3)) = 1.0;
      echoinput << "create mirror_mask: " << mirror_mask(f) << endl;
      echoinput << "end check on min-max ranges for size selex=11" << endl;
    }
  
    parmcount += N_selparmvec(f);
  }
  for (f = 1; f <= Nfleet; f++)
  {
    if (seltype(f + Nfleet, 1) == 11) //  setting min-max age range
    {
      echoinput << "check on age selex min-max for fleet: " << f << " " << selparm_1(parmcount + 1, 3) << " " << selparm_1(parmcount + 2, 3) << " nages: " << nages << endl;
      i = int(selparm_1(parmcount + 1, 3));
      j = int(selparm_1(parmcount + 2, 3));
      echoinput << "set to no prior and not estimated, just in case " << endl;
      selparm_1(parmcount + 1, 6) = 0;
      selparm_1(parmcount + 2, 6) = 0;
      selparm_1(parmcount + 1, 7) = -99;
      selparm_1(parmcount + 2, 7) = -99;
      if ((selparm_1(parmcount + 1, 3) - i) > 0.)
      {
        warnstream << "fleet: " << f << " age selex range min read is: " << selparm_1(parmcount + 1, 3) << "; SS3 expected an integer and will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 1, 3) = i;
      }
      if ((selparm_1(parmcount + 2, 3) - j) > 0.)
      {
        warnstream << "fleet: " << f << " age selex range max read is: " << selparm_1(parmcount + 2, 3) << "; SS3 expected an integer and will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = j;
      }
      if (selparm_1(parmcount + 2, 3) > nages)
      {
        warnstream << "fleet: " << f << " age selex range max read is: " << selparm_1(parmcount + 2, 3) << "; is >nages; SS3 will convert ";
        write_message (ADJUST, 0);
        selparm_1(parmcount + 2, 3) = nages;
      }
      echoinput << " accepted range: " << selparm_1(parmcount + 1, 3) << " " << selparm_1(parmcount + 2, 3) << endl;
      mirror_mask_a(f) = 0;
      mirror_mask_a(f)(selparm_1(parmcount + 1, 3), selparm_1(parmcount + 2, 3)) = 1.0;
      echoinput << "create mirror_mask: " << mirror_mask_a(f) << endl;
      echoinput << "end check on min-max ranges for age selex=11" << endl;
    }
    //  seltype 41 check on the min-max age range could go here, rather than in selex calcs
    parmcount += N_selparmvec(f + Nfleet);
  }
  // clang-format off
 END_CALCS

  int timevary_parm_cnt_sel;
  int timevary_parm_start_sel;
  ivector selparm_timevary(1,N_selparm)  //  holds index of timevary used by this base parameter
  imatrix timevary_sel(styr-3,YrMax+1,1,2*Nfleet)
  int TwoD_AR_do;
  int TwoD_AR_cnt
  int makefishsel_yr
  ivector TwoD_AR_use(1,2*Nfleet);

 LOCAL_CALCS
  // clang-format on
  timevary_parm_start_sel = 0;
  timevary_parm_cnt_sel = 0;
  timevary_sel.initialize();
  selparm_timevary.initialize();
  TwoD_AR_use.initialize();
  timevary_used = 0;
  for (j = 1; j <= N_selparm; j++)
  {
    echoinput << j << " sel " << selparm_1(j) << endl;
    k = selparm_fleet(j);
    if (selparm_1(j, 13) == 0 && selparm_1(j, 8) == 0 && selparm_1(j, 9) == 0)
    {
      //  no time-vary parameter effects
    }
    else if (k == 0)
    {
      warnstream << "Comp_err parameters cannot have timevary effects ";
      write_message (WARN, 0);
    }
    else //  set up a timevary parameter defintion
    {
      timevary_pass = column(timevary_sel, k); // year vector for this category of selparm
      timevary_used = 1;
      ivector timevary_setup(1, 14); //  temporary vector for timevary specs
      timevary_setup.initialize();
      if (timevary_parm_start_sel == 0) timevary_parm_start_sel = timevary_parm_cnt + 1;
      echoinput << endl
                << " timevary for sel parameter: " << j << endl;
      timevary_cnt++; //  count parameters with time-vary effect
      selparm_timevary(j) = timevary_cnt; //  base parameter will use this timevary specification
      timevary_setup(1) = 5; //  indicates a sel parm
      timevary_setup(2) = j; //  index of base parm within that type of parameter
      timevary_setup(13) = firstselparm + j; //  index of base parm relative to ParCount which is continuous across all types of parameters
      timevary_setup(3) = timevary_parm_cnt + 1; //  first TV parameter within total list of all timevary parms
      z = selparm_1(j, 13); // specified block or trend definition
  
      k = int(abs(selparm_1(j, 8)) / 100); //  find the env link code
      timevary_setup(6) = k; //  link code for env
      if (selparm_1(j, 8) > 0) //  env variable used
      {
        timevary_setup(7) = int(abs(selparm_1(j, 8))) - k * 100;
        k = timevary_setup(7);
        //         for(y=styr-1;y<=YrMax;y++) env_data_pass(y)=env_data_RD(y,k);
        env_data_pass(1) = env_data_minyr(k);
        env_data_pass(2) = env_data_maxyr(k);
      }
        else if (abs(selparm_1(j, 8) > 0)) //  density-dependence
      {
        timevary_setup(7) = -int(abs(selparm_1(j, 8)) - k * 100);
        do_densitydependent = 1;
        k = 0;
        env_data_pass.initialize();
      }
      if (z > 0) //  doing blocks
      {
        if (z > N_Block_Designs)
        {
          warnstream << "selex block request exceeds N_block patterns";
          write_message (FATAL, 0); // EXIT!
        }
        create_timevary(selparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), selparm_fleet(j), Block_Design(z), env_data_pass, N_parm_dev, finish_starter);
      }
      else
      {
        create_timevary(selparm_1(j), timevary_setup, timevary_pass, autogen_timevary(timevary_setup(1)), selparm_fleet(j), block_design_null, env_data_pass, N_parm_dev, finish_starter);
      }
      timevary_def.push_back(timevary_setup(1, 14));
      for (y = styr - 3; y <= YrMax + 1; y++) {
        timevary_sel(y, selparm_fleet(j)) = timevary_pass(y);
      } // year vector for this category
    }
  }
    if (do_densitydependent == 1 && Fcast_timevary_Selex == 1) {
      warnstream << "Fcast_timevary_Selex is 1 (do averages); user should change to 0 (timevary) because density dependence affects a selectivity parameter or growth "<<endl;
      write_message(WARN, 0);
    }

  
  timevary_setup.initialize();
  timevary_setup(3) = timevary_parm_cnt + 1; //  one past last one used
  timevary_def.push_back(timevary_setup(1, 14));
  
  N_selparm3 = N_selparm;
  if (timevary_parm_start_sel > 0)
  {
    if (timevary_used == 1) autogen_timevary(5) = 1; //  indicate that some parameter is time-varying
    timevary_parm_cnt_sel = timevary_parm_cnt; //  last timevary_selparm
    N_selparm3 = N_selparm + timevary_parm_cnt_sel - timevary_parm_start_sel + 1;
  }
  N_selparm2 = N_selparm3; //  for distinguishing the 2D_AR parms
  
  //  now add parameters for the 2D_AR1 approach
  //  Input in first parameter line several setup factors:  rho_y, rho_a, ymin, ymax, amin, amax, use_rho, sigma_amax, null9, null10, null11, null12, null13,null14
  //  then one to several parameter lines containing age-specific sigma for ages amin to sigma_amax
  //  note that parm_dev_minyr and parm_dev_maxyr need to map onto the matrix defined by  ymin, ymax, amin, amax,
  TwoD_AR_cnt = 0;
  echoinput << " now read 0/1 for 2D_AR" << endl;
  *(ad_comm::global_datafile) >> TwoD_AR_do;
  echoinput << TwoD_AR_do << "  #_ 0/1 to request experimental 2D_AR selectivity deviations " << endl;
  
  if (TwoD_AR_do > 0)
  {
      //  elements 1-11 are read from control.ss;  12 and 13 are calculated internally
      //  1-fleet, 2-ymin, 3-ymax, 4-amin, 5-amax, 6-sigma_amax, 7-use_rho, 8-age/len, 9-dev_phase
      //  10-before yr range, 11=after yr range, 12-N_parm_dev,  13-selparm_location
      //  rho is used only to calculate the cor matrix in prelim_calcs; it can never be estimated
      //  sigma_sel is generally best fixed to a value of 1.0, estimation should not be undertaken without thorough investigation
    ivector tempvec(1, 13);
    tempvec.initialize();
    TwoD_AR_def.push_back(tempvec); //  bypass that pesky zeroth row
    TwoD_AR_def_rd.push_back(tempvec); //  bypass that pesky zeroth row
    echoinput << "read specification for first 2D_AR1:  fleet, ymin, ymax, amin, amax, sigma_amax, use_rho, len1/age2, phase, before, after" << endl;
    ender = 0;
    do
    {
      ivector tempvec(1, 13);
      ivector tempvec2(1, 13);
      tempvec.initialize();
      tempvec2.initialize();
      *(ad_comm::global_datafile) >> tempvec(1, 11);
      tempvec2 = tempvec;
      echoinput << tempvec(1, 11) << endl;
      f = tempvec(1);
      if (f < 0)
      {
        ender = 1;
      }
      else
      {
        N_parm_dev++;
        TwoD_AR_cnt++;
        if (tempvec(8) == 1)
        {
          anystring = "LEN";
          fs = f;
          TwoD_AR_use(fs) = TwoD_AR_cnt;
        }
        else
        {
          anystring = "AGE";
          fs = f + Nfleet;
          TwoD_AR_use(fs) = TwoD_AR_cnt;
        }
  
        //         save_sigmaval=tempvec(6);  //  to restore into TwoD_AR_def_rd later
        if (tempvec(6) < tempvec(4)) tempvec(6) = tempvec(4);
        if (tempvec(6) > tempvec(5)) tempvec(6) = tempvec(5);
        int sigma_amax = tempvec(6);
        int use_rho = tempvec(7);
        int amin = tempvec(4);
  
        TwoD_AR_def_rd.push_back(tempvec2); //  saves the values as read for writing to control.ss_new
  
        tempvec(12) = N_parm_dev;
        //         apply two lines below later when the timevary_setup is created
        //         tempvec(12)=1;  //  used for dimensioning the dev vectors in SS_param   parm_dev_minyr(k)
        //         tempvec(13)=(tempvec(3)-tempvec(2)+1)*(tempvec(5)-amin+1);   //parm_dev_maxyr(k)
        tempvec(13) = N_selparm2 + 1;
        z = f;
        if (tempvec(8) == 2) z = f + Nfleet;
        for (y = tempvec(2); y <= tempvec(3) + 1; y++) {
          timevary_sel(y, z) = 1;
        }
        TwoD_AR_def.push_back(tempvec);
        echoinput << "now read a parameter line with the sigma for each age from: " << amin << " to sigma_amax: " << sigma_amax << endl;
        for (j = amin; j <= sigma_amax; j++)
        {
          dvector dtempvec(1, 7); //  Lo, Hi, init, prior, prior_sd, prior_type, phase;
          dtempvec.initialize();
          *(ad_comm::global_datafile) >> dtempvec(1, 7);
          timevary_parm_rd.push_back(dtempvec);
          echoinput << " sigmasel for " << anystring << " " << j << " " << dtempvec(3) << endl;
          if (timevary_parm_start_sel == 0) {
            timevary_parm_start_sel = timevary_parm_cnt + 1;
            timevary_parm_cnt_sel = timevary_parm_cnt;
          }
          ParCount++;
          timevary_parm_cnt++;
          timevary_parm_cnt_sel++;
          N_selparm2++;
          ParmLabel += "sigmasel_" + fleetname(f) + "(" + NumLbl(f) + ")_" + anystring + "(" + NumLbl(max(1, j)) + ")";
          if (dtempvec(7) > 0)
          {
            warnstream << "2DAR Sigmasel parameter is not normally estimable; adequate performance usually obtained by fixing to value of 1.0";
            write_message (WARN, 0);
          }
        }
        if (use_rho == 1)
        {
          warnstream << "2DAR rho is incompletely implemented; it should only be used experimentally and never estimated";
          write_message (WARN, 0);
          echoinput << "read one parameter line for rho_yr,  then one for rho_age (or length)" << endl;
          {
            dvector dtempvec(1, 7); //  Lo, Hi, init, prior, prior_sd, prior_type, phase;
            dtempvec.initialize();
            *(ad_comm::global_datafile) >> dtempvec(1, 7);
            dtempvec(7) = -1;  //  force no estimation
            timevary_parm_rd.push_back(dtempvec);
            echoinput << " rho year: " << dtempvec(3) << endl;
            ParCount++;
            timevary_parm_cnt++;
            timevary_parm_cnt_sel++;
            N_selparm2++;
            ParmLabel += "rho_yr_" + fleetname(f) + "(" + NumLbl(f) + ")_" + anystring;
          }
          {
            dvector dtempvec(1, 7); //  Lo, Hi, init, prior, prior_sd, prior_type, phase;
            dtempvec.initialize();
            *(ad_comm::global_datafile) >> dtempvec(1, 7);
            dtempvec(7) = -1;  //  force no estimation
            timevary_parm_rd.push_back(dtempvec);
            echoinput << " rho " << anystring << ": " << dtempvec(3) << endl;
            ParCount++;
            timevary_parm_cnt++;
            timevary_parm_cnt_sel++;
            N_selparm2++;
            ParmLabel += "rho_" + fleetname(f) + "(" + NumLbl(f) + ")" + anystring;
          }
        }
        echoinput << "ready to read next fleet's 2DAR specs, or terminate by reading line starting with negative fleet" << endl;
      }
    } while (ender == 0);
  }
  echoinput << "N_selparm: " << N_selparm << " with timevary: " << N_selparm3 << " with TV and 2D_AR: " << N_selparm2 << " timevary parm range for sel: " << timevary_parm_start_sel << " " << timevary_parm_cnt_sel << " " << timevary_parm_cnt << endl;
  
  if (timevary_parm_cnt > 0)
  {
    echoinput << "list all parms used for timevary implementation" << endl;
    for (y = 1; y <= timevary_parm_cnt; y++)
    {
      echoinput << y << " parm " << timevary_parm_rd[y](1, 7) << endl;
    }
  }
  // clang-format off
 END_CALCS

!!// SS_Label_Info_4.9.xx #Create arrays needed for timevary_parameters
  vector baseparm_min(1,timevary_parm_cnt)
  vector baseparm_max(1,timevary_parm_cnt)

!!//  SS_Label_Info_4.9.9 #Create arrays for the total set of selex parameters
  vector selparm_LO(1,N_selparm2)
  vector selparm_HI(1,N_selparm2)
  vector selparm_RD(1,N_selparm2)
  vector selparm_PR(1,N_selparm2)
  vector selparm_PRtype(1,N_selparm2)
  vector selparm_CV(1,N_selparm2)
  ivector selparm_PH(1,N_selparm2)
  ivector selparm_PH_soft(1,N_selparm2)

 LOCAL_CALCS
   // clang-format on
   //  SS_Label_Info_4.9.12 #Create vectors, e.g. selparm_PH(), that will be used to create actual array of estimted parameters
   for (f = 1; f <= N_selparm; f++)
  {
    selparm_LO(f) = selparm_1(f, 1);
    selparm_HI(f) = selparm_1(f, 2);
    selparm_RD(f) = selparm_1(f, 3);
    selparm_PR(f) = selparm_1(f, 4);
    selparm_PRtype(f) = selparm_1(f, 6);
    selparm_CV(f) = selparm_1(f, 5);
    selparm_PH(f) = selparm_1(f, 7);
  }
  j = N_selparm;
  if (timevary_parm_start_sel > 0)
  {
    for (f = timevary_parm_start_sel; f <= timevary_parm_cnt_sel; f++)
    {
      j++;
      selparm_LO(j) = timevary_parm_rd[f](1);
      selparm_HI(j) = timevary_parm_rd[f](2);
      selparm_RD(j) = timevary_parm_rd[f](3);
      selparm_PR(j) = timevary_parm_rd[f](4);
      selparm_PRtype(j) = timevary_parm_rd[f](6);
      selparm_CV(j) = timevary_parm_rd[f](5);
      selparm_PH(j) = timevary_parm_rd[f](7);
    }
  }
  
  //  SS_Label_Info_4.9.10 #Special bound checking for size selex parameters
  z = 0; // parameter counter within this section
  for (f = 1; f <= Nfleet; f++)
  {
    if (seltype(f, 1) == 8 || seltype(f, 1) == 22 || seltype(f, 1) == 23 || seltype(f, 1) == 24 || seltype(f, 1) == 2)
    {
      if (selparm_1(z + 1, 1) < len_bins_m(2))
      {
        warnstream << "Fleet:_" << f << "min bound on parameter for size at peak is " << selparm_1(z + 1, 1) << "; should be >= midsize bin 2 (" << len_bins_m(2) << ")";
        write_message (WARN, 0);
      }
      if (selparm_1(z + 1, 1) < len_bins_dat(1) && (seltype(f, 1) == 24 || seltype(f, 1) == 2))
      {
        warnstream << "Fleet:_" << f << "min bound on parameter for size at peak is " << selparm_1(z + 1, 1) << "; which is < min databin (" << len_bins_dat(1) << "), so illogical.";
        write_message (WARN, 0);
      }
      if (selparm_1(z + 1, 2) > len_bins_m(nlength - 1))
      {
        warnstream << "Fleet:_" << f << "max bound on parameter for size at peak is " << selparm_1(z + 1, 2) << "; should be <= midsize bin N-1 (" << len_bins_m(nlength - 1) << ")";
        write_message (WARN, 0);
      }
    }
    z += N_selparmvec(f);
  }
  // end special bound checking
  
  //  SS_Label_Info_4.9.11  #Create time/fleet array indicating when changes in selex occcur
  timevary_sel(styr - 3) = 1;
  timevary_sel(styr) = 1;
  timevary_sel(endyr + 1) = 1;
  
  for (y = styr + 1; y <= endyr; y++)
  {
    z = 0; // parameter counter within this section
    for (f = 1; f <= 2 * Nfleet; f++)
    {
      if (seltype(f, 1) == 5 || seltype(f, 1) == 15) // mirror
      {
        if (f <= Nfleet) {
          timevary_sel(y, f) = timevary_sel(y, seltype(f, 4));
        }
        else
        {
          timevary_sel(y, f) = timevary_sel(y, seltype(f, 4) + Nfleet);
        }
        z += seltype_Nparam(seltype(f, 1));
      }
      if (f <= Nfleet && seltype(f, 2) < 0) //  retention is being mirrored
      {
        k = -seltype(f, 2);
        if (timevary_sel(y, k) > 0) timevary_sel(y, f) = 1;
      }
      if (f <= Nfleet)
      {
        //  CHECK:  why is below needed for WTage_rd>0
        if (timevary_MG(y, 2) > 0 || timevary_MG(y, 3) > 0 || WTage_rd > 0)
        {
          timevary_sel(y, f) = 1;
        }
      }
    } // end type
  
  } // end years
  echoinput << "Recalc_flag_for_length_selex_recalc_by_year" << endl;
  for (f = 1; f <= Nfleet; f++)
  {
    echoinput << f << " " << fleetname(f) << " " << column(timevary_sel, f) << endl;
  }
  echoinput << "Recalc_flag_for_age_selex_recalc_by_year" << endl;
  for (f = 1; f <= Nfleet; f++)
  {
    int f2 = f + Nfleet;
    echoinput << f << " " << fleetname(f) << " " << column(timevary_sel, f2) << endl;
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.10 #Read tag recapture parameter setup
// if Tags are used, the read parameters for initial tag loss, chronic tag loss, andd
// fleet-specific tag reporting.  Of these, only reporting rate will be allowed to be time-varying
  init_int TG_custom;  // 1=read; 0=create default parameters
!! echoinput<<TG_custom<<" TG_custom (need to read even if no tag data ); tag_data?: "<<Do_TG<<" N_Fleet: "<<Nfleet1<<endl;
!! k=TG_custom*Do_TG*(3*N_TG+2*Nfleet1);
!!
  init_matrix TG_parm1(1,k,1,14);  // read initial values
!! if(k>0) echoinput<<" Tag parameters as read "<<endl<<TG_parm1<<endl;
!! k=Do_TG*(3*N_TG+2*Nfleet1);
  matrix TG_parm2(1,k,1,14);
!!if(Do_TG>0) {k1=k;} else {k1=1;}
  vector TG_parm_LO(1,k1);
  vector TG_parm_HI(1,k1);
  ivector TG_parm_PH(1,k1);
  int firsttagparm;
 LOCAL_CALCS
  // clang-format on
  if (Do_TG > 0)
  {
    if (TG_custom == 1)
    {
      TG_parm2 = TG_parm1; // assign to the read values
    }
    else
    {
      TG_parm2.initialize();
      onenum = "    ";
      for (j = 1; j <= N_TG; j++)
      {
        TG_parm2(j, 1) = -10; // min
        TG_parm2(j, 2) = 10; // max
        TG_parm2(j, 3) = -7.; // init
        TG_parm2(j, 4) = -7.; // prior
        TG_parm2(j, 5) = 0.001; //  prior is quite diffuse
        TG_parm2(j, 6) = 1.; // default prior type is symmetric beta
        if (j == 1)
        {
          TG_parm2(j, 7) = -4;
        } // phase
        else
        {
          TG_parm2(j, 7) = -1000;
        } // phase
      }
  
      for (j = 1; j <= N_TG; j++)
      {
        TG_parm2(j + N_TG) = TG_parm2(1); // set chronic tag retention equal to initial tag_retention
      }
      for (j = 1; j <= N_TG; j++) // set overdispersion
      {
        TG_parm2(j + 2 * N_TG, 1) = 1; // min
        TG_parm2(j + 2 * N_TG, 2) = 10; // max
        TG_parm2(j + 2 * N_TG, 3) = 2.; // init
        TG_parm2(j + 2 * N_TG, 4) = 2.; // prior
        TG_parm2(j + 2 * N_TG, 5) = 0.001; //  prior is quite diffuse
        TG_parm2(j + 2 * N_TG, 6) = 1.; // default prior type is symmetric beta
        if (j == 1)
        {
          TG_parm2(j + 2 * N_TG, 7) = -4;
        } // phase
        else
        {
          TG_parm2(j + 2 * N_TG, 7) = -1000;
        } // phase
      }
      for (j = 1; j <= Nfleet1; j++)
      {
        TG_parm2(j + 3 * N_TG, 1) = -10; // min
        TG_parm2(j + 3 * N_TG, 2) = 10; // max
        TG_parm2(j + 3 * N_TG, 3) = 7.; // init
        TG_parm2(j + 3 * N_TG, 4) = 7.; // prior
        TG_parm2(j + 3 * N_TG, 5) = 0.001; //  prior is quite diffuse
        TG_parm2(j + 3 * N_TG, 6) = 1.; // default prior type is symmetric beta
        if (j == 1)
        {
          TG_parm2(j + 3 * N_TG, 7) = -4;
        } // phase
        else
        {
          TG_parm2(j + 3 * N_TG, 7) = -1000;
        } // phase
      }
      // set tag reporting decay to nil decay rate
      for (j = 1; j <= Nfleet1; j++)
      {
        k = j + 3 * N_TG + Nfleet1;
        TG_parm2(k, 1) = -4.;
        TG_parm2(k, 2) = 0.;
        TG_parm2(k, 3) = 0.;
        TG_parm2(k, 4) = 0.; // prior of zero
        TG_parm2(k, 5) = 2.; // sd dev of prior
        TG_parm2(k, 6) = 6.; // default prior type is squared dev
        if (j == 1)
        {
          TG_parm2(k, 7) = -4;
        } // phase
        else
        {
          TG_parm2(k, 7) = -1000;
        } // phase
      }
    }
  
    TG_parm_LO = column(TG_parm2, 1);
    TG_parm_HI = column(TG_parm2, 2);
    k = 3 * N_TG + 2 * Nfleet1;
    for (j = 1; j <= k; j++) TG_parm_PH(j) = TG_parm2(j, 7); // write it out due to no typecast available
  
    echoinput << "create tag labels " << endl;
    //  SS_Label_Info_4.10.1 #Create parameter count and parameter names for tag parameters
    onenum = "    ";
    firsttagparm = ParCount;
    for (j = 1; j <= N_TG; j++)
    {
      sprintf(onenum, "%d", j);
      ParCount++;
      ParmLabel += "TG_loss_init_" + onenum + CRLF(1);
    }
    for (j = 1; j <= N_TG; j++)
    {
      sprintf(onenum, "%d", j);
      ParCount++;
      ParmLabel += "TG_loss_chronic_" + onenum + CRLF(1);
    }
    for (j = 1; j <= N_TG; j++)
    {
      sprintf(onenum, "%d", j);
      ParCount++;
      ParmLabel += "TG_overdispersion_" + onenum + CRLF(1);
      if (TG_parm_LO(2 * N_TG + j) < 1.0)
      {
        warnstream << "Overdispersion par_min is <1.0 for TG= " << j << "; value = " << TG_parm_LO(2 * N_TG + j) << "; changed to 1.001 for run";
        write_message (ADJUST, 0);
        TG_parm_LO(2 * N_TG + j) = 1.001;
      }
      if (TG_parm2(2 * N_TG + j, 3) < 1.0)
      {
        warnstream << "Overdispersion parameter is <1.0 for TG= " << j << "; value = " << TG_parm2(2 * N_TG + j, 3) << "; changed to 1.001 for run";
        write_message (ADJUST, 0);
        TG_parm2(2 * N_TG + j, 3) = 1.001;
      }
    }
    for (j = 1; j <= Nfleet; j++)
    {
      if (fleet_type(j) <= 2)
      {
        sprintf(onenum, "%d", j);
        ParCount++;
        ParmLabel += "TG_report_fleet:_" + onenum + CRLF(1);
      }
    }
    for (j = 1; j <= Nfleet; j++)
    {
      if (fleet_type(j) <= 2)
      {
        sprintf(onenum, "%d", j);
        ParCount++;
        ParmLabel += "TG_rpt_decay_fleet:_" + onenum + CRLF(1);
      }
    }
  
    echoinput << " Processed/generated Tag parameters " << endl
              << TG_parm2 << endl;
  }
  else
  {
    TG_parm_LO.initialize();
    TG_parm_HI.initialize();
    TG_parm_PH.initialize();
  }
  // clang-format off
 END_CALCS

   ivector parm_dev_minyr(1,N_parm_dev);
   ivector parm_dev_maxyr(1,N_parm_dev);
   ivector parm_dev_PH(1,N_parm_dev);
   int Do_Var_adjust

   ivector parm_dev_type(1,N_parm_dev);  //  distinguish parameter dev vectors from 2DAR devs
   ivector parm_dev_use_rho(1,N_parm_dev);  //  uses rho parameter, or not
   ivector parm_dev_info(1,N_parm_dev);  //  pointer from list of devvectors to 2DAR list
   ivector TwoD_AR_ymin(1,TwoD_AR_cnt)
   ivector TwoD_AR_ymax(1,TwoD_AR_cnt)
   ivector TwoD_AR_amin(1,TwoD_AR_cnt)
   ivector TwoD_AR_amax(1,TwoD_AR_cnt)
   ivector TwoD_AR_before(1,TwoD_AR_cnt) //  what to do in years before the year range
   ivector TwoD_AR_after(1,TwoD_AR_cnt)  //  what to do in years after the year range
   ivector TwoD_AR_degfree(1,TwoD_AR_cnt)  //  N years with observations * nages in the 2D_AR range
   ivector TwoD_AR_cor_dim(1,TwoD_AR_cnt)

 LOCAL_CALCS
      // clang-format on
      parm_dev_use_rho.initialize();
  if (timevary_cnt > 0)
  {
    for (j = 1; j <= timevary_cnt; j++) //  loop all timevary to set up devs; note that 2D_AR1 is counted in N_parm_dev, but not in timevary_cnt
    {
      ivector timevary_setup(1, 14);
      timevary_setup(1, 14) = timevary_def[j](1, 14);
      if (timevary_setup(8) > 0)
      {
        k = timevary_setup(8); //  dev vector used
        parm_dev_minyr(k) = timevary_setup(10); //  used for dimensioning the dev vectors in SS_param
        parm_dev_maxyr(k) = timevary_setup(11);
        parm_dev_PH(k) = timevary_setup(12);
        echoinput << " dev vector #:  " << k << " setup: " << timevary_setup << " phase: " << parm_dev_PH(k) << endl;
        f = timevary_setup(13); //  index of base parameter
        int picker = timevary_setup(9);
        parm_dev_type(k) = 1; //  so P'=P+dev*se with objfun using  -log(1); so expects se of devs to be approx unit normal
                              //  parm_dev_type is used in SS_objfunc.tpl
        if (picker > 20)
        {
          picker -= 20;
          timevary_setup(14) = 1; //  flag to continue last dev through to YrMax
          timevary_def[j](14) = 1; //  save in array also
          echoinput << j << " setting flag to continue last dev " << Fcast_timevary_Selex << " " << firstselparm << " " << f << " " << firstselparm + N_selparm << " " << endl;
          if (Fcast_timevary_Selex == 1 && f >= firstselparm && f <= (firstselparm + N_selparm))
          {
            warnstream << "for selectivity parmdevs, must change Fcast_timevary_Selex to 0 when using continue last dev";
            write_message (WARN, 1);
          }
        }
        if (picker > 10)
        {
          parm_dev_type(k) = 3; // P'=P+dev; objfun using -log(se) to match 3.30.12 and earlier
          picker -= 10;
        }
        if (picker == 6) parm_dev_type(k) = 4; //  add penalty to keep rmse near 1. Needs to estimate stddev factor
        //  this works, but slow final convergence because getting stddev exactly to 1.0 causes high correlation among devs
        timevary_setup(9) = picker; //  set to its core function because parm_dev_type has been setup
        timevary_def[j](9) = picker; //  save in array also
  
        parm_dev_use_rho(k) = 0;
        // require rho to be used for some dev approaches
        if (picker == 4 || picker == 5 || picker == 6) parm_dev_use_rho(k) = 1;
        for (y = parm_dev_minyr(k); y <= parm_dev_maxyr(k); y++)
        {
          sprintf(onenum, "%d", y);
          ParCount++;
          if (picker == 1)
          {
            ParmLabel += ParmLabel(f) + "_DEVmult_" + onenum + CRLF(1);
          }
          else if (picker == 2)
          {
            ParmLabel += ParmLabel(f) + "_DEVadd_" + onenum + CRLF(1);
          }
          else if (picker == 3)
          {
            ParmLabel += ParmLabel(f) + "_DEVrwalk_" + onenum + CRLF(1);
          }
          else if (picker == 4)
          {
            ParmLabel += ParmLabel(f) + "_DEV_MR_rwalk_" + onenum + CRLF(1);
          }
          else if (picker == 5)
          {
            ParmLabel += ParmLabel(f) + "_DEV_MR_rwalk_bnd_" + onenum + CRLF(1);
          } //  for bounding result on base parm min-max
          else if (picker == 6)
          {
            ParmLabel += ParmLabel(f) + "_DEV_MR_rwalk_pen_" + onenum + CRLF(1);
          } //  like 3.24
          else
          {
            warnstream << "illegal parmdevtype for parm " << f;
            write_message (FATAL, 0); // EXIT!
          }
        }
      }
    }
  }
  
  //  now add dev vectors for the 2D_AR1
  TwoD_AR_degfree.initialize();
  for (f = 1; f <= TwoD_AR_cnt; f++)
  {
    ivector TwoD_AR_setup(1, 13);
    //  1-fleet, 2-ymin, 3-ymax, 4-amin, 5-amax, 6-sigma_amax, 7-use_rho, 8-age/len, 9-dev_phase
    //  10-mindimension, 11=maxdim, 12-N_parm_dev, 13-selparm_location
    //  note that elements 10 and 11 have different usages when used for time-varying parameters
    TwoD_AR_setup(1, 13) = TwoD_AR_def[f](1, 13);
    echoinput << f << " 2D_AR1 setup " << TwoD_AR_setup << endl;
    k = TwoD_AR_setup(12); //  dev vector used
    parm_dev_minyr(k) = 1; //  used for dimensioning the dev vectors in SS_param   parm_dev_minyr(k)
    parm_dev_maxyr(k) = (TwoD_AR_setup(3) - TwoD_AR_setup(2) + 1) * (TwoD_AR_setup(5) - TwoD_AR_setup(4) + 1); //parm_dev_maxyr(k)
    parm_dev_PH(k) = TwoD_AR_setup(9);
    parm_dev_type(k) = 2; //  distinguish 2D_AR devs from parameter devs
    parm_dev_use_rho(k) = 0; //  need to update when implemented
    parm_dev_info(k) = f; //  pointer from parmdev list to the 2D_AR list
    TwoD_AR_ymin(f) = TwoD_AR_setup(2);
    TwoD_AR_ymax(f) = TwoD_AR_setup(3);
    TwoD_AR_amin(f) = TwoD_AR_setup(4);
    TwoD_AR_amax(f) = TwoD_AR_setup(5);
    TwoD_AR_before(f) = TwoD_AR_setup(10);
    TwoD_AR_after(f) = TwoD_AR_setup(11);
    TwoD_AR_cor_dim(f) = (TwoD_AR_ymax(f) - TwoD_AR_ymin(f) + 1) * (TwoD_AR_amax(f) - TwoD_AR_amin(f) + 1);
    for (y = TwoD_AR_ymin(f); y <= TwoD_AR_ymax(f); y++)
    {
      TwoD_AR_degfree(f) += have_data_yr(y, timevary_setup(1));
      for (a = TwoD_AR_amin(f); a <= TwoD_AR_amax(f); a++)
      {
        sprintf(onenum, "%d", y);
        sprintf(anystring, "%d", a);
        ParCount++;
        if (TwoD_AR_setup(8) == 1)
        {
          ParmLabel += fleetname(TwoD_AR_setup(1)) + "_ARDEV_y" + onenum + "_Lbin" + anystring + CRLF(1);
        }
        else
        {
          ParmLabel += fleetname(TwoD_AR_setup(1)) + "_ARDEV_y" + onenum + "_A" + anystring + CRLF(1);
        }
      }
    }
    echoinput << " total years, and with data  " << TwoD_AR_ymax(f) - TwoD_AR_ymin(f) + 1 << " " << TwoD_AR_degfree(f) << "  times nages: ";
    TwoD_AR_degfree(f) *= (TwoD_AR_amax(f) - TwoD_AR_amin(f) + 1);
    echoinput << TwoD_AR_degfree(f) << endl;
  }
  
  echoinput << " read var_adjust list until -9999" << endl;
  ender = 0;
  do
  {
    dvector tempvec(1, 3);
    *(ad_comm::global_datafile) >> tempvec(1, 3);
    echoinput << tempvec << endl;
    if (tempvec(1) == -9999.) ender = 1;
    var_adjust_data.push_back(tempvec(1, 3));
  } while (ender == 0);
  Do_Var_adjust = var_adjust_data.size() - 1;
  echoinput << " number of variance adjustment records = " << Do_Var_adjust << endl;
  // clang-format off
 END_CALCS
  matrix var_adjust(1,7,1,Nfleet)
  // init_matrix var_adjust_list(1,Do_Var_adjust+1,1,3)

 LOCAL_CALCS
      // clang-format on
      var_adjust.initialize();
  for (j = 4; j <= 7; j++)
  {
    var_adjust(j) = 1.0; //  null value
  }
  if (Do_Var_adjust > 0)
  {
    for (j = 1; j <= Do_Var_adjust; j++)
    {
      var_adjust(var_adjust_data[j - 1](1), var_adjust_data[j - 1](2)) = var_adjust_data[j - 1](3);
    }
    echoinput << " Var_adjustments as read " << endl
              << var_adjust << endl;
  }
  else
  {
    var_adjust(1) = 0.;
    var_adjust(2) = 0.;
    var_adjust(3) = 0.;
    var_adjust(4) = 1.;
    var_adjust(5) = 1.;
    var_adjust(6) = 1.;
    var_adjust(7) = 1.;
  }
  // clang-format off
 END_CALCS

  init_int max_lambda_phase
  init_number sd_offset

 LOCAL_CALCS
      // clang-format on
      echoinput
      << max_lambda_phase << " max_lambda_phase " << endl;
  if (max_lambda_phase < 1) max_lambda_phase = 1;
  echoinput << sd_offset << " sd_offset (adds log(s)); needed if variance parameters are estimated " << endl;
  if (sd_offset == 0)
  {
    if (varparm_estimated(1) == 1)
    {
      warnstream << "growth variance is estimated parameter, so change sd_offset to 1";
      write_message (FATAL, 0); // EXIT!
    }
    if (varparm_estimated(2) == 1)
    {
      warnstream << "recruitment sigmaR is estimated parameter, so change sd_offset to 1";
      write_message (FATAL, 0); // EXIT!
    }
    if (varparm_estimated(3) == 1)
    {
      warnstream << "survey extraSD is estimated parameter, so change sd_offset to 1";
      write_message (FATAL, 0); // EXIT!
    }
  }
  if (depletion_fleet > 0 && depletion_type < 2 && max_lambda_phase < 2)
  {
    max_lambda_phase = 2;
    warnstream << "Increase max_lambda_phase to 2 because depletion fleet is being used";
    write_message (ADJUST, 0);
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.11.1 #Define type_phase arrays for lambdas
  matrix surv_lambda(1,Nfleet,1,max_lambda_phase)
  matrix disc_lambda(1,Nfleet,1,max_lambda_phase)
  matrix mnwt_lambda(1,Nfleet,1,max_lambda_phase)
  matrix length_lambda(1,Nfleet,1,max_lambda_phase)
  matrix age_lambda(1,Nfleet,1,max_lambda_phase)
  matrix sizeage_lambda(1,Nfleet,1,max_lambda_phase)
  matrix init_equ_lambda(1,Nfleet,1,max_lambda_phase)
  matrix catch_lambda(1,Nfleet,1,max_lambda_phase)
  vector recrdev_lambda(1,max_lambda_phase)
  vector regime_lambda(1,max_lambda_phase)
  vector parm_prior_lambda(1,max_lambda_phase)
  vector parm_dev_lambda(1,max_lambda_phase)
  vector CrashPen_lambda(1,max_lambda_phase)
  vector Morphcomp_lambda(1,max_lambda_phase)
  matrix SzFreq_lambda(1,SzFreq_N_Like,1,max_lambda_phase)
  matrix TG_lambda1(1,N_TG2,1,max_lambda_phase)
  matrix TG_lambda2(1,N_TG2,1,max_lambda_phase)
  vector F_ballpark_lambda(1,max_lambda_phase)

!!//  SS_Label_Info_4.11.2 #Read and process any lambda adjustments
  int N_lambda_changes
  int N_changed_lambdas
 LOCAL_CALCS
  // clang-format on
  echoinput << endl << "LAMBDA" << endl
  << " each line has 5 values: like_code, fleet, beginning_phase, value, code_for_sizefreq "<< endl
  << " terminate reading with like_code = -9999" << endl
  << " like_code options are:  1=surv; 2=disc; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=catch; 9=init_equ_catch; " << endl
  << " 10=recrdev; 11=parm_prior; 12=parm_dev; 13=CrashPen; 14=Morphcomp; 15=Tag-comp; 16=Tag-negbin; 17=F_ballpark; 18=initEQregime." << endl
  << " 2nd value (fleet) only used for like_codes 1 - 9, which are fleet-specific, except" << endl
  << "   2nd value is used for Tag-Group, instead of fleet, for like_codes 15 & 16." << endl
  << " 5th value is used only for like_code=6 and specifies the SizeFreq method used, which is in addition to fleet designation." << endl;

  ender = 0;  //  begin reading lambda changes
  do
  {
    dvector tempvec(1, 5);
    *(ad_comm::global_datafile) >> tempvec(1, 5);
    if (tempvec(1) == -9999.) ender = 1;
    lambda_change_data.push_back(tempvec(1, 5));
  } while (ender == 0);
  N_lambda_changes = lambda_change_data.size() - 1;
  // clang-format off
 END_CALCS

  matrix Lambda_changes(1,N_lambda_changes,1,5)
 LOCAL_CALCS
  // clang-format on
  for (f = 1; f <= N_lambda_changes; f++) Lambda_changes(f) = lambda_change_data[f - 1];
  if (N_lambda_changes > 0) echoinput << N_lambda_changes << " lambda changes: " << endl
                                      << Lambda_changes << endl;
  surv_lambda = 1.; // 1
  disc_lambda = 1.; // 2
  mnwt_lambda = 1.; // 3
  length_lambda = 1.; // 4
  age_lambda = 1.; // 5
  SzFreq_lambda = 1.; // 6
  sizeage_lambda = 1.; // 7
  catch_lambda = 1.; // 8
  init_equ_lambda = 1.; // 9
  recrdev_lambda = 1.; // 10
  parm_prior_lambda = 1.; // 11
  parm_dev_lambda = 1.; // 12
  CrashPen_lambda = 1.; // 13
  Morphcomp_lambda = 1.; // 14
  TG_lambda1 = 1.; // 15
  TG_lambda2 = 1.; //16
  F_ballpark_lambda = 1.; // 17
  regime_lambda = 1.; //  18
  
  if (depletion_fleet > 0 && depletion_type < 2)
  {
    for (f = 1; f <= Nfleet; f++)
    {
      surv_lambda(f, 1) = 0.0;
      init_equ_lambda(f, 1) = 0.0;
      disc_lambda(f, 1) = 0.0;
      mnwt_lambda(f, 1) = 0.0;
      length_lambda(f, 1) = 0.0;
      age_lambda(f, 1) = 0.0;
      sizeage_lambda(f, 1) = 0.0;
      //        catch_lambda(f,1)=0.0;  //  keep this positive to prevent crashes from bad fit to catch
    }
    if (SzFreq_Nmeth > 0)
    {
      for (z = 1; z <= SzFreq_N_Like; z++)
      {
        SzFreq_lambda(z, 1) = 0.0;
      }
    }
    if (N_TG2 > 0)
    {
      for (z = 1; z <= N_TG2; z++)
      {
        TG_lambda1(z, 1) = 0.0;
        TG_lambda2(z, 1) = 0.0;
      }
    }
    recrdev_lambda(1) = 0.0;
    Morphcomp_lambda(1) = 0.0;
    F_ballpark_lambda(1) = 0.0;
  
    surv_lambda(depletion_fleet, 1) = 1.0;
  }
  
  N_changed_lambdas = 0;
  for (j = 1; j <= N_lambda_changes; j++)
  {
    k = Lambda_changes(j, 1); // like component
    f = Lambda_changes(j, 2); // fleet
    s = Lambda_changes(j, 3); // phase
    if (k <= 9)   //  only check those codes that are fleet-specific
    {
      if (f > Nfleet)
      {
        k = 0;
        warnstream << "Illegal fleet/survey for lambda change at row: " << j << " fleet: " << f << " > Nfleet";
        write_message (ADJUST, 0);
      }
    }
    else if (k == 15 || k == 16) // tag data
    {
      if (f > N_TG2)
      {
        k = 0;
        warnstream << "Illegal tag group for lambda change at row: " << j << " Tag: " << f << " > N_taggroups";
        write_message (ADJUST, 0);
      }
    }
    else if (k > 18)
    {
      k = 0;
      warnstream << "Illegal lambda_type for lambda change at row: " << j << " Method: " << k << " > 17";
      write_message (ADJUST, 0);
    }
    if (s > max_lambda_phase)
    {
      k = 0;
      warnstream << "Illegal request for lambda change at row: " << j << " phase: " << s << " > max_lambda_phase: " << max_lambda_phase;
      write_message (ADJUST, 0);
    }
    //      if(s>Turn_off_phase) s=max(1,Turn_off_phase);
    temp = Lambda_changes(j, 4); // value
    if (temp != 0.0 && temp != 1.0) N_changed_lambdas++;
    z = Lambda_changes(j, 5); // special for sizefreq
    switch (k)
    {
      case 0: // do nothing
      {
        break;
      }
      case 1: // survey
      {
        surv_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 2: // discard
      {
        disc_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 3: // meanbodywt
      {
        mnwt_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 4: // lengthcomp
      {
        length_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 5: // agecomp
      {
        age_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 6: // sizefreq comp
      {
        z = Lambda_changes(j, 5); //  sizefreq method
        if (z > SzFreq_Nmeth)
        {
          warnstream << "reading sizefreq lambda change for method > Nmeth " << Lambda_changes(j, 5);
          write_message (FATAL, 0); // EXIT!
        }
        SzFreq_lambda(SzFreq_LikeComponent(f, z))(s, max_lambda_phase) = temp;
        break;
      }
      case 7: // size-at-age
      {
        sizeage_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 8: // catch
      {
        catch_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 9: // init_equ_catch
      {
        init_equ_lambda(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 10: // recr_dev
      {
        recrdev_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 11: // parm_prior
      {
        parm_prior_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 12: // parm_dev
      {
        parm_dev_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 13: // crash_penalty
      {
        CrashPen_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 14: // morphcomp
      {
        Morphcomp_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 15: // Tag - multinomial by fleet  where f is now tag group
      {
        TG_lambda1(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 16: // Tag - total by time where f is now tag group
      {
        TG_lambda2(f)(s, max_lambda_phase) = temp;
        break;
      }
      case 17: // F ballpark
      {
        F_ballpark_lambda(s, max_lambda_phase) = temp;
        break;
      }
      case 18: // regime lambda - only for initial equilibrium
      {
        regime_lambda(s, max_lambda_phase) = temp;
        break;
      }
    }
  }
  for (f = 1; f <= Nfleet; f++)
  {
    if (Svy_N_fleet(f) == 0) surv_lambda(f) = 0.;
    if (disc_N_fleet(f) == 0) disc_lambda(f) = 0.;
    if (Nobs_l(f) == 0) length_lambda(f) = 0.;
    if (Nobs_a(f) == 0) age_lambda(f) = 0.;
    if (Nobs_ms(f) == 0) sizeage_lambda(f) = 0.;
  }
  if (nobs_mnwt == 0) mnwt_lambda = 0.; //  more complicated to turn off for each fleet
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.12 #Read setup for more derived quantities to include in the STD report
  init_int Do_More_Std   // option (currently 0, 1, or 2)
  int More_Std_N_Inputs; // count of inputs (depends on option above)
 LOCAL_CALCS
  // clang-format on
  More_Std_N_Inputs = 0;
  if (Do_More_Std == 1) {
    More_Std_N_Inputs = 9;
  }
  if (Do_More_Std == 2) {
    More_Std_N_Inputs = 13;
  }
  // clang-format off
 END_CALCS
  ivector More_Std_Input(1,13); // read dimensions
  init_ivector temp_std_input(1,More_Std_N_Inputs)
 LOCAL_CALCS
      // clang-format on
      echoinput
      << Do_More_Std << " # extra stdev reporting: 0 = skip, 1 = read specs for reporting stdev for selectivity, size, and numbers, 2 = add option for M, dyn. Bzero & Smrybio " << endl;
  More_Std_Input.initialize();
  if (Do_More_Std > 0)
  {
    echoinput << "inpt_as_read: " << temp_std_input << endl;
    More_Std_Input(1, More_Std_N_Inputs) = temp_std_input(1, More_Std_N_Inputs);
    echoinput << More_Std_Input(1, 4) << " # Selectivity: (1) 0 to skip or fleet, (2) 1=len/2=age/3=combined, (3) year, (4) N selex bins; NOTE: combined reports in age bins" << endl;
    echoinput << More_Std_Input(5, 6) << " # Growth: (1) 0 to skip or growth pattern, (2) growth ages; NOTE: does each sex" << endl;
    echoinput << More_Std_Input(7, 9) << " # Numbers-at-age: (1) 0 to skip or area(-1 for all), (2) year, (3) N ages;  NOTE: sums across morphs" << endl;
  }
  if (Do_More_Std >= 2)
  {
    echoinput << More_Std_Input(10, 11) << " # Mortality: (1) 0 to skip or growth pattern, (2) N ages for mortality; NOTE: does each sex" << endl;
    echoinput << More_Std_Input(12) << " # Dyn_Bzero: 0 to skip, 1 to do, 2 w/ recr" << endl;
    echoinput << More_Std_Input(13) << " # SmryBio: 0 to skip, 1 to do" << endl;
  }
  // clang-format off
 END_CALCS

  int Do_Selex_Std;
  int Selex_Std_AL;
  int Selex_Std_Year;
  int Selex_Std_Cnt;
  int Do_Growth_Std;
  int Growth_Std_Cnt;
  int Do_NatAge_Std;
  int NatAge_Std_Year;
  int NatAge_Std_Cnt;
  int Do_NatM_Std;
  int NatM_Std_Cnt;
  int Do_Dyn_Bzero;
  int Do_se_smrybio;
  int Do_se_LnSSB;
  int Extra_Std_N;   //  dimension for the sdreport vector Selex_Std which also contains the Growth_Std

 LOCAL_CALCS
  // clang-format on
  Extra_Std_N = 0;
  
  // Itialize all switches for extra std inputs
  Do_Selex_Std = 0;
  Selex_Std_AL = 1;
  Selex_Std_Year = endyr;
  Selex_Std_Cnt = 0;
  Do_Growth_Std = 0;
  Growth_Std_Cnt = 0;
  Do_NatAge_Std = 0;
  NatAge_Std_Cnt = 0;
  NatAge_Std_Year = endyr;
  Do_NatM_Std = 0;
  NatM_Std_Cnt = 0;
  Do_Dyn_Bzero = 0;
  Do_se_smrybio = 0;
  Do_se_LnSSB = 0;
  
  // read standard extra std inputs (only option prior to 3.30.15)
  if (Do_More_Std > 0)
  {
    Do_Selex_Std = More_Std_Input(1);
    Selex_Std_AL = More_Std_Input(2);
    Selex_Std_Year = More_Std_Input(3);
    if (Selex_Std_Year < 0) Selex_Std_Year = endyr;
    Selex_Std_Cnt = More_Std_Input(4);
    Do_Growth_Std = More_Std_Input(5);
    Growth_Std_Cnt = More_Std_Input(6);
    Do_NatAge_Std = More_Std_Input(7);
    NatAge_Std_Year = More_Std_Input(8);
    if (NatAge_Std_Year < 0) NatAge_Std_Year = endyr + 1;
    NatAge_Std_Cnt = More_Std_Input(9);
    if (Do_Selex_Std <= 0) Selex_Std_Cnt = 0;
    if (Do_Growth_Std <= 0) Growth_Std_Cnt = 0;
    if (Do_NatAge_Std == 0) NatAge_Std_Cnt = 0;
    Do_NatM_Std = 0; // value replaced below if Do_More_Std==2
    NatM_Std_Cnt = 0; // value replaced below if Do_More_Std==2
    // read additional extra std inputs for NatM (added in 3.30.15)
    if (Do_More_Std == 2)
    {
      Do_NatM_Std = More_Std_Input(10);
      NatM_Std_Cnt = More_Std_Input(11);
      if (Do_NatM_Std <= 0) NatM_Std_Cnt = 0;
      Do_Dyn_Bzero = More_Std_Input(12);
      Do_se_smrybio = More_Std_Input(13);
    }
  }
  
  // clang-format off
 END_CALCS

  // get vector of length bins or ages for selex std (either input or autogenerate)
  init_ivector Selex_Std_Pick(1,Selex_Std_Cnt);
 LOCAL_CALCS
  // clang-format on
  if (Do_Selex_Std > 0)
  {
    echoinput << Selex_Std_Pick << " # vector with selex std bins (-1 in first bin to self-generate)" << endl;
    if (Selex_Std_Pick(1) < 0) //  then self-generate even bin selection
    {
      if (Selex_Std_AL == 1) // length-based selex
      {
        if (Selex_Std_Cnt == 1)
        {
          Selex_Std_Pick(1) = nlength / 2;
        }
        else if (Selex_Std_Cnt == 2)
        {
          Selex_Std_Pick(1) = nlength / 2;
          Selex_Std_Pick(2) = nlength;
        }
        else
        {
          j = nlength / (Selex_Std_Cnt - 1);
          Selex_Std_Pick(1) = j / 2;
          for (i = 2; i <= Selex_Std_Cnt - 1; i++) Selex_Std_Pick(i) = Selex_Std_Pick(i - 1) + j;
          Selex_Std_Pick(Selex_Std_Cnt) = nlength;
        }
        echoinput << "generate length selex std for fleet: " << Do_Selex_Std << " in year: " << Selex_Std_Year << " at bins: " << Selex_Std_Pick << endl;
      }
      else // age-based or age-length-combined selex
      {
        if (Selex_Std_Cnt == 1)
        {
          Selex_Std_Pick(1) = nages / 2;
        }
        else if (Selex_Std_Cnt == 2)
        {
          Selex_Std_Pick(1) = nages / 2;
          Selex_Std_Pick(2) = nages;
        }
        else
        {
          j = nages / (Selex_Std_Cnt - 1);
          Selex_Std_Pick(1) = j / 2;
          for (i = 2; i <= Selex_Std_Cnt - 1; i++) Selex_Std_Pick(i) = Selex_Std_Pick(i - 1) + j;
          Selex_Std_Pick(Selex_Std_Cnt) = nages;
        }
        echoinput << "generate age selex std for fleet: " << Do_Selex_Std << " in year: " << Selex_Std_Year << " at ages: " << Selex_Std_Pick << endl;
      }
    }
    // adjust values to keep in range
    for (i = 1; i <= Selex_Std_Cnt; i++)
    {
      if (Selex_Std_AL == 1) // length-based selex
      {
        if (Selex_Std_Pick(i) <= 0) Selex_Std_Pick(i) = 1;
        if (Selex_Std_Pick(i) > nlength)
        {
          warnstream << "Selex_std requested output past nlength, resets to nlength, may produce duplicates";
          write_message (ADJUST, 0);
          Selex_Std_Pick(i) = nlength;
        }
      }
      else // age-based or age-length-combined selex
      {
        if (Selex_Std_Pick(i) < 0) Selex_Std_Pick(i) = 0;
        if (Selex_Std_Pick(i) > nages)
        {
          warnstream << "Selex_std requested output past nages, resets to nages, may produce duplicates";
          write_message (ADJUST, 0);
          Selex_Std_Pick(i) = nages;
        }
      }
    }
    // increment count
    Extra_Std_N = gender * Selex_Std_Cnt;
  }
  // clang-format off
 END_CALCS

  // get vector of bins for growth std (either input or autogenerate)
  init_ivector Growth_Std_Pick(1,Growth_Std_Cnt);
 LOCAL_CALCS
  // clang-format on
  if (Do_Growth_Std > 0)
  {
    echoinput << Growth_Std_Pick << " # vector with growth std ages (-1 in first bin to self-generate)" << endl;
    // turn off growth extra stderr for growth if no estimated growth parameters
    if (MG_active(2) == 0)
    {
      warnstream << "Growth output stderr requested but no growth parameters are estimated, changing growth stddev reporting specifications to 0";
      write_message (ADJUST, 0);
      Do_Growth_Std = 0;
      //  		More_Std_Input(5)=0;
      //  		More_Std_Input(6)=0;
      Growth_Std_Cnt = 0;
    }
    else
    {
      // there are active growth parameters so proceed with processing stderr
      if (Growth_Std_Pick(1) < 0)
      {
        Growth_Std_Pick(1) = AFIX;
        Growth_Std_Pick(Growth_Std_Cnt) = nages;
        if (Growth_Std_Cnt > 2)
        {
          k = Growth_Std_Cnt / 2;
          for (i = 2; i <= k; i++) Growth_Std_Pick(i) = Growth_Std_Pick(i - 1) + 1;
          j = (nages - Growth_Std_Pick(k)) / (Growth_Std_Cnt - k);
          for (i = k + 1; i <= Growth_Std_Cnt - 1; i++) Growth_Std_Pick(i) = Growth_Std_Pick(i - 1) + j;
        }
      }
      for (i = 1; i <= Growth_Std_Cnt; i++)
      {
        if (Growth_Std_Pick(i) < 0) Growth_Std_Pick(i) = 0;
        if (Growth_Std_Pick(i) > nages) Growth_Std_Pick(i) = nages;
      }
    }
    Extra_Std_N += gender * Growth_Std_Cnt;
  }
  // clang-format off
 END_CALCS

  // get vector of bins for N-at-age std (either input or autogenerate)
  init_ivector NatAge_Std_Pick(1,NatAge_Std_Cnt);
 LOCAL_CALCS
  // clang-format on
  if (Do_NatAge_Std != 0)
  {
    echoinput << NatAge_Std_Pick << " # vector with NatAge std bins (-1 in first bin to self-generate)" << endl;
    if (NatAge_Std_Pick(1) < 0)
    {
      NatAge_Std_Pick(1) = 1;
      NatAge_Std_Pick(NatAge_Std_Cnt) = nages;
      if (NatAge_Std_Cnt > 2)
      {
        k = NatAge_Std_Cnt / 2;
        for (i = 2; i <= k; i++) NatAge_Std_Pick(i) = NatAge_Std_Pick(i - 1) + 1;
        j = (nages - NatAge_Std_Pick(k)) / (NatAge_Std_Cnt - k);
        for (i = k + 1; i <= NatAge_Std_Cnt - 1; i++) NatAge_Std_Pick(i) = NatAge_Std_Pick(i - 1) + j;
      }
    }
    for (i = 1; i <= NatAge_Std_Cnt; i++)
    {
      if (NatAge_Std_Pick(i) <= 0) NatAge_Std_Pick(i) = 0;
      if (NatAge_Std_Pick(i) > nages) NatAge_Std_Pick(i) = nages;
    }
    Extra_Std_N += gender * NatAge_Std_Cnt;
  }
  
  // clang-format off
 END_CALCS

  // get vector of bins for NatM std (either input or autogenerate)
  init_ivector NatM_Std_Pick(1,NatM_Std_Cnt);
 LOCAL_CALCS
  // clang-format on
  if (Do_NatM_Std > 0)
  {
    echoinput << NatM_Std_Pick << " # vector with NatM std ages (-1 in first bin to self-generate)" << endl;
    // autogenerate the ages
    if (NatM_Std_Pick(1) < 0)
    {
      // set first and last to reference ages
      NatM_Std_Pick(1) = AFIX;
      NatM_Std_Pick(NatM_Std_Cnt) = nages;
      // if there is more than 2, fill in the middle
      if (NatM_Std_Cnt > 2)
      {
        // first half of values increment by 1
        k = NatM_Std_Cnt / 2;
        for (i = 2; i <= k; i++) {
          NatM_Std_Pick(i) = NatM_Std_Pick(i - 1) + 1;
        }
        // remainder are evently distributed across range
        j = (nages - NatM_Std_Pick(k)) / (NatM_Std_Cnt - k);
        for (i = k + 1; i <= NatM_Std_Cnt - 1; i++) {
          NatM_Std_Pick(i) = NatM_Std_Pick(i - 1) + j;
        }
      }
    }
    // shift any negative values to 0 and any that are too large down to nages
    for (i = 1; i <= NatM_Std_Cnt; i++)
    {
      if (NatM_Std_Pick(i) < 0) NatM_Std_Pick(i) = 0;
      if (NatM_Std_Pick(i) > nages) NatM_Std_Pick(i) = nages;
    }
    // increment counter
    Extra_Std_N += gender * NatM_Std_Cnt;
  }
  
  if (Do_Dyn_Bzero > 0)
  {
    Do_Dyn_Bzero = Extra_Std_N + 1; //  start spot for Dynamic Bzero
    Extra_Std_N += YrMax - (styr - 2) + 1;
    if (More_Std_Input(12) == 2) Extra_Std_N += YrMax - (styr - 2) + 1; //  for recruitment
  }
  // add 3 values for ln(SSBio)
  // (years are automatically generated as startyr, mid-point, and endyr)
  Do_se_LnSSB = Extra_Std_N + 1;
  Extra_Std_N += 3;
  
  if (Do_se_smrybio > 0)
  {
    Do_se_smrybio = Extra_Std_N + 1; //  start spot
    Extra_Std_N += YrMax - (styr - 2) + 1;
  }
  // else  smrybio will be written anyway, but without se
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.13 #End of reading from control file
  init_int fim // end of file indicator

 LOCAL_CALCS
   // clang-format on
   if (fim == 999)
  {
    cout << "End of control file successful! " << fim << endl;
    echoinput << "End of control file successful! " << fim << endl;
  }
  else
  {
    cout << " Unsuccessful end of control file. Check echoinput for clues.  Last read is: " << fim << endl;
    exit(1);
  }
  // clang-format off
 END_CALCS

!!//  SS_Label_Info_4.14 #Create count of active parameters and derived quantities
  int CoVar_Count;
  int active_count;    // count the active parameters
  int active_parms;    // count the active parameters
  int deriv_start;  //  start index for derived quantities
  int deriv_covar_start

 LOCAL_CALCS
      // clang-format on
      if (Do_Benchmark > 0)
  {
    N_STD_Mgmt_Quant = 22;
    if (Do_Benchmark == 3) N_STD_Mgmt_Quant += 3; //  for Blimit
  }
  else
  {
    N_STD_Mgmt_Quant = 4;
  }
  Fcast_catch_start = N_STD_Mgmt_Quant;
  if (max(Do_Retain) > 0) {
    j = 1;
  }
  else
  {
    j = 0;
  }
  if (Do_Forecast > 0) {
    N_STD_Mgmt_Quant += N_Fcast_Yrs * (1 + j) + N_Fcast_Yrs;
  }
  k = ParCount + 2 * N_STD_Yr + N_STD_Yr_Dep + N_STD_Yr_Ofish + N_STD_Yr_F + N_STD_Mgmt_Quant + gender * Selex_Std_Cnt + gender * Growth_Std_Cnt + gender * NatAge_Std_Cnt + gender * NatM_Std_Cnt;
  if (Do_More_Std >= 2)
  {
    k += Do_Dyn_Bzero * (YrMax - (styr - 2) - 1);
    if (More_Std_Input(12) == 2) k += (YrMax - (styr - 2) - 1); //  for recruits
    k += Do_se_smrybio * (YrMax - (styr - 2) - 1);
  }
  k += 3 + Svy_N_sdreport;
  echoinput << "N parameters: " << ParCount << endl
            << "Parameters plus derived quant: " << k << endl;
  // clang-format off
 END_CALCS
  ivector active_parm(1,k)  //  pointer from active list to the element of the full parameter list to get label later

//***********************************************
!!//  SS_Label_Info_4.14.1 #Adjust the phases to negative if beyond turn_off_phase and find resultant max_phase
  int max_phase;
  int Turn_off_phase2

 LOCAL_CALCS
      // clang-format on
      echoinput
      << "Adjust the phases " << endl;
  Turn_off_phase2 = Turn_off_phase;
  echoinput << " requested turn_off phase: " << Turn_off_phase << endl;
  if (depletion_fleet > 0 && depletion_type == 1)
  {
    Turn_off_phase2 = 1;
    echoinput << "depletion fleet and type are: " << depletion_fleet << " " << depletion_type << " so set turn-off to phase 1 " << endl;
  }
  max_phase = 1;
  active_count = 0;
  active_parm(1, ParCount) = 0;
  ParCount = 0;
  
  j = MGparm_PH.indexmax();
  
  for (k = 1; k <= j; k++)
  {
    ParCount++;
    if (MGparm_PH(k) == -9999) {
      MGparm_RD(k) = prof_var(prof_var_cnt);
      prof_var_cnt += 1;
    }
    if (depletion_fleet > 0 && depletion_type < 2 && MGparm_PH(k) > 0) MGparm_PH(k)++; //  add 1 to phase if using depletion fleet
    if (MGparm_PH(k) > Turn_off_phase2) MGparm_PH(k) = -1;
    if (MGparm_PH(k) > max_phase) max_phase = MGparm_PH(k);
    if (MGparm_PH(k) >= 0)
    {
      active_count++;
      active_parm(active_count) = ParCount;
    }
  }
  
  for (j = 1; j <= SRparm_PH.indexmax(); j++)
  {
    ParCount++;
    if (SRparm_PH(j) == -9999) {
      SRparm_1(j, 3) = prof_var(prof_var_cnt);
      SRparm_RD(j, 3) = SRparm_1(j, 3);
      prof_var_cnt += 1;
    }
    if (depletion_fleet > 0 && depletion_type < 2 && SRparm_PH(j) > 0) SRparm_PH(j)++; //  add 1 to phase if using depletion fleet
    if (depletion_fleet > 0 && depletion_type < 2 && j == 1) SRparm_PH(1) = 1; //  R0 active in phase 1, unless type==2
    if (SRparm_PH(j) > Turn_off_phase2) SRparm_PH(j) = -1;
    if (SRparm_PH(j) > max_phase) max_phase = SRparm_PH(j);
    if (SRparm_PH(j) >= 0)
    {
      active_count++;
      active_parm(active_count) = ParCount;
    }
  }

  // flag to bypass steepness calculations
  use_steepness = 1; // default
  // following test will occur in preliminary calcs such that it will work even if values are read from ss3.par
  // if (SR_fxn == 3)
  // {
  //  if (SRparm_PH(2) < 0 || SRparm(2) >= 0.999999) use_steepness = 0;
  // }
  
  if (recdev_cycle > 0)
  {
    for (y = 1; y <= recdev_cycle; y++)
    {
      ParCount++;
      recdev_cycle_LO(y) = recdev_cycle_parm_RD(y, 1);
      recdev_cycle_HI(y) = recdev_cycle_parm_RD(y, 2);
      recdev_cycle_PH(y) = recdev_cycle_parm_RD(y, 7);
      if (depletion_fleet > 0 && depletion_type < 2 && recdev_cycle_PH(y) > 0) recdev_cycle_PH(y)++; //  add 1 to phase if using depletion fleet
      if (recdev_cycle_PH(y) > Turn_off_phase2) recdev_cycle_PH(y) = -1;
      if (recdev_cycle_PH(y) > max_phase) max_phase = recdev_cycle_PH(y);
      if (recdev_cycle_PH(y) >= 0) {
        active_count++;
        active_parm(active_count) = ParCount;
      }
    }
  }
  
  if (depletion_fleet > 0 && depletion_type < 2 && recdev_early_PH_rd > 0) recdev_early_PH_rd++; //  add 1 to phase if using depletion fleet
  if (recdev_early_PH_rd > Turn_off_phase2)
  {
    recdev_early_PH = -1;
  }
  else
  {
    recdev_early_PH = recdev_early_PH_rd;
  }
  
  if (recdev_early_PH > max_phase) max_phase = recdev_early_PH;
  
  if (recdev_do_early > 0)
  {
    for (y = recdev_early_start; y <= recdev_early_end; y++)
    {
      ParCount++;
      if (recdev_early_PH >= 0) {
        active_count++;
        active_parm(active_count) = ParCount;
      }
    }
  }
  
  if (depletion_fleet > 0 && depletion_type < 2 && recdev_PH > 0) recdev_PH++; //  add 1 to phase if using depletion fleet
  if (recdev_PH > Turn_off_phase2) recdev_PH = -1;
  if (recdev_PH > max_phase) max_phase = recdev_PH;
  if (do_recdev > 0)
  {
    for (y = recdev_start; y <= recdev_end; y++)
    {
      ParCount++;
      if (recdev_PH >= 0) {
        active_count++;
        active_parm(active_count) = ParCount;
      }
    }
  }
  
  Fcast_recr_PH2 = max_phase + 1;
  Fcast_recr_PH = Fcast_recr_PH_rd;
  if (Do_Forecast > 0)
  {
    if (Turn_off_phase > 0)
    {
      if (Fcast_recr_PH_rd != 0) // read value for forecast_PH
      {
        Fcast_recr_PH2 = Fcast_recr_PH;
        if (depletion_fleet > 0 && depletion_type < 2 && Fcast_recr_PH2 > 0) Fcast_recr_PH2++;
        if (Fcast_recr_PH2 > Turn_off_phase2) Fcast_recr_PH2 = -1;
        if (Fcast_recr_PH2 > max_phase) max_phase = Fcast_recr_PH2;
      }
      if (depletion_fleet > 0 && depletion_type == 1)
      {
        max_phase = 1;
        Fcast_recr_PH2 = -1;
      }
    }
    else
    {
      Fcast_recr_PH2 = -1;
    }
  
    if (do_recdev != 0) {
      for (y = recdev_end + 1; y <= YrMax; y++)
      {
        ParCount++;
        if (Fcast_recr_PH2 > -1) {
          active_count++;
          active_parm(active_count) = ParCount;
        }
      }
    }
    if (Do_Impl_Error > 0) {
      for (y = endyr + 1; y <= YrMax; y++)
      {
        ParCount++;
        if (Fcast_recr_PH2 > -1)
        {
          active_count++;
          active_parm(active_count) = ParCount;
        }
      }
    }
  }
  else
  {
    Fcast_recr_PH2 = -1;
  }
  
  echoinput << "Fcast_dev_phase (read and adjusted): " << Fcast_recr_PH_rd << " " << Fcast_recr_PH2 << endl;
  
  for (s = 1; s <= nseas; s++)
    for (f = 1; f <= Nfleet; f++)
    {
      if (init_F_loc(s, f) > 0)
      {
        j = init_F_loc(s, f);
        ParCount++;
        if (init_F_PH(j) == -9999) {
          init_F_parm_1(j, 3) = prof_var(prof_var_cnt);
          init_F_RD(j) = init_F_parm_1(j, 3);
          prof_var_cnt++;
        }
        if (depletion_fleet > 0 && depletion_type < 2 && init_F_PH(j) > 0) init_F_PH(j)++;
        if (init_F_PH(j) > Turn_off_phase2) init_F_PH(j) = -1;
        if (init_F_PH(j) > max_phase) max_phase = init_F_PH(j);
        if (init_F_PH(j) >= 0)
        {
          active_count++;
          active_parm(active_count) = ParCount;
        }
      }
    }
  
  if (N_Fparm > 0)
  {
    Fparm_PH_dim.deallocate();
    Fparm_PH_dim.allocate(1, N_Fparm);
    for (g = 1; g <= N_Fparm; g++)
    {
      ParCount++;
      if (depletion_fleet > 0 && depletion_type < 2 && Fparm_PH[g] > 0) Fparm_PH[g]++; //  increase phase by 1
      if (Fparm_PH[g] > Turn_off_phase2) Fparm_PH[g] = -1;
      if (Fparm_PH[g] > max_phase) max_phase = Fparm_PH[g];
      Fparm_PH_dim(g) = Fparm_PH[g];  //  move values into ivector
      if (Fparm_PH[g] > 0)
      {
        active_count++;
        active_parm(active_count) = ParCount;
      }
    echoinput<<g<<" dim  "<<Fparm_PH_dim(g)<<endl;
    }
  }
  
  for (f = 1; f <= Q_Npar2; f++)
  {
    ParCount++;
    if (Q_parm_PH(f) == -9999) {
      Q_parm_1(f, 3) = prof_var(prof_var_cnt);
      Q_parm_RD(f, 3) = prof_var(prof_var_cnt);
      prof_var_cnt++;
    }
    if (depletion_fleet > 0 && depletion_type < 2 && Q_parm_PH(f) > 0) Q_parm_PH(f)++;
    if (Q_parm_PH(f) > Turn_off_phase2) Q_parm_PH(f) = -1;
    if (Q_parm_PH(f) > max_phase) max_phase = Q_parm_PH(f);
    if (Q_parm_PH(f) >= 0)
    {
      active_count++;
      active_parm(active_count) = ParCount;
    }
  }
  
  //  SS_Label_Info_4.14.2 #Auto-generate cubic spline setup while inside this parameter counting loop
  Ip = 0;
  int N_knots;
  for (f = 1; f <= 2 * Nfleet; f++) //  check for cubic spline setup
  {
    if (f <= Nfleet)
    {
      fs = f;
    }
    else
    {
      fs = f - Nfleet;
    }
    if (seltype(f, 1) == 27 || seltype(f, 1) == 42) //  reset the cubic spline knots for size or age comp
    {
      // TODO - may need adjustments below for selex pattern 42
  
      k = int(selparm_RD(Ip + 1)); // setup method
      N_knots = seltype(f, 4); //  number of knots
  
      if (k == 0 || k == 10)
      {
      } //  do nothing
      else if (k == 1 || k == 2 || k == 11 || k == 12) //  get new knots according to cumulative distribution of data
      {
        echoinput << "Adjust the ";
        if (f <= Nfleet)
        {
          echoinput << "size-based ";
        }
        else
        {
          echoinput << "age-based ";
        }
        echoinput << "cubic spline setup for fleet: " << fs << endl;
  
        j = 4; // counter for which knot is being set (first knot is 4th spline parameter line)
        z = 1; //  counter for  bins in cumulative distribution
        if (N_knots >= 3)
        {
          temp = 0.025;
          temp1 = 0.950 / float(N_knots - 1); //  increment
        }
        else
        {
          warnstream << "There must be at least 3 knots in spline ";
          write_message (FATAL, 0); // EXIT!
        }
        if (f <= Nfleet) // doing size Selex
        {
          // exit if no length data available on which to base the knots
          if (Nobs_l(fs) == 0)
          {
            warnstream << "No length data for fleet " << fs << ": can't autogenerate cubic spline knots ";
            write_message (FATAL, 0); // EXIT!
          }
          // calculate cumulative length distribution
          dvector templen(1, nlen_bin);
          templen.initialize();
          for (s = 1; s <= nseas; s++)
          {
            templen += obs_l_all(2, s, f);
          }
          templen /= double(nseas);
          while (temp <= 0.975001)
          {
            while (templen(z) < temp)
            {
              z++;
            }
            //  intermediate knots are calculated from data_length_bins
            if (z > 1)
            {
              selparm_RD(Ip + j) = len_bins_dat(z - 1) + (temp - templen(z - 1)) / (templen(z) - templen(z - 1)) * (len_bins_dat(z) - len_bins_dat(z - 1));
            }
            else
            {
              selparm_RD(Ip + j) = len_bins_dat(z);
            }
            j++;
            temp += temp1;
          }
          echoinput << "len_bins_dat: " << len_bins_dat << endl;
          echoinput << "Cum_comp: " << templen << endl;
          echoinput << "Knots: " << selparm_RD(Ip + 3 + 1, Ip + 3 + N_knots) << endl;
        }
        else //  age selex
        {
          // exit if no age data available on which to base the knots
          if (Nobs_a(fs) == 0)
          {
            warnstream << "no age data for fleet " << fs << ": can't autogenerate cubic spline knots ";
            write_message (FATAL, 0); // EXIT!
          }
          // calculate cumulative age distribution
          dvector tempage(1, n_abins);
          tempage.initialize();
          for (s = 1; s <= nseas; s++)
          {
            tempage += obs_a_all(2, s, fs);
          }
          tempage /= double(nseas);
          while (temp <= 0.975001)
          {
            while (tempage(z) < temp)
            {
              z++;
            }
            //  intermediate knots are calculated from age_bins
            if (z > 1)
            {
              selparm_RD(Ip + j) = age_bins(z - 1) + (temp - tempage(z - 1)) / (tempage(z) - tempage(z - 1)) * (age_bins(z) - age_bins(z - 1));
            }
            else
            {
              selparm_RD(Ip + j) = age_bins(z);
            }
            j++;
            temp += temp1;
          }
          echoinput << "age_bins: " << age_bins << endl;
          echoinput << "Cum_comp: " << tempage(1, n_abins) << endl;
          echoinput << "Knots: " << selparm_RD(Ip + 3 + 1, Ip + 3 + N_knots) << endl;
        }
        if (k == 2 || k == 12) //  create default bounds, priors, etc.
        {
          echoinput << "Do complete setup of lo, hi, prior, etc. for cubic spline" << endl;
          for (z = Ip + 4; z <= Ip + 3 + N_knots; z++)
          {
            // set bounds at outer limits of data bins
            if (f <= Nfleet)
            {
              selparm_LO(z) = len_bins_dat(1);
              selparm_HI(z) = len_bins_dat(nlen_bin);
            }
            else
            {
              selparm_LO(z) = age_bins(1);
              selparm_HI(z) = age_bins(n_abins);
            }
            // set prior at mid-point
            selparm_PR(z) = int((selparm_LO(z) + selparm_HI(z)) / 2.);
            // set prior type to 0 and SD to 1.0
            selparm_PRtype(z) = 0;
            selparm_CV(z) = 1.0;
            // set phase for knots to negative
            selparm_PH(z) = -99;
          }
  
          if (N_knots == 3)
          {
            p = 8;
          }
          else if (N_knots == 4)
          {
            p = 10;
          }
          else
          {
            p = 3 + N_knots + 1 + 0.5 * N_knots;
          }
          // loop over parameters for splines value at each knot
          for (z = N_knots + 1 + 3; z <= 3 + 2 * N_knots; z++)
          {
            a = Ip + z;
            // set initial value for each parameter
            if (z <= p)
            {
              selparm_RD(a) = -5. + float(z - (N_knots + 4)) / float(p - (N_knots + 4)) * 4.;
            }
            else
            {
              selparm_RD(a) = 0.0;
            }
            // set bounds and symmetric beta prior
            selparm_LO(a) = -9.;
            selparm_HI(a) = 7.;
            selparm_PR(a) = 0.;
            selparm_PRtype(a) = 1; //  symmetric beta
            selparm_CV(a) = 0.001;
            selparm_PH(a) = 2;
          }
          // fix one of the parameters at 0 (because rescaling removes a degree of freedom)
          selparm_PH(Ip + p) = -99;
          selparm_PRtype(Ip + p) = 0;
          selparm_CV(Ip + p) = 1.0;
          // set values for gradient parameters
          p = Ip + 1;
          selparm_LO(p) = 0.;
          selparm_HI(p) = 2.;
          selparm_PR(p) = 0.;
          selparm_PRtype(p) = 0;
          selparm_CV(p) = 1.0;
          selparm_PH(p) = -99;
          p++;
          selparm_LO(p) = -0.001;
          selparm_HI(p) = 1.;
          selparm_RD(p) = 0.1; // moderate positive gradient at bottom
          selparm_PR(p) = 0.;
          selparm_PRtype(p) = 1; // SYMMETRIC BETA
          selparm_CV(p) = 0.001;
          selparm_PH(p) = 3;
          p++;
          selparm_LO(p) = -1.;
          selparm_HI(p) = 0.001;
          if (N_knots >= 3)
          {
            selparm_RD(p) = -0.001; // small negative gradient at top
            selparm_PR(p) = 0.;
            selparm_PRtype(p) = 1;
            selparm_CV(p) = 0.001;
            selparm_PH(p) = 3;
          }
          else
          {
            selparm_RD(p) = 0.00;
            selparm_PR(p) = 0.;
            selparm_PRtype(p) = 0;
            selparm_CV(p) = 1.0;
            selparm_PH(p) = -99;
          }
  
          for (z = Ip + 1; z <= Ip + 3 + 2 * N_knots; z++)
          {
            selparm_1(z, 1) = selparm_LO(z);
            selparm_1(z, 2) = selparm_HI(z);
            selparm_1(z, 3) = selparm_RD(z);
            selparm_1(z, 4) = selparm_PR(z);
            selparm_1(z, 6) = selparm_PRtype(z);
            selparm_1(z, 5) = selparm_CV(z);
            selparm_1(z, 7) = selparm_PH(z);
          }
        }
      }
    }
    Ip += N_selparmvec(f);
  }
  selparm_PH_soft = selparm_PH;
  for (k = 1; k <= selparm_PH.indexmax(); k++)
  {
    ParCount++;
    if (selparm_PH(k) == -9999) {
      selparm_RD(k) = prof_var(prof_var_cnt);
      selparm_1(k) = prof_var(prof_var_cnt);
      prof_var_cnt++;
    }
    if (depletion_fleet > 0 && depletion_type < 2 && selparm_PH(k) > 0) selparm_PH(k)++;
    if (selparm_PH(k) > Turn_off_phase2) selparm_PH(k) = -1;
    if (selparm_PH(k) > max_phase) max_phase = selparm_PH(k);
    if (selparm_PH(k) >= 0)
    {
      active_count++;
      active_parm(active_count) = ParCount;
    }
  }
  
  if (Do_TG > 0)
  {
    for (k = 1; k <= 3 * N_TG + 2 * Nfleet1; k++)
    {
      ParCount++;
      if (depletion_fleet > 0 && depletion_type < 2 && TG_parm_PH(k) > 0) TG_parm_PH(k)++;
      if (TG_parm_PH(k) > Turn_off_phase2) TG_parm_PH(k) = -1;
      if (TG_parm_PH(k) > max_phase) max_phase = TG_parm_PH(k);
      if (TG_parm_PH(k) >= 0)
      {
        active_count++;
        active_parm(active_count) = ParCount;
      }
    }
  }
  
  if (timevary_cnt > 0)
  {
    for (j = 1; j <= timevary_cnt; j++) //  loop all timevary to set up devs; note that 2D_AR1 is counted in N_parm_dev, but not in timevary_cnt
    {
      ivector timevary_setup(1, 14);
      timevary_setup(1, 14) = timevary_def[j](1, 14);
      if (timevary_setup(8) > 0)
      {
        k = timevary_setup(8); //  dev vector used
        if (depletion_fleet > 0 && depletion_type < 2 && parm_dev_PH(k) > 0) parm_dev_PH(k)++; //  add 1 to phase if using depletion fleet
        if (parm_dev_PH(k) > Turn_off_phase2) parm_dev_PH(k) = -1;
        if (parm_dev_PH(k) > max_phase) max_phase = parm_dev_PH(k);
      }
    }
  }
  
  if (TwoD_AR_cnt > 0)
  {
    for (j = 1; j <= TwoD_AR_cnt; j++) //  loop all timevary to set up devs; note that 2D_AR1 is counted in N_parm_dev, but not in timevary_cnt
    {
      ivector TwoD_AR_setup(1, 13);
      TwoD_AR_setup(1, 13) = TwoD_AR_def[j](1, 13);
      if (TwoD_AR_setup(12) > 0)
      {
        k = TwoD_AR_setup(12); //  dev vector used
        if (depletion_fleet > 0 && depletion_type < 2 && parm_dev_PH(k) > 0) parm_dev_PH(k)++; //  add 1 to phase if using depletion fleet
        if (parm_dev_PH(k) > Turn_off_phase2) parm_dev_PH(k) = -1;
        if (parm_dev_PH(k) > max_phase) max_phase = parm_dev_PH(k);
      }
    }
  }
  
  if (N_parm_dev > 0)
  {
    for (k = 1; k <= N_parm_dev; k++)
    {
      for (y = parm_dev_minyr(k); y <= parm_dev_maxyr(k); y++)
      {
        ParCount++;
        if (parm_dev_PH(k) >= 0)
        {
          active_count++;
          active_parm(active_count) = ParCount;
        }
      }
    }
  }
  
  if (Do_Forecast > 0 && Turn_off_phase > 0)
  {
    if (Fcast_recr_PH == 0) // read value for forecast_PH.  This code is repeats earlier code in case other parameters have changed maxphase
    {
      if (depletion_fleet > 0 && depletion_type == 1)
      {
      }
      else
      {
        Fcast_recr_PH2 = max_phase + 1;
      }
    }
  }
  
  echoinput << "ParCount " << ParCount << "   Active parameters: " << active_count << endl
            << "Turn_off_phase " << Turn_off_phase << endl
            << " max_phase " << max_phase << endl;
  echoinput << active_parm.indexmax() << endl;
  
  if (Turn_off_phase <= 0)
  {
    func_eval(1) = 1;
  }
  else
  {
    func_conv(max_phase) = final_conv;
    func_eval(max_phase) = 10000;
    func_conv(max_phase + 1) = final_conv;
    func_eval(max_phase + 1) = 10000;
  }
  
  //  SS_Label_Info_4.14.3 #Add count of derived quantities and create labels for these quantities
  j = ParCount;
  active_parms = active_count;
  CoVar_Count = active_count;
  deriv_start = ParCount;
  deriv_covar_start = active_count;
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  echoinput << "deriv_start " << deriv_start << " " << deriv_covar_start << endl;
  onenum = "    ";
  for (y = styr - 2; y <= YrMax; y++)
  {
    if (STD_Yr_Reverse(y) > 0)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      if (y == styr - 2)
      {
        ParmLabel += "SSB_Virgin";
      }
      else if (y == styr - 1)
      {
        ParmLabel += "SSB_Initial";
      }
      else
      {
        //      _itoa(y,onenum,10);
        sprintf(onenum, "%d", y);
        ParmLabel += "SSB_" + onenum + CRLF(1);
      }
    }
  }
  
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  for (y = styr - 2; y <= YrMax; y++)
  {
    if (STD_Yr_Reverse(y) > 0)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      if (y == styr - 2)
      {
        ParmLabel += "Recr_Virgin";
      }
      else if (y == styr - 1)
      {
        ParmLabel += "Recr_Initial";
      }
      else
      {
        //      _itoa(y,onenum,10);
        sprintf(onenum, "%d", y);
        ParmLabel += "Recr_" + onenum + CRLF(1);
      }
    }
  }
  
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  for (y = styr; y <= YrMax; y++)
  {
    if (STD_Yr_Reverse_Ofish(y) > 0)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      //      _itoa(y,onenum,10);
      sprintf(onenum, "%d", y);
      ParmLabel += "SPRratio_" + onenum + CRLF(1);
    }
  }
  
  //F_std
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  for (y = styr; y <= YrMax; y++)
  {
    if (STD_Yr_Reverse_F(y) > 0)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      //      _itoa(y,onenum,10);
      sprintf(onenum, "%d", y);
      ParmLabel += "F_" + onenum + CRLF(1);
    }
  }
  
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  for (y = styr; y <= YrMax; y++)
  {
    if (STD_Yr_Reverse_Dep(y) > 0)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      //      _itoa(y,onenum,10);
      sprintf(onenum, "%d", y);
      ParmLabel += "Bratio_" + onenum + CRLF(1);
    }
  }
  echoinput << "parm " << j << " covar " << CoVar_Count << endl;
  //  create labels for Mgmt_Quant
  if (Do_Benchmark > 0)
  {
    ParmLabel += "SSB_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Totbio_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SmryBio_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Recr_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    if (Do_Benchmark == 1 || Do_Benchmark == 3)
    {
      ParmLabel += "SSB_Btgt" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "SPR_Btgt" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "annF_Btgt" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "Dead_Catch_Btgt" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
    }
    else if (Do_Benchmark == 2)
    {
      ParmLabel += "SSB_F01" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "SPR_F01" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "annF_F01" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "Dead_Catch_F01" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
    }
    ParmLabel += "SSB_SPR" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "annF_SPR" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dead_Catch_SPR" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SSB_MSY" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SPR_MSY" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "annF_MSY" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dead_Catch_MSY" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Ret_Catch_MSY" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "B_MSY/SSB_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
// add quantities needed when time-vary life history is used; but report here for all cases; elements 18-21 of mgmt_quant
    ParmLabel += "Recr_MSY_bmarkbio" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Depletion_denom" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "HCR_inflect" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "R0_for_SRR_bench" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SSB_for_SRR_bench" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;

    if (Do_Benchmark == 3)
    {
      ParmLabel += "SSB_Blim" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "annF_Blim" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      ParmLabel += "Dead_Catch_Blim" + CRLF(1);
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
    }
  }
  else
  {
    ParmLabel += "Bzero_again" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Totbio_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SmryBio_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Recr_unfished" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
  }
  
  echoinput << "parm " << j << " covar " << CoVar_Count << "  after benchmark " << endl;
  if (Do_Forecast > 0)
  {
    for (y = endyr + 1; y <= YrMax; y++)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      sprintf(onenum, "%d", y);
      ParmLabel += "ForeCatch_" + onenum + CRLF(1);
    }
    for (y = endyr + 1; y <= YrMax; y++)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      sprintf(onenum, "%d", y);
      ParmLabel += "OFLCatch_" + onenum + CRLF(1);
    }
    if (max(Do_Retain) > 0)
    {
      for (y = endyr + 1; y <= YrMax; y++)
      {
        CoVar_Count++;
        j++;
        active_parm(CoVar_Count) = j;
        sprintf(onenum, "%d", y);
        ParmLabel += "ForeCatchret_" + onenum + CRLF(1);
      }
    }
  }
  echoinput << "parm " << j << " covar " << CoVar_Count << "  after forecast " << endl;
  
  // do labels for Selex_Std
  if (Do_Selex_Std > 0)
  {
    echoinput << " do selex std labels " << Selex_Std_Cnt << " " << Selex_Std_AL << endl;
    for (g = 1; g <= gender; g++)
      for (i = 1; i <= Selex_Std_Cnt; i++)
      {
        CoVar_Count++;
        j++;
        active_parm(CoVar_Count) = j;
        if (Selex_Std_AL == 1)
        {
          if (Selex_Std_Pick(i) > nlength)
          {
            warnstream << "cannot select stdev for length bin greater than nlength " << Selex_Std_Pick(i) << " > " << nlength;
            write_message (FATAL, 0); // EXIT!
          }
          ParmLabel += "LenSelex_std_" + NumLbl(Do_Selex_Std) + "_" + GenderLbl(g) + "_L_" + NumLbl(len_bins(Selex_Std_Pick(i))) + CRLF(1);
        }
        else if (Selex_Std_AL == 2)
        {
          if (Selex_Std_Pick(i) > nages)
          {
            warnstream << "cannot select stdev for age bin greater than maxage " << Selex_Std_Pick(i) << " > " << nages;
            write_message (FATAL, 0); // EXIT!
          }
          ParmLabel += "AgeSelex_std_" + NumLbl(Do_Selex_Std) + "_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(Selex_Std_Pick(i)) + 1) + CRLF(1);
        }
        else if (Selex_Std_AL == 3)
        {
          if (Selex_Std_Pick(i) > nages)
          {
            warnstream << "cannot select stdev for age bin greater than maxage " << Selex_Std_Pick(i) << " > " << nages;
            write_message (FATAL, 0); // EXIT!
          }
          ParmLabel += "AgeLenSelex_std_" + NumLbl(Do_Selex_Std) + "_GP1_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(Selex_Std_Pick(i)) + 1) + CRLF(1);
        }
      }
  }
  if (Do_Growth_Std > 0)
  {
    echoinput << " do growth std labels " << Growth_Std_Cnt << endl;
    for (g = 1; g <= gender; g++)
      for (i = 1; i <= Growth_Std_Cnt; i++)
      {
        CoVar_Count++;
        j++;
        active_parm(CoVar_Count) = j;
        ParmLabel += "Grow_std_GP:_" + NumLbl(Do_Growth_Std) + "_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(Growth_Std_Pick(i)) + 1) + CRLF(1);
      }
  }
  
  if (Do_NatAge_Std != 0)
  {
    echoinput << " do natage std labels " << NatAge_Std_Cnt << endl;
    for (g = 1; g <= gender; g++)
      for (i = 1; i <= NatAge_Std_Cnt; i++)
      {
        CoVar_Count++;
        j++;
        active_parm(CoVar_Count) = j;
        if (Do_NatAge_Std > 0)
        {
          ParmLabel += "NatAge_std_" + NumLbl(Do_NatAge_Std) + "_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(NatAge_Std_Pick(i)) + 1) + CRLF(1);
        }
        else
        {
          ParmLabel += "NatAge_std_All_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(NatAge_Std_Pick(i)) + 1) + CRLF(1);
        }
      }
  }
  
  if (Do_NatM_Std > 0)
  {
    echoinput << " do NatM std labels " << NatM_Std_Cnt << endl;
    for (g = 1; g <= gender; g++)
      for (i = 1; i <= NatM_Std_Cnt; i++)
      {
        CoVar_Count++;
        j++;
        active_parm(CoVar_Count) = j;
        // cout<<"i: "<<i<<endl;
        // cout<<"NatM_Std_Pick(i): "<<NatM_Std_Pick(i)<<endl;
        // cout<<"age_vector(NatM_Std_Pick(i)): "<<age_vector(NatM_Std_Pick(i))<<endl;
        // cout<<"NumLbl0(age_vector(NatM_Std_Pick(i))+1): "<<NumLbl0(age_vector(NatM_Std_Pick(i))+1)<<endl;
        ParmLabel += "NatM_std_GP:_" + NumLbl(Do_NatM_Std) + "_" + GenderLbl(g) + "_A_" + NumLbl0(age_vector(NatM_Std_Pick(i)) + 1) + CRLF(1);
      }
  }
  
  if (Do_Dyn_Bzero > 0)
  {
    echoinput << " do Dyn Bzero std labels " << endl;
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dyn_Bzero_Virg" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dyn_Bzero_InitEq" + CRLF(1);
    for (y = styr; y <= YrMax; y++)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      sprintf(onenum, "%d", y);
      ParmLabel += "Dyn_Bzero_" + onenum + CRLF(1);
    }
  }
  else if (depletion_basis_rd == 5)
  {
    warnstream << "must select dyn_bzero in control file extra_std for it to be used as depletion denominator ";
    write_message (FATAL, 0); // EXIT!
  }
  if (More_Std_Input(12) == 2)
  {
    echoinput << " do Dyn Bzero Recruits std labels " << endl;
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dyn_Recr_Virg" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "Dyn_Recr_InitEq" + CRLF(1);
    for (y = styr; y <= YrMax; y++)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      sprintf(onenum, "%d", y);
      ParmLabel += "Dyn_Recr_" + onenum + CRLF(1);
    }
  }
  
  //  output ln(SSB) std for selected years
  echoinput << " do ln(SSB) std labels for 3 years" << endl;
  CoVar_Count++;
  j++;
  active_parm(CoVar_Count) = j;
  sprintf(onenum, "%d", styr);
  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
  CoVar_Count++;
  j++;
  active_parm(CoVar_Count) = j;
  sprintf(onenum, "%d", int((endyr + styr) / 2));
  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
  CoVar_Count++;
  j++;
  active_parm(CoVar_Count) = j;
  sprintf(onenum, "%d", endyr);
  ParmLabel += "ln(SSB)_" + onenum + CRLF(1);
  
  if (Do_se_smrybio > 0)
  {
    echoinput << " do SmryBio std labels " << endl;
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SmryBio_Virg" + CRLF(1);
    CoVar_Count++;
    j++;
    active_parm(CoVar_Count) = j;
    ParmLabel += "SmryBio_InitEq" + CRLF(1);
    for (y = styr; y <= YrMax; y++)
    {
      CoVar_Count++;
      j++;
      active_parm(CoVar_Count) = j;
      sprintf(onenum, "%d", y);
      ParmLabel += "SmryBio_" + onenum + CRLF(1);
    }
  }
  
  //  output Svy_sdreport value std for selected years
  echoinput << " do Svy_sdreport labels " << Svy_N_sdreport << endl;
  if (Svy_N_sdreport > 0)
  {
    k = 0;
    for (f = 1; f <= Nfleet; ++f)
    {
      if (Svy_sdreport(f) > 0)
      {
        for (i = 1; i <= Svy_N_fleet(f); i++)
        {
          CoVar_Count++;
          j++;
          active_parm(CoVar_Count) = j;
          sprintf(onenum, "%d", Svy_yr(f, i));
          ParmLabel += fleetname(f) + "_" + onenum + CRLF(1);
        }
      }
    }
  }
  
  // additional labels
  echoinput << "parm " << j << " covar " << CoVar_Count << "  after all derived quantities " << endl;
  sprintf(onenum, "%d", int(100 * depletion_level));
  switch (depletion_basis)
  {
    case 0:
    {
      depletion_basis_label += "no_depletion_basis";
      break;
    }
    case 1:
    {
      depletion_basis_label += " " + onenum + "%*Virgin_Biomass";
      break;
    }
    case 2:
    {
      depletion_basis_label += " " + onenum + "%*B_MSY";
      break;
    }
    case 3:
    {
      depletion_basis_label += " " + onenum + "%*StartYr_Biomass";
      break;
    }
    case 4:
    {
      depletion_basis_label += " " + onenum + "%*EndYr_Biomass";
      break;
    }
    case 5:
    {
      depletion_basis_label += " " + onenum + "%*Dyn_Bzero";
      break;
    }
    case 6:
    {
      depletion_basis_label += " " + onenum + "%*Bmark_Biomass";
      break;
    }
  }
  if (depletion_log == 1) depletion_basis_label += ";log";
  if (depletion_multi > 1)
  {
    sprintf(onenum, "%d", depletion_multi);
    depletion_basis_label += ";multi:" + onenum;
  }
  
  switch (SPR_reporting)
  {
    case 0: // skip SPR reporting
    {
      SPR_report_label += " raw_SPR";
      break;
    }
    case 5: // keep as raw %SPR value
    {
      SPR_report_label += " raw_SPR";
      break;
    }
    case 1: // compare to SPR
    {
      sprintf(onenum, "%d", int(100. * SPR_target));
      SPR_report_label += " (1-SPR)/(1-SPR_" + onenum + "%)";
      break;
    }
    case 2: // compare to SPR_MSY
    {
      SPR_report_label += " (1-SPR)/(1-SPR_MSY)";
      break;
    }
    case 3: // compare to SPR_Btarget
    {
      sprintf(onenum, "%d", int(100. * BTGT_frac));
      SPR_report_label += " (1-SPR)/(1-SPR_at_B" + onenum + "%)";
      break;
    }
    case 4:
    {
      SPR_report_label += " 1-SPR";
      break;
    }
  }
  
  switch (F_std_basis)
  {
    case 0: // raw
    {
      F_report_label = "_abs_F";
      break;
    }
    case 1:
    {
      sprintf(onenum, "%d", int(100. * SPR_target));
      F_report_label = "(F)/(F" + onenum + "%SPR)";
      break;
    }
    case 2:
    {
      F_report_label = "(F)/(Fmsy)";
      break;
    }
    case 3:
    {
      sprintf(onenum, "%d", int(100. * BTGT_frac));
      F_report_label = "(F)/(F_at_B" + onenum + "%)";
      break;
    }
  }
  
  switch (F_reporting)
  {
    case 0: // keep as raw value
    {
      F_report_label += ";_no_F_report";
      break;
    }
    case 1: // exploitation rate in biomass
    {
      F_report_label += ";_with_F=Exploit(bio)";
      break;
    }
    case 2: // exploitation rate in numbers
    {
      F_report_label += ";_with_F=Exploit(num)";
      break;
    }
    case 3: // sum of F mults
    {
      F_report_label += ";_with_F=sum(full_Fs)";
      break;
    }
    case 4: // F=Z-M for specified ages
    {
      F_report_label += ";_with_F=Z-M;_for_ages_";
      sprintf(onenum, "%d", int(F_reporting_ages(1)));
      F_report_label += onenum;
      sprintf(onenum, "%d", int(F_reporting_ages(2)));
      F_report_label += "_" + onenum;
      break;
    }
    case 5: // F=Z-M for specified ages (unweighted)
    {
      F_report_label += ";_with_F=Z-M;_for_ages_unweighted_";
      sprintf(onenum, "%d", int(F_reporting_ages(1)));
      F_report_label += onenum;
      sprintf(onenum, "%d", int(F_reporting_ages(2)));
      F_report_label += "_" + onenum;
      break;
    }
  }
  if (F_std_log == 1) F_report_label += ";log";
  if (F_std_multi > 1)
  {
    sprintf(onenum, "%d", F_std_multi);
    F_report_label += ";multi:" + onenum;
  }
  
  echoinput << "Active parameters plus derived quantities:  " << CoVar_Count << endl;
  // clang-format off
 END_CALCS

//  containers for parameter values after jitter
    vector MGparm_use(1,N_MGparm2)
    vector SRparm_use(1,N_SRparm3);
    vector recdev_cycle_use(1,recdev_cycle);
    vector recdev_use(recdev_first,YrMax);
    vector recdev_RD(recdev_first,YrMax);
    vector Q_parm_use(1,Q_Npar2);
    vector init_F_use(1,N_init_F);
    vector Fparm_use(1,N_Fparm);
    vector selparm_use(1,N_selparm2);
!!k=Do_TG*(3*N_TG+2*Nfleet1);
    vector TG_parm_use(1,k);
    matrix parm_dev_RD(1,N_parm_dev,parm_dev_minyr,parm_dev_maxyr);
    matrix parm_dev_use(1,N_parm_dev,parm_dev_minyr,parm_dev_maxyr);

!!k=gmorph*(YrMax-styr+1);
!!//  SS_Label_Info_4.14.4 #Create matrix CoVar and set it to receive the covariance output
  matrix save_G_parm(1,k,1,22);
  matrix save_seas_parm(1,nseas,1,10);
  matrix CoVar(1,CoVar_Count,1,CoVar_Count+1);
!!save_G_parm.initialize();
!!CoVar.initialize();
!!set_covariance_matrix(CoVar);

  //  SS_Label_Info_4.15 #Prepare for read empirical wt-at-age, which happens in prelim
  int N_WTage_rd
  int N_WTage_maxage
  int y2
  ivector last_yr_read(-2,Nfleet)
  ivector filled_once(-2,Nfleet)
  int f2