SS_readstarter.tpl

// clang-format off
// SS_Label_file  #1. **SS_readstarter.tpl**
// SS_Label_file  #  * define many global constants, also see GLOBALS_SECTION
// SS_Label_file  #  * create list of pick_report_name values
// SS_Label_file  #  * read and process *starter.ss*
// SS_Label_file  #  * read *runnumber.ss*
// SS_Label_file  #  * read *profilevalues.ss*
// SS_Label_file  #

//*********COUNTERS*************************
  int z;  // counters for size (length)
  int z1; // min for z counter
  int z2; // max for z counter
  int L1; //  for selecting sex specific length data
  int L2; //  used for l+nlength to get length bin for males
  int A2; //  used for a+nages+1 to get true age bin for males
  int a1; // use to track a subset of ages
  int f;  // counter for fleets and surveys.  total is Ntypes
  int f1; // another fleet counter
  int fs; //  counter for fleets when looping across size and ageselex; so = f-Ntypes

  int gmorph; // number of biological entities:  gender*GP*BirthEvent*Platoon
  int g;  // counter for biological entity
  int GPat; //  counter for Gpattern (morph)
  int gg; // counter for sex
  int gp; //  counter for sex*GPat  or for Gpat
  int gp2; //  used to loop platoons within Gpattern

  int a;  // counter for ages
  int b;  // counter for age bins
  int p;  // counter for area
  int p1;
  int p2; // counter for destination area in migration
  int i;  // counter for observations
  int y;  // counter for year
  int yz; // year, but not allowed to extend past endyr
  int s;  // counter for seasons
  int s2; // destination season
  int mid_subseas; //  index of the subseas that corresponds to the middle of the season
  int subseas; //  subseas, mostly used to calc ALK_idx
  int ALK_idx; //  index to which subseas within current year to use for the ALK  ALK_idx=(s-1)*N_subseas+subseas
  int ALK_time; //  continuous index to subseas =(y-styr)*nseas*N_subseas+ALK_idx
  int ALK_idx_mid; //  index of subseason at middle of season
  int t;  // counter for time, combining year and season
  int mo; //  month (1-12), not (0-11)
  int j;
  int j1;
  int j2;
  int k;
  int k1;
  int k2;
  int k3;
  int special_flag; //  reserved for ephemeral use while developing code
  int s_off; // offset for male section of vectors
  int Fishon; // whether or not to do fishery catch in equil_calc
  int NP; // number of parameters
  int Ip; // parameter counter
  int firstseas; // used to start season loops at the birthseason
  int t_base;  //
  int niter; // iteration count
  int loop;
  int TG_t;  // time counter (in seasons) for tag groups

  int Fcast_catch_start;
//  int ParCount;
  int retParCount;
  int N_SC; // counter for starter comments
  int N_DC;
  int N_CC;
  int N_FC;

  int catch_mult_pointer;

  int frac_female_pointer;
  int finished_minimize;
  int icycle;
  int No_Report; // flag to skip output reports after MCMC and MCeval
  int mcmcFlag;
  int noest_flag;
  number temp;
  number temp1;
  int save_for_report;
  int bigsaver; // (save_for_report>0) || ((sd_phase() || mceval_phase()) && (initial_params::mc_phase==0))
  int write_bodywt;
  int write_bodywt_save;
  int save_gparm;
  int save_gparm_print;
!! save_for_report = 0;
!! bigsaver = 0;
!! write_bodywt = 0;
!! write_bodywt_save = 0;
!! special_flag = 0;

  int Nparm_on_bound;
  int on;
  int SDmode;
  int maxI;

 LOCAL_CALCS
  // clang-format on
  maxI = 999;
  on = 0;
  No_Report = 0;
  Ncycle = 3;
  z = 0;
  z1 = 0;
  z2 = 0;
  L1 = 0;
  L2 = 0;
  A2 = 0;
  a1 = 0;
  f = 0;
  f1 = 0;
  fs = 0;
  gmorph = 0;
  g = 0;
  GPat = 0;
  gg = 0;
  gp = 0;
  gp2 = 0;
  a = 0;
  b = 0;
  p = 0;
  p1 = 0;
  p2 = 0;
  i = 0;
  y = 0;
  yz = 0;
  s = 0;
  s2 = 0;
  mid_subseas = 0;
  subseas = 0;
  ALK_idx = 0;
  ALK_time = 0;
  ALK_idx_mid = 0;
  t = 0;
  mo = 0;
  j = 0;
  j1 = 0;
  j2 = 0;
  k = 0;
  k1 = 0;
  k2 = 0;
  k3 = 0;
  s_off = 0;
  Fishon = 0;
  NP = 0;
  Ip = 0;
  firstseas = 0;
  t_base = 0;
  niter = 0;
  loop = 0;
  TG_t = 0;
  Fcast_catch_start = 0;
  retParCount = 0;
  N_SC = 0;
  N_DC = 0;
  N_CC = 0;
  N_FC = 0;
  catch_mult_pointer = 0;
  frac_female_pointer = 0;
  icycle = 0;
  No_Report = 0;
  mcmcFlag = 0;
  noest_flag = 0;
  temp = 0;
  temp1 = 0;
  save_gparm_print = 0;
  finished_minimize = 0;
  // SS_Label_Info_1.1.2 #arrays for parameter labels are created in GLOBAL
  // adstring_array NumLbl;
  // adstring_array GenderLbl;   // gender label
  // adstring_array CRLF;   // blank to terminate lines

  MessageIntro += " Information: "; // information that could be useful
  MessageIntro += " Suggestion: ";  // a possible better way
  MessageIntro += " Performance: "; // can help performance
  MessageIntro += " : ";            // might be a problem, execution continues anyway
  MessageIntro += " Adjustment: ";  // adjustment has been made, execution continues
  MessageIntro += " Fatal Error! "; // major problem, program will exit

  CRLF += "";
  GenderLbl += "Fem";
  GenderLbl += "Mal";
  GP_Lbl += "_GP_1";
  GP_Lbl += "_GP_2";
  GP_Lbl += "_GP_3";
  GP_Lbl += "_GP_4";
  GP_Lbl += "_GP_5";
  GP_Lbl += "_GP_6";
  onenum = "    ";
  for (i = 1; i <= 199; i++) /* SS_loop: fill string NumLbl with numbers (start at 1) */
  {
    sprintf(onenum, "%d", i);
    NumLbl += onenum + CRLF(1);
  }
  for (i = 0; i <= 198; i++) /* SS_loop: fill string NumLbl0 with numbers (start at 0) */
  {
    sprintf(onenum, "%d", i);
    NumLbl0 += onenum + CRLF(1);
  }
  pick_report_name += "DEFINITIONS report:1";
  pick_report_use += "N";
  pick_report_name += "LIKELIHOOD report:2";
  pick_report_use += "N";
  pick_report_name += "Input_Variance_Adjustment report:3";
  pick_report_use += "N";
  pick_report_name += "Parm_devs_detail report:4";
  pick_report_use += "N";
  pick_report_name += "PARAMETERS report:5";
  pick_report_use += "N";
  pick_report_name += "DERIVED_QUANTITIES report:6";
  pick_report_use += "N";
  pick_report_name += "MGparm_By_Year_after_adjustments report:7";
  pick_report_use += "N";
  pick_report_name += "selparm(Size)_By_Year_after_adjustments report:8";
  pick_report_use += "N";
  pick_report_name += "selparm(Age)_By_Year_after_adjustments report:9";
  pick_report_use += "N";
  pick_report_name += "RECRUITMENT_DIST report:10";
  pick_report_use += "N";
  pick_report_name += "MORPH_INDEXING report:11";
  pick_report_use += "N";
  pick_report_name += "SIZEFREQ_TRANSLATION report:12";
  pick_report_use += "N";
  pick_report_name += "MOVEMENT report:13";
  pick_report_use += "N";
  pick_report_name += "EXPLOITATION report:14";
  pick_report_use += "N";
  pick_report_name += "CATCH report:15";
  pick_report_use += "N";
  pick_report_name += "TIME_SERIES report:16";
  pick_report_use += "N";
  pick_report_name += "SPR_SERIES report:17";
  pick_report_use += "N";
  pick_report_name += "Kobe_Plot report:18";
  pick_report_use += "N";
  pick_report_name += "SPAWN_RECRUIT report:19";
  pick_report_use += "N";
  pick_report_name += "SPAWN_RECR_CURVE report:20";
  pick_report_use += "N";
  pick_report_name += "INDEX_1 report:21 summary";
  pick_report_use += "N";
  pick_report_name += "INDEX_2 report:22 annual";
  pick_report_use += "N";
  pick_report_name += "INDEX_3 report:23 Qparms";
  pick_report_use += "N";
  pick_report_name += "DISCARD_SPECIFICATION report:24";
  pick_report_use += "N";
  pick_report_name += "DISCARD_OUTPUT report:25";
  pick_report_use += "N";
  pick_report_name += "MEAN_BODY_WT_OUTPUT report:26";
  pick_report_use += "N";
  pick_report_name += "FIT_LEN_COMPS report:27";
  pick_report_use += "N";
  pick_report_name += "FIT_AGE_COMPS report:28";
  pick_report_use += "N";
  pick_report_name += "FIT_SIZE_COMPS report:29";
  pick_report_use += "N";
  pick_report_name += "OVERALL_COMPS report:30";
  pick_report_use += "N";
  pick_report_name += "LEN_SELEX report:31";
  pick_report_use += "N";
  pick_report_name += "AGE_SELEX report:32";
  pick_report_use += "N";
  pick_report_name += "ENVIRONMENTAL_DATA report:33";
  pick_report_use += "N";
  pick_report_name += "TAG_Recapture report:34";
  pick_report_use += "N";
  pick_report_name += "NUMBERS_AT_AGE report:35";
  pick_report_use += "N";
  pick_report_name += "BIOMASS_AT_AGE report:36";
  pick_report_use += "N";
  pick_report_name += "NUMBERS_AT_LENGTH report:37";
  pick_report_use += "N";
  pick_report_name += "BIOMASS_AT_LENGTH report:38";
  pick_report_use += "N";
  pick_report_name += "F_AT_AGE report:39";
  pick_report_use += "N";
  pick_report_name += "CATCH_AT_AGE report:40";
  pick_report_use += "N";
  pick_report_name += "DISCARD_AT_AGE report:41";
  pick_report_use += "N";
  pick_report_name += "BIOLOGY report:42";
  pick_report_use += "N";
  pick_report_name += "Natural_Mortality report:43";
  pick_report_use += "N";
  pick_report_name += "AGE_SPECIFIC_K report:44";
  pick_report_use += "N";
  pick_report_name += "Growth_Parameters report:45";
  pick_report_use += "N";
  pick_report_name += "Seas_Effects report:46";
  pick_report_use += "N";
  pick_report_name += "Biology_at_age_in_endyr report:47";
  pick_report_use += "N";
  pick_report_name += "MEAN_BODY_WT(Begin) report:48";
  pick_report_use += "N";
  pick_report_name += "MEAN_SIZE_TIMESERIES report:49";
  pick_report_use += "N";
  pick_report_name += "AGE_LENGTH_KEY report:50";
  pick_report_use += "N";
  pick_report_name += "AGE_AGE_KEY report:51";
  pick_report_use += "N";
  pick_report_name += "COMPOSITION_DATABASE report:52";
  pick_report_use += "N";
  pick_report_name += "SELEX_database report:53";
  pick_report_use += "N";
  pick_report_name += "SPR/YPR_Profile report:54";
  pick_report_use += "N";
  pick_report_name += "GLOBAL_MSY report:55";
  pick_report_use += "N";
  pick_report_name += "SS_summary.sso report:56";
  pick_report_use += "N";
  pick_report_name += "rebuilder.sso report:57";
  pick_report_use += "N";
  pick_report_name += "SIStable.sso report:58";
  pick_report_use += "N";
  pick_report_name += "Dynamic_Bzero report:59";
  pick_report_use += "N";
  pick_report_name += "wtatage.ss_new report:60";
  pick_report_use += "N";
  pick_report_name += "ANNUAL_TIME_SERIES report:61";
  pick_report_use += "N";

  // check command line inputs

  if ((on = option_match(argc, argv, "-noest")) > -1)
  {
    warnstream << "SS3 is not configured to work with -noest; use -stopph <maxphase> instead which overrides maxphase in starter.ss";
    write_message(FATAL, 0);
  }

  if ((on = option_match(argc, argv, "-maxI")) > -1 || (on = option_match(argc, argv, "-stopph")) > -1)
  {
    // if maxI > 999, maxphase will reset to maxI
    maxI = atoi(ad_comm::argv[on + 1]);
    echoinput << "read max phase to override starter file's maxphase " << maxI << endl;
  }

  if ((on = option_match(argc, argv, "modelname")) > -1 )
  {
    base_modelname = ad_comm::argv[on + 1];
    echoinput << "read basemodel name to use instead of ss3 " << base_modelname << endl;
  cout << " base name " << base_modelname << endl;
  }

  SDmode = 1;
  if ((on = option_match(argc, argv, "-nohess")) > -1)
  {
    SDmode = 0;
  }
  echoinput << " -nohess flag (1 means do Hessian): " << SDmode << endl;
  adstring sw; //  used for reading of ADMB switches from command line
  mcmcFlag = 0;
  noest_flag = 0;
  for (i = 0; i < argc; i++) /* SS_loop: check command line arguments for mcmc commands */
  {
    sw = argv[i];
    j = strcmp(sw, "-mcmc");
    if (j == 0)
    {
      mcmcFlag = 1;
    }
    j = strcmp(sw, "-mceval");
    if (j == 0)
    {
      mcmcFlag = 1;
    }
  }
  // clang-format off

  // SS_Label_Info_1.2  #Read the starter.ss file
  // SS_Label_Flow  read starter.ss
  ad_comm::change_datafile_name("starter.ss"); //  get filenames
  cout << " reading from starter.ss" << endl;
  adstring checkchar;
  line_adstring readline;
  checkchar = "";
  ifstream Starter_Stream("starter.ss");
  //  this opens a different logical file with a separate pointer from the pointer that ADMB uses when reading using init command to read from global_datafile
  k = 0;
  N_SC = 0;
  while (k == 0)
  {
    Starter_Stream >> readline; // reads a single 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_SC++;
        Starter_Comments += readline;
      }
    }
  }
  echoinput << version_info(1) << version_info(2) << version_info(3) << endl
            << version_info2 << endl;
  warning << version_info(1) << version_info(2) << version_info(3) << endl
          << version_info2 << endl;
  warning << "This file contains warnings, suggestions and notes generated as files are read and processed" << endl
          << endl;
 END_CALCS


  init_adstring datfilename
!!echoinput << datfilename << "  datfilename" << endl;
  init_adstring ctlfilename
!!echoinput << ctlfilename << "  ctlfilename" << endl;
  init_int readparfile
!!echoinput << readparfile << "  readparfile" << endl;
  init_int rundetail
!!echoinput << rundetail << "  rundetail" << endl;
  init_int reportdetail
  int rd_background

 LOCAL_CALCS
      // clang-format on
      struct stat pathinfo;
  if (stat("./ssnew", &pathinfo) != 0)
  {
    ssnew_pathname = "";
  }
  else
  {
    ssnew_pathname = "./ssnew/";
  }

  if (stat("./sso", &pathinfo) != 0)
  {
    sso_pathname = "";
  }
  else
  {
    sso_pathname = "./sso/";
  }

  warning.open(sso_pathname + "warning.sso");
  echoinput.open(sso_pathname + "echoinput.sso");
  ParmTrace.open(sso_pathname + "ParmTrace.sso");
  report5.open(sso_pathname + "Forecast-report.sso");
  report2.open(sso_pathname + "CumReport.sso", ios::app);
  bodywtout.open(ssnew_pathname + "wtatage.ss_new");
  // clang-format off
 END_CALCS


 LOCAL_CALCS
  // clang-format on
  if (reportdetail < 0 || reportdetail > 3)
    reportdetail = 0;
  echoinput << reportdetail << "  reportdetail 0=minimal for data-limited, 1=all, 2=no growth, 3=custom" << endl;
  if (reportdetail == 3)
  {
    // -101 means to select all
    // -100 means to select data-limited
    // -102 means to select no growth or length
    // positive integer means to add that item to selected list
    // negative integer means to remove selected item from list
    // -999 means to stop reading items for the list
    ender = 0;
    do
    {
      ivector tempin(1, 1);
      *(ad_comm::global_datafile) >> tempin(1, 1);
      if (tempin(1) == -999)
        ender = 1;
      reportdetail_list.push_back(tempin(1, 1));
    } while (ender == 0);
    int Nrec = reportdetail_list.size() - 2;
    for (int j = 0; j <= Nrec; j++)
    {
      if (reportdetail_list[j](1) == -100) rd_background = 0;
      if (reportdetail_list[j](1) == -101) rd_background = 1;
      if (reportdetail_list[j](1) == -102) rd_background = 2;
    }
  }
  else
  {
    rd_background = reportdetail; // 0=limited; 2=brief; 1=all
  }

  // set background set of picked reports; then set custom if reportdetail==3
  for (k = 1; k <= 60; k++)
  {
    pick_report_use(k) = "N"; // all off
  }
  if (rd_background == 0) // limited
  {
    pick_report_use(1) = "Y";
    pick_report_use(2) = "Y";
    pick_report_use(5) = "Y";
    pick_report_use(6) = "Y";
    pick_report_use(14) = "Y";
    pick_report_use(15) = "Y";
    pick_report_use(16) = "Y";
    pick_report_use(61) = "Y";
  }
  else if (rd_background == 2) // brief, no growth or length
  {
    for (k = 1; k <= 61; k++)
    {
      pick_report_use(k) = "Y"; // start with all on
    }
    pick_report_use(7) = "N";
    pick_report_use(8) = "N";
    pick_report_use(11) = "N";
    pick_report_use(12) = "N";
    pick_report_use(13) = "Y";
    pick_report_use(17) = "N";
    pick_report_use(18) = "N";
    pick_report_use(24) = "N";
    pick_report_use(25) = "N";
    pick_report_use(26) = "N";
    pick_report_use(27) = "N";
    pick_report_use(29) = "N";
    pick_report_use(31) = "N";
    pick_report_use(33) = "N";
    pick_report_use(34) = "N";
    pick_report_use(37) = "N";
    pick_report_use(38) = "N";
    pick_report_use(44) = "N";
    pick_report_use(45) = "N";
    pick_report_use(46) = "N";
    pick_report_use(47) = "N";
    pick_report_use(48) = "N";
    pick_report_use(49) = "N";
    pick_report_use(50) = "N";
    pick_report_use(53) = "N";
    pick_report_use(55) = "N";
    pick_report_use(57) = "N";
    pick_report_use(58) = "N";
    pick_report_use(59) = "N";
  }
  else // all on
  {
    for (k = 1; k <= 61; k++)
    {
      pick_report_use(k) = "Y";
    }
  }
  if (reportdetail == 3)
  {
    for (unsigned j = 0; j <= reportdetail_list.size() - 2; j++)
    {
      if (reportdetail_list[j](1) > 0 && reportdetail_list[j](1) <= 60)
      {
        pick_report_use(reportdetail_list[j](1)) = "Y";
      }
      else if (reportdetail_list[j](1) >= -60)
      {
        pick_report_use(-reportdetail_list[j](1)) = "N";
      }
      else if (reportdetail_list[j](1) > -100)
      {
        warnstream << "custom report number: " << reportdetail_list[j](1) << " is out of range and ignored";
        write_message(WARN, 0);
      }
    }
  }

  for (k = 1; k <= 60; k++)
    echoinput << k << " " << pick_report_use(k) << " " << pick_report_name(k) << endl;
  // clang-format off
 END_CALCS

  init_int docheckup;           // flag for ending dump to "checkup.SS"
!!echoinput<<docheckup<<"  docheckup"<<endl;
  init_int Do_ParmTrace;
!!echoinput<<Do_ParmTrace<<"  Do_ParmTrace"<<endl;
  init_int Do_CumReport;
!!echoinput<<Do_CumReport<<"  Do_CumReport"<<endl;
  init_int Do_all_priors;
!!echoinput<<Do_all_priors<<"  Do_all_priors"<<endl;
  int prior_ignore_warning;
!!prior_ignore_warning=0;
  init_int SoftBound;
!!echoinput<<SoftBound<<"  SoftBound"<<endl;
  init_int N_nudata_read;
  int N_nudata;
!! N_nudata=N_nudata_read;
!!echoinput<<N_nudata<<"  N_nudata"<<endl;
  int Turn_off_phase;
  init_int Turn_off_phase_rd;
   !!echoinput<<Turn_off_phase_rd<<"  Turn_off_phase"<<endl;
   !!if(maxI<999) { Turn_off_phase=maxI; echoinput<<"-stopph resets it to: "<<Turn_off_phase<<endl;} else {Turn_off_phase=Turn_off_phase_rd;}

// read in burn and thinning intervals
  init_int burn_intvl;
!!echoinput<<burn_intvl<<"  MCeval burn_intvl"<<endl;
  init_int thin_intvl;
!!echoinput<<thin_intvl<<"  MCeval thin_intvl"<<endl;

  init_number jitter;
!!echoinput<<jitter<<"  jitter fraction for initial parm values"<<endl;

  int STD_Yr_min;
  int STD_Yr_max;
  init_int STD_Yr_min_rd; // min yr for sdreport
!!echoinput<<STD_Yr_min_rd<<"  STD_Yr_min"<<endl;
!!STD_Yr_min=STD_Yr_min_rd;
  init_int STD_Yr_max_rd; // max yr for sdreport
!!echoinput<<STD_Yr_max_rd<<"  STD_Yr_max (-1 for endyr; -2 for YrMax)"<<endl;
  init_int N_STD_Yr_RD ; // N extra years to read
!!echoinput<<N_STD_Yr_RD<<"  N extra STD years to read"<<endl;
!!STD_Yr_max=STD_Yr_max_rd;
  int N_STD_Yr;
  init_ivector STD_Yr_RD(1,N_STD_Yr_RD);
!!if(N_STD_Yr_RD>0) echoinput<<STD_Yr_RD<<"  vector of extra STD years"<<endl;
  // wait to process the above until after styr, endyr, N-forecast_yrs are read in data and forecast sections below

// set up the mcmc chain counter
  int mceval_counter;
  int mceval_header;
!! mceval_counter = 0;
!! mceval_header = 0;
  int mcmc_counter;
!! mcmc_counter = 0;
  int done_run;
!! done_run=0;

// set up the convergence criteria
  vector func_eval(1,50);
  vector func_conv(1,50);
//  number final_conv;
  init_number final_conv;
!!echoinput<<final_conv<<"  final_conv"<<endl;

!! func_eval.fill_seqadd(100,0);
!! func_conv.fill_seqadd(1,0);
!! func_conv(1)=10.;
!! func_conv(2)=10.;

  init_int retro_yr;             //  introduce year for retrospective analysis
!!echoinput << retro_yr << "  retro_yr" << endl;
  int fishery_on_off;
!! fishery_on_off = 1;

  init_int Smry_Age;
!!echoinput << Smry_Age << "  Smry_Age" << endl;
  int depletion_basis;
  int depletion_multi;
  int depletion_log;
  init_number depletion_basis_rd; // 0=skip; 1=B0; 2=Bmsy; 3=B_styr; 4=B_endyr; 5=dynamic_Bzero; values >=11 invoke multiyr with 10's digit; append .1 to invoke log(ratio) with hundreds digit
 LOCAL_CALCS
  // clang-format on
  echoinput << depletion_basis_rd << "  depletion_basis as read; this is also known as Bratio and is a std quantity; has multi-yr and log(ratio) options" << endl;
  depletion_multi = 0;
  depletion_log = 0;
  depletion_basis = int( depletion_basis_rd ); // discard decimal
  k = depletion_basis;

  if (depletion_basis_rd > float( depletion_basis) ) // invokes log(ratio) if decimal value exists
  {
    depletion_log = 1;
  }

  if (k > 10) //  invokes multiyr
  {
    depletion_multi = int(k / 10);
    depletion_basis = k - 10 * depletion_multi;
  }

  echoinput << "Parse into: depletion_log(ratio): " << depletion_log << " depletion_multi-yr: " << depletion_multi << " depletion_basis: " << depletion_basis << endl;
  // clang-format off
 END_CALCS

  init_number depletion_level;
!!echoinput << depletion_level << "  depletion_level" << endl;
  init_int SPR_reporting; // 0=skip; 1=SPR; 2=SPR_MSY; 3=SPR_Btarget; 4=(1-SPR)
!!echoinput << SPR_reporting << "  SPR_reporting" << endl;
  init_int F_reporting; // 0=skip; 1=exploit(Bio); 2=exploit(Num); 3=sum(frates); 4=true F for range of ages; 5=unweighted avg F for range of ages
 LOCAL_CALCS
  // clang-format on
  echoinput << F_reporting << "  F_reporting quantity, e.g. 3=sum(apical Fs)" << endl;
  if (F_reporting == 4 || F_reporting == 5) {
    k = 2;
  }
  else
  {
    k = 0;
  }
  // clang-format off
 END_CALCS
  init_ivector F_reporting_ages_R(1,k);
  //  convert to F_reporting_ages later after nages is read.
 LOCAL_CALCS
  // clang-format on
  if (k > 0)
  {
    echoinput << F_reporting_ages_R << "  F_reporting_ages_R" << endl;
    echoinput << "Will be checked against maxage later " << endl;
  }
  // clang-format off
 END_CALCS

  init_number F_std_basis_rd; // 0=raw; 1=rel Fspr; 2=rel Fmsy ; 3=rel Fbtgt; values >=11 invoke multiyr with 10's digit; >=100 invoke log(ratio) with hundreds digit
  number finish_starter;
  int mcmc_output_detail;
  number MCMC_bump; // value read and added to ln(R0) when starting into MCMC
  number ALK_tolerance;
  number tempin;
  int ender;
  int irand_seed;
  int irand_seed_rd;
  int F_std_multi; // for multi-year averaging of F_std
  int F_std_log; // for log(ratio) of F_std
  int F_std_basis;

 LOCAL_CALCS
  // clang-format on
  {
    F_std_multi = 0;
    F_std_log = 0;
    echoinput << F_std_basis_rd << "  F_std basis as read" << endl;
    F_std_basis = int(F_std_basis_rd);  // discards the decimal
    k = F_std_basis;  // temp value

    if (F_std_basis_rd > float( F_std_basis) ) // invokes log(ratio) if decimal value exists
    {
      F_std_log = 1;
    }

    if (k > 10) //  invokes multiyr
    {
      F_std_multi = int(k / 10);
      F_std_basis = k - 10 * F_std_multi;
    }

    echoinput << "Parse into: F_std_log(ratio): " << F_std_log << " F_std_multi: " << F_std_multi << " F_std_basis: " << F_std_basis << endl;
    if (F_std_multi > 1)
    {
      warnstream << "new feature for multiyr F_std reporting, be sure STD reporting covers all years from styr to endyr";
      write_message(NOTE, 0);
    }
    echoinput << "For Kobe plot, set depletion_basis=2; depletion_level=1.0; F_reporting=your choice; F_std_basis=2" << endl;

    mcmc_output_detail = 0;
    MCMC_bump = 0.;
    ALK_tolerance = 0.0;
    irand_seed_rd = -1;
    irand_seed = -1;
    ender = 0;
    //embed following reads in a do-while such that additional reads can be added while retaining backward compatibility with files that do not have the added elements
    //  element list:
    //  1.  MCMC_output_detail.MCMC_bump
    //  2.  ALK_tolerance
    //  3.  irand_seed;  added for 3.30.15
    //  xx.  finish_starter
    do
    {
      *(ad_comm::global_datafile) >> tempin;
      finish_starter = tempin;
      if (tempin == 3.30 || tempin == 999)
        ender = 1;

      if (tempin == 999.) // finish read in 3.24 format for ss_trans
      {
        echoinput << "SS read 999 from starter.ss, so will read files in 3.24 format" << endl
                  << endl;
        if (readparfile > 0)
        {
          warnstream << " ss_trans does not read the PAR file; readparfile set to 0" << endl;
          write_message(WARN, 0);
          readparfile = 0;
        }
      }
      else // reading in 3.30 format
      {
        finish_starter = 3.30;
        echoinput << "Read files in 3.30 format" << endl;
        echoinput << "SS will continue reading from starter.ss until it reads 3.30" << endl;

        echoinput << "read MCMC_output_detail.MCMC_bump as a single real number;  separate values will be parsed from integer and fraction" << endl;
        mcmc_output_detail = int(tempin);
        MCMC_bump = tempin - mcmc_output_detail;
        if (mcmc_output_detail < 0 || mcmc_output_detail > 2)
          mcmc_output_detail = 0;
        echoinput << "MCMC output detail(1=more_detail_to_posts; 2=write_report_for_each_mceval):  " << mcmc_output_detail << endl;
        echoinput << "MCMC bump to R0:  " << MCMC_bump << endl;

        echoinput << "Now read ALK tolerance which is deprecated. If not 0, it will be reset to 0." << endl;
        *(ad_comm::global_datafile) >> ALK_tolerance;
        if (ALK_tolerance > 0.0 || ALK_tolerance < 0.0)
        {
          warnstream << "ALK tolerance is now deprecated and is set to 0" ;
          write_message(ADJUST, 1);
          ALK_tolerance = 0;
        }
        echoinput << "ALK tolerance:  " << ALK_tolerance << endl;

        echoinput << "Now get random number seed; enter -1 to use long(time) as the seed" << endl;
        *(ad_comm::global_datafile) >> tempin;
        if (tempin == 3.30)
        {
          ender = 1;
          irand_seed_rd = -1;
          irand_seed = -1;
        }
        else
        {
          irand_seed_rd = int(tempin);
          irand_seed = irand_seed_rd;
          echoinput << "random number seed:  " << irand_seed << endl;
          tempin = 0;
        }
        if (ender == 0)
        {
          *(ad_comm::global_datafile) >> tempin;
          if (tempin == 3.30)
          {
            ender = 1;
          }
          else
          {
            echoinput << endl
                      << "starter.ss should have read 3.30 here; it read: " << tempin << endl;
            warnstream << "starter.ss has extra input lines; check echoinput to verify read";
            write_message(FATAL, 0);
          }
        }
      }
    } while (ender == 0);
    echoinput << "  finish reading starter.ss" << endl
              << endl;
  }
  // clang-format off
 END_CALCS

  //  end reading  from Starter file

  number pi
!! pi = 3.14159265358979;

  number neglog19
!! neglog19 = -log(19.);

  number NilNumbers           //  used as the minimum for posfun and similar checks
!! NilNumbers = 0.0000001;
// !!   NilNumbers = 0.000;

!!//  SS_Label_Info_1.2.1 #Set up a dummy datum for use when max phase = 0
  number dummy_datum;
  int dummy_phase;
!! dummy_datum = 1.;
!! if (Turn_off_phase <= 0) {dummy_phase = 0;} else {dummy_phase = -6;}

  int runnumber;
  int N_prof_var;
  int prof_var_cnt;
  int prof_junk;

 LOCAL_CALCS
  // clang-format on
  // SS_Label_Info_1.3 #Read runnumber.ss
  ifstream fin1("runnumber.ss", ios::in);
  if (fin1)
  {
    fin1 >> runnumber;
    runnumber++;
    fin1.close();
  }
  else
  {
    runnumber = 1;
  }
  // SS_Label_Info_1.3.1 #Increment runnumber and write to file
  ofstream fin2("runnumber.ss", ios::out);
  fin2 << runnumber;
  fin2.close();

  // SS_Label_Info_1.4 #Read Profilevalues.ss file
  N_prof_var = 998;
  ifstream fin3("profilevalues.ss", ios::in);
  fin3 >> N_prof_var; // if file is null this will not return anything
  if (N_prof_var == 998)
  {
    N_prof_var = 0;
    prof_junk = 0;
  }
  else
  {
    prof_junk = 1;
  }
  fin3.close();
  if (N_prof_var > 0)
  {
    ad_comm::change_datafile_name("profilevalues.ss");
  }
  else // just to have something in scope
  {
    ad_comm::change_datafile_name("runnumber.ss");
  }
  prof_var_cnt = (runnumber - 1) * N_prof_var + 2;
  // clang-format off
 END_CALCS
  init_vector prof_var(1,prof_junk+runnumber*N_prof_var);