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SS_write_ssnew.tpl
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SS_write_ssnew.tpl
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// SS_Label_file #18. **SS_write_ssnew.tpl**
// SS_Label_file # * <u>write_nudata()</u> // produces *starter.ss_new*, *forecast.ss_new*, *data_echo.ss_new*, *data_expval.ss*, bootstraps
// SS_Label_file # * <u>write_nucontrol()</u> // produces *control.ss_new*
// SS_Label_file #
//********************************************************************
/* SS_Label_FUNCTION 38 write_nudata */
FUNCTION void write_nudata()
{
// code for multinomial distribution developed by Ian Stewart, Oct 2005
dvector temp_mult(1, 50000);
dvector temp_probs(1, nlen_bin2);
int compindex = 0;
dvector temp_probs2(1, n_abins2);
int Nudat = 0;
int Nubootdat = 0;
int Nsamp_DM = 0;
adstring newdatfilename;
adstring datinfostring;
// create bootstrap data files; except first file just replicates the input and second is the estimate without error
if (irand_seed < 0)
irand_seed = long(time(&start));
random_number_generator radm(irand_seed);
for (i = 1; i <= 1234; i++)
{
temp = randn(radm);
}
for (Nudat = 1; Nudat <= N_nudata; Nudat++)
{
if (Nudat == 1)
{
echoinput << "Begin writing data_echo.ss_new file" << endl;
newdatfilename = "data_echo.ss_new";
datinfostring = "echo_input_data";
}
else if (Nudat == 2)
{
echoinput << "Begin writing data_expval.ss file" << endl;
newdatfilename = "data_expval.ss";
datinfostring = "expected_values";
}
else // data_boot files
{
echoinput << "Begin writing bootstrap data file(s)" << endl;
Nubootdat = Nudat - 2;
anystring2 = " ";
sprintf(anystring2, "%d", Nubootdat);
if (Nubootdat < 10)
{
newdatfilename = "data_boot_00" + anystring2 + ".ss";
}
else if (Nubootdat < 100)
{
newdatfilename = "data_boot_0" + anystring2 + ".ss";
}
else // Nubootdat > 99
{
newdatfilename = "data_boot_" + anystring2 + ".ss";
}
datinfostring = "bootstrap";
}
anystring = ssnew_pathname + newdatfilename;
report1.open(anystring);
report1 << version_info(1) << version_info(2) << version_info(3) << endl
<< version_info2 << endl
<< "#_Start_time: " << ctime(&start);
report1 << "#_" << datinfostring << endl;
report1 << Data_Comments << endl;
if (Nudat > 2)
report1 << "#_bootstrap file: " << Nubootdat << " irand_seed: " << irand_seed << " first rand#: " << randn(radm) << endl;
report1 << version_info(1) << version_info(2) << version_info(3) << endl;
report1 << styr << " #_StartYr" << endl;
report1 << endyr << " #_EndYr" << endl;
report1 << nseas << " #_Nseas" << endl;
report1 << 12. * seasdur << " #_months/season" << endl;
report1 << N_subseas << " #_Nsubseasons (even number, minimum is 2)" << endl;
report1 << spawn_month << " #_spawn_month" << endl;
report1 << gender_rd << " #_Nsexes: 1, 2, -1 (use -1 for 1 sex setup with SSB multiplied by female_frac parameter)" << endl;
report1 << nages << " #_Nages=accumulator age, first age is always age 0" << endl;
report1 << pop << " #_Nareas" << endl;
report1 << Nfleet << " #_Nfleets (including surveys)" << endl;
report1 << "#_fleet_type: 1=catch fleet; 2=bycatch only fleet; 3=survey; 4=predator(M2) " << endl;
report1 << "#_sample_timing: -1 for fishing fleet to use season-long catch-at-age for observations, or 1 to use observation month; (always 1 for surveys)" << endl;
report1 << "#_fleet_area: area the fleet/survey operates in " << endl;
report1 << "#_units of catch: 1=bio; 2=num (ignored for surveys; their units read later)" << endl;
report1 << "#_catch_mult: 0=no; 1=yes" << endl;
report1 << "#_rows are fleets" << endl
<< "#_fleet_type fishery_timing area catch_units need_catch_mult fleetname" << endl;
for (f = 1; f <= Nfleet; f++)
{
report1 << fleet_setup(f) << " " << fleetname(f) << " # " << f << endl;
}
report1 << "#Bycatch_fleet_input_goes_next" << endl;
report1 << "#a: fleet index" << endl;
report1 << "#b: 1=include dead bycatch in total dead catch for F0.1 and MSY optimizations and forecast ABC; 2=omit from total catch for these purposes (but still include the mortality)" << endl;
report1 << "#c: 1=Fmult scales with other fleets; 2=bycatch F constant at input value; 3=bycatch F from range of years" << endl;
report1 << "#d: F or first year of range" << endl;
report1 << "#e: last year of range" << endl;
report1 << "#f: not used" << endl;
report1 << "# a b c d e f " << endl;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) == 2)
report1 << bycatch_setup(f) << " # " << fleetname(f) << endl;
}
if (Nudat == 1) // report back the input data
{
report1 << "#_Catch data: year, seas, fleet, catch, catch_se" << endl;
report1 << "#_catch_se: standard error of log(catch)" << endl;
report1 << "#_NOTE: catch data is ignored for survey fleets" << endl;
k = 0;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (y = styr - 1; y <= endyr; y++)
{
for (s = 1; s <= nseas; s++)
{
k++;
t = styr + (y - styr) * nseas + s - 1;
if (y == styr - 1)
{
g = -999;
}
else
{
g = y;
}
report1 << g << " " << s << " " << f << " " << catch_ret_obs(f, t) << " " << catch_se(t, f) << endl;
}
}
}
}
report1 << "-9999 0 0 0 0" << endl
<< "#" << endl;
report1 << "#_CPUE_and_surveyabundance_and_index_observations" << endl;
report1 << "#_units: 0=numbers; 1=biomass; 2=F; 30=spawnbio; 31=exp(recdev); 36=recdev; 32=spawnbio*recdev; 33=recruitment; 34=depletion(&see Qsetup); 35=parm_dev(&see Qsetup)" << endl;
report1 << "#_errtype: -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
report1 << "#_fleet units errtype SD_report" << endl;
for (f = 1; f <= Nfleet; f++)
report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
report1 << "#_year month fleet obs stderr" << endl;
if (Svy_N > 0)
for (f = 1; f <= Nfleet; f++)
for (i = 1; i <= Svy_N_fleet(f); i++)
{
t = Svy_time_t(f, i);
ALK_time = Svy_ALK_time(f, i);
report1 << Show_Time(t, 1) << " " << Svy_super(f, i) * data_time(ALK_time, f, 1) << " " << f * Svy_use(f, i) << " ";
report1 << Svy_obs(f, i) << " " << Svy_se_rd(f, i) << " #_ " << fleetname(f) << endl;
}
report1 << "-9999 1 1 1 1 # terminator for survey observations " << endl;
report1 << "#" << endl
<< Ndisc_fleets << " #_N_fleets_with_discard" << endl;
report1 << "#_discard_units (1=same_as_catchunits(bio/num); 2=fraction; 3=numbers)" << endl;
report1 << "#_discard_errtype: >0 for DF of T-dist(read CV below); 0 for normal with CV; -1 for normal with se; -2 for lognormal; -3 for trunc normal with CV" << endl;
report1 << "# note: only enter units and errtype for fleets with discard " << endl;
report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
report1 << "#_fleet units errtype" << endl;
if (Ndisc_fleets > 0)
{
for (f = 1; f <= Nfleet; f++)
if (disc_units(f) > 0)
report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
report1 << "#_year month fleet obs stderr" << endl;
for (f = 1; f <= Nfleet; f++)
for (i = 1; i <= disc_N_fleet(f); i++)
{
ALK_time = disc_time_ALK(f, i);
report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
report1 << obs_disc(f, i) << " " << cv_disc(f, i) << " #_ " << fleetname(f) << endl;
}
}
else
{
report1 << "# ";
}
report1 << "-9999 0 0 0.0 0.0 # terminator for discard data " << endl;
report1 << "#" << endl
<< do_meanbodywt << " #_use meanbodysize_data (0/1)" << endl;
if (nobs_mnwt_rd == 0)
report1 << "#_COND_";
report1 << DF_bodywt << " #_DF_for_meanbodysize_T-distribution_like" << endl;
report1 << "# note: type=1 for mean length; type=2 for mean body weight " << endl;
report1 << "#_year month fleet part type obs stderr" << endl;
if (nobs_mnwt > 0)
{
for (i = 1; i <= nobs_mnwt; i++)
{
f = abs(mnwtdata(3, i));
report1 << Show_Time(mnwtdata(1, i), 1) << " " << mnwtdata(2, i) << " " << mnwtdata(3, i) << " " << mnwtdata(4, i) << " " << mnwtdata(5, i) << " " << mnwtdata(6, i) << " " << mnwtdata(7, i) - var_adjust(3, f) << " #_ " << fleetname(f) << endl;
}
}
if (do_meanbodywt == 0)
report1 << "# ";
report1 << " -9999 0 0 0 0 0 0 # terminator for mean body size data " << endl;
report1 << "#" << endl
<< "# set up population length bin structure (note - irrelevant if not using size data and using empirical wtatage" << endl;
report1 << LenBin_option << " # length bin method: 1=use databins; 2=generate from binwidth,min,max below; 3=read vector" << endl;
if (LenBin_option == 1)
{
report1 << "# no additional input for option 1" << endl;
report1 << "# read binwidth, minsize, lastbin size for option 2" << endl;
report1 << "# read N poplen bins, then vector of bin lower boundaries, for option 3" << endl;
}
else if (LenBin_option == 2)
{
report1 << binwidth2 << " # binwidth for population size comp " << endl;
report1 << minLread << " # minimum size in the population (lower edge of first bin and size at age 0.00) " << endl;
report1 << maxLread << " # maximum size in the population (lower edge of last bin) " << endl;
}
else
{
report1 << nlength << " # number of population size bins " << endl;
report1 << len_bins << endl;
}
report1 << use_length_data << " # use length composition data (0/1/2) where 2 invokes new comp_control format" << endl;
if (use_length_data > 0)
{
report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
report1 << "#_addtocomp: after accumulation of tails; this value added to all bins" << endl;
report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
report1 << "#_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation" << endl;
report1 << "#_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << "#_ParmSelect: consecutive index for dirichlet or MV_Tweedie" << endl;
report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
report1 << "#" << endl;
if(use_length_data == 1)
{
report1 << "#_Using old format for composition controls" << endl;
report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (f = 1; f <= Nfleet; f++)
{
report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
}
}
else if (use_length_data == 2)
{
report1 << "#_Using new list format for composition controls" << endl;
report1 << "#_use negative fleet value to fill for all higher numbered fleets (recommended!)" << endl;
report1 << "#_must enter in fleet, partition order; but only need to enter for used combos" << endl;
report1 << "#_fleet = -9999 to terminate list" << endl;
report1 << "#_fleet partition mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (int i = 0; i <= comp_control_L_count; i++)
report1 << comp_control_L[i] << endl;
}
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: (0=combined; 1=discard; 2=retained" << endl;
report1 << nlen_bin << " #_N_LengthBins; then enter lower edge of each length bin" << endl
<< len_bins_dat << endl;
// report1<<nobsl_rd<<" #_N_Length_obs"<<endl;
report1 << "#_year month fleet sex part Nsamp datavector(female-male)" << endl;
if (nobsl_rd > 0)
{
for (i = 0; i <= nobsl_rd - 1; i++)
{
report1 << lendata[i] << endl;
}
}
report1 << -9999. << " ";
for (j = 2; j <= 6 + nlen_bin2; j++)
report1 << "0 ";
report1 << endl;
}
else
{
report1 << "# see manual for format of length composition data " << endl;
}
report1 << "#" << endl
<< n_abins << " #_N_age_bins" << endl;
if (n_abins > 0)
{
report1 << age_bins1 << endl;
}
else
{
report1 << "# ";
}
report1 << N_ageerr << " #_N_ageerror_definitions" << endl;
if (N_ageerr > 0)
report1 << age_err_rd << endl;
report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
report1 << "#_addtocomp: after accumulation of tails; this value added to all bins" << endl;
report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
report1 << "#_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation" << endl;
report1 << "#_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << "#_ParmSelect: consecutive index for dirichlet or MV_Tweedie" << endl;
report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
report1 << "#" << endl;
report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (f = 1; f <= Nfleet; f++)
{
if (n_abins <= 0)
report1 << "# ";
report1 << min_tail_A(f) << " " << min_comp_A(f) << " " << CombGender_A(f) << " " << AccumBin_A(f) << " " << Comp_Err_A(f) << " " << Comp_Err_A2(f) << " " << min_sample_size_A(f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
}
if (n_abins <= 0)
report1 << "# ";
report1 << Lbin_method << " #_Lbin_method_for_Age_Data: 1=poplenbins; 2=datalenbins; 3=lengths" << endl;
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: (0=combined; 1=discard; 2=retained" << endl;
report1 << "#_year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp datavector(female-male)" << endl;
if (nobsa_rd > 0)
{
for (i = 0; i <= nobsa_rd - 1; i++)
{
report1 << Age_Data[i] << endl;
}
}
f = exp_a_temp.size() + 8;
if (n_abins <= 0)
report1 << "# ";
report1 << "-9999 ";
for (i = 1; i <= f; i++)
report1 << " 0";
report1 << endl;
report1 << "#" << endl
<< use_meansizedata << " #_Use_MeanSize-at-Age_obs (0/1)" << endl;
if (use_meansizedata > 0)
{
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: 0=combined; 1=discard; 2=retained" << endl;
report1 << "# ageerr codes: positive means mean length-at-age; negative means mean bodywt_at_age" << endl;
report1 << "#_year month fleet sex part ageerr ignore datavector(female-male)" << endl;
report1 << "# samplesize(female-male)" << endl;
if (nobs_ms_rd > 0)
{
if (finish_starter == 999)
{
for (i = 1; i <= nobs_ms_rd; i++)
{
report1 << sizeAge_Data[i] << endl;
}
}
else
{
for (i = 0; i <= nobs_ms_rd - 1; i++)
{
report1 << sizeAge_Data[i] << endl;
}
}
report1 << "-9999 ";
for (j = 1; j <= 6 + 2 * n_abins2; j++)
report1 << " 0";
report1 << endl;
}
}
report1 << "#" << endl
<< N_envvar << " #_N_environ_variables" << endl;
report1 << "# -2 in year will subtract mean for that env_var; -1 will subtract mean and divide by stddev (e.g. Z-score)" << endl;
report1 << "#_year variable value" << endl;
if (N_envvar > 0)
{
for (i = 0; i <= N_envdata - 1; i++)
report1 << env_temp[i] << endl;
report1 << "-9999 0 0" << endl;
}
report1 << "#" << endl << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
report1 << SzFreq_Nmeth_rd << " # N sizefreq methods to read (or -1 for expanded options)" << endl;
if (SzFreq_Nmeth_rd < 0) {
report1 << SzFreq_Nmeth << " # N sizefreq methods to read" << endl;
}
if (SzFreq_Nmeth != 0)
{
report1 << "# each row below has entry for each sizefreq method " << endl;
report1 << "#_ ";
for (int j = 1; j <= SzFreq_Nmeth; j++ )
{ report1 << j << " ";}
report1 << " # Method" << endl;
report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
report1 << SzFreq_scale << " #_Sizefreq scale(1=kg/2=lbs/3=cm/4=inches)" << endl;
report1 << SzFreq_mincomp << " #_Sizefreq: small constant to add to comps" << endl;
report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
if (SzFreq_Nmeth_rd < 0) {
report1 << Comp_Err_Sz << " #_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << Comp_Err_Sz2 << " #_ParmSelect: consecutive index for dirichlet or MV_Tweedie comp_error" << endl;
}
report1 << "#_Sizefreq bins. one row for each method" << endl
<< "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
for (i = 1; i <= SzFreq_Nmeth; i++)
{ report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
report1 << "#_method year month fleet sex part Nsamp <data> " << endl << SzFreq_obs1 << endl;
}
// begin tagging data section #1 (observed data)
report1 << "# " << endl
<< Do_TG_rd << " # do tags (0/1/2); where 2 allows entry of TG_min_recap" << endl;
if (Do_TG_rd > 0)
{
// info on dimensions of tagging data
report1 << N_TG << " # N tag groups" << endl;
report1 << N_TG_recap << " # N recap events" << endl;
report1 << TG_mixperiod << " # TG_mixperiod ## (latency) is the first period in which logL is calculated for this tag group (0 = release period)" << endl;
report1 << TG_maxperiods << " # max periods ## to track recaptures (units=seasons), after which tags are still read into this accumulator period" << endl;
if (Do_TG_rd == 2)
{
report1 << TG_min_recap << " # TG_min_recap ## tag group's N recaps >=mixperiod must be >= min_recap to include tag group in logL)" << endl;
}
else
{
report1 << "# COND: TG_min_recap ## use Do_TG=2 to invoke reading TG_min_recap after TG_maxperiods" << endl;
}
// tag releases
report1 << "# Release data for each tag group. Tags are considered to be released at the beginning of a season (period)" << endl;
report1 << "#<TG> area year seas <tfill> sex age Nrelease (note that the TG and tfill values are placeholders and are replaced by program generated values)" << endl;
report1 << TG_release << endl;
// tag recaptures
report1 << "#_TG year seas fleet Nrecap" << endl;
for (j = 1; j <= N_TG_recap; j++)
{
// fill in first 4 columns:
for (k = 1; k <= 5; k++)
report1 << TG_recap_data(j, k) << " ";
report1 << endl;
}
}
// end tagging data section #1 (observed data)
report1 << "#" << endl
<< Do_Morphcomp << " # morphcomp data(0/1) " << endl;
if (Do_Morphcomp > 0)
{
report1 << Morphcomp_nobs_rd << " # Nobs" << endl;
report1 << Morphcomp_nmorph << " # Nmorphs" << endl;
report1 << Morphcomp_mincomp << " # add_to_comp" << endl;
report1 << "#_year, month, fleet, null, Nsamp, datavector_by_Nmorphs" << endl;
for (i = 1; i <= Morphcomp_nobs_rd; i++)
{
report1 << Morphcomp_obs_rd << endl;
}
}
else
{
report1 << "# Nobs, Nmorphs, mincomp" << endl;
report1 << "#_year, seas, type, partition, Nsamp, datavector_by_Nmorphs" << endl;
}
report1 << "#" << endl
<< Do_SelexData << " # Do dataread for selectivity priors(0/1)" << endl;
report1 << "#_year, seas, fleet, age/size, bin, selex_prior, prior_sd" << endl;
report1 << "# feature not yet implemented" << endl;
report1 << "#" << endl
<< "999" << endl
<< endl;
}
else if (Nudat == 2) // report expected value with no added error
{
report1 << "#_Catch data: year, seas, fleet, catch, catch_se" << endl;
report1 << "#_catch_se: standard error of log(catch)" << endl;
report1 << "#_NOTE: catch data is ignored for survey fleets" << endl;
k = 0;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (y = styr - 1; y <= endyr; y++)
{
for (s = 1; s <= nseas; s++)
{
k++;
t = styr + (y - styr) * nseas + s - 1;
if (y == styr - 1)
{ report1 << -999 << " "; }
else
{ report1 << y << " "; }
report1 << s << " " << f << " ";
if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0)
{
report1 << 0.1 << " " << catch_se(t, f) << endl; // for bycatch only fleet
}
else if (catchunits(f) == 1)
{
report1 << catch_fleet(t, f, 3) << " " << catch_se(t, f) << endl;
}
else
{
report1 << catch_fleet(t, f, 6) << " " << catch_se(t, f) << endl;
}
}
}
}
}
report1 << "-9999 0 0 0 0" << endl
<< "#" << endl;
report1 << "#_CPUE_and_surveyabundance_and_index_observations" << endl;
report1 << "#_units: 0=numbers; 1=biomass; 2=F; 30=spawnbio; 31=exp(recdev); 36=recdev; 32=spawnbio*recdev; 33=recruitment; 34=depletion(&see Qsetup); 35=parm_dev(&see Qsetup)" << endl;
report1 << "#_errtype: -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
report1 << "#_fleet units errtype SD_report" << endl;
for (f = 1; f <= Nfleet; f++)
report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
report1 << "#_year month index obs err" << endl;
if (Svy_N > 0)
for (f = 1; f <= Nfleet; f++)
for (i = 1; i <= Svy_N_fleet(f); i++)
{
t = Svy_time_t(f, i);
ALK_time = Svy_ALK_time(f, i);
report1 << Show_Time(t, 1) << " " << Svy_super(f, i) * data_time(ALK_time, f, 1) << " " << f * Svy_use(f, i) << " ";
if (Svy_errtype(f) == -1) // normal
{
report1 << Svy_est(f, i);
}
else if (Svy_errtype(f) == -2) // gamma
{
// need gamma here
}
else
{
report1 << mfexp(Svy_est(f, i)); // lognormal or T-dist or lognormal w/bias
}
report1 << " " << Svy_se_rd(f, i) << " #_orig_obs: " << Svy_obs(f, i) << " " << fleetname(f) << endl;
}
report1 << "-9999 1 1 1 1 # terminator for survey observations " << endl;
report1 << "#" << endl
<< Ndisc_fleets << " #_N_fleets_with_discard" << endl;
report1 << "#_discard_units (1=same_as_catchunits(bio/num); 2=fraction; 3=numbers)" << endl;
report1 << "#_discard_errtype: >0 for DF of T-dist(read CV below); 0 for normal with CV; -1 for normal with se; -2 for lognormal; -3 for trunc normal with CV" << endl;
report1 << "# note: only enter units and errtype for fleets with discard " << endl;
report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
report1 << "#_fleet units errtype" << endl;
if (Ndisc_fleets > 0)
{
for (f = 1; f <= Nfleet; f++)
if (disc_units(f) > 0)
report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
report1 << "#_year month fleet obs stderr" << endl;
for (f = 1; f <= Nfleet; f++)
if (disc_N_fleet(f) > 0)
for (i = 1; i <= disc_N_fleet(f); i++)
{
ALK_time = disc_time_ALK(f, i);
report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
{
report1 << exp_disc(f, i);
}
report1 << " " << cv_disc(f, i) << " #_orig_obs: " << obs_disc(f, i) << " #_ " << fleetname(f) << endl;
}
}
else
{
report1 << "# ";
}
report1 << "-9999 0 0 0.0 0.0 # terminator for discard data " << endl;
report1 << "#" << endl
<< do_meanbodywt << " #_use meanbodysize_data (0/1)" << endl;
if (nobs_mnwt_rd == 0)
report1 << "#_COND_";
report1 << DF_bodywt << " #_DF_for_meanbodysize_T-distribution_like" << endl;
report1 << "# note: type=1 for mean length; type=2 for mean body weight " << endl;
report1 << "#_year month fleet part type obs stderr" << endl;
if (nobs_mnwt > 0)
{
for (i = 1; i <= nobs_mnwt; i++)
{
f = abs(mnwtdata(3, i));
report1 << Show_Time(mnwtdata(1, i), 1) << " " << mnwtdata(2, i) << " " << mnwtdata(3, i) << " " << mnwtdata(4, i) << " " << mnwtdata(5, i) << " " << exp_mnwt(i) << " " << mnwtdata(7, i) - var_adjust(3, f) << " #_orig_obs: " << mnwtdata(6, i) << " #_ " << fleetname(f) << endl;
}
}
if (do_meanbodywt == 0)
report1 << "# ";
report1 << " -9999 0 0 0 0 0 0 # terminator for mean body size data " << endl;
report1 << "#" << endl
<< "# set up population length bin structure (note - irrelevant if not using size data and using empirical wtatage" << endl;
report1 << LenBin_option << " # length bin method: 1=use databins; 2=generate from binwidth,min,max below; 3=read vector" << endl;
if (LenBin_option == 1)
{
report1 << "# no additional input for option 1" << endl;
report1 << "# read binwidth, minsize, lastbin size for option 2" << endl;
report1 << "# read N poplen bins, then vector of bin lower boundaries, for option 3" << endl;
}
else if (LenBin_option == 2)
{
report1 << binwidth2 << " # binwidth for population size comp " << endl;
report1 << minLread << " # minimum size in the population (lower edge of first bin and size at age 0.00) " << endl;
report1 << maxLread << " # maximum size in the population (lower edge of last bin) " << endl;
}
else
{
report1 << nlength << " # number of population size bins " << endl;
report1 << len_bins << endl;
}
report1 << use_length_data << " # use length composition data (0/1/2) where 2 invokes new comp_comtrol format" << endl;
if (use_length_data > 0)
{
report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
report1 << "#_addtocomp: after accumulation of tails; this value added to all bins" << endl;
report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
report1 << "#_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation" << endl;
report1 << "#_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << "#_ParmSelect: consecutive index for dirichlet or MV_Tweedie" << endl;
report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
report1 << "#" << endl;
if(use_length_data == 1)
{
report1 << "#_Using old format for composition controls" << endl;
report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (f = 1; f <= Nfleet; f++)
{
report1 << min_tail_L(0, f) << " " << min_comp_L(0, f) << " " << CombGender_L(0, f) << " " << AccumBin_L(0, f) << " " << Comp_Err_L(0, f) << " " << Comp_Err_L2(0, f) << " " << min_sample_size_L(0, f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
}
}
else if (use_length_data == 2)
{
report1 << "#_Using new list format for composition controls" << endl;
report1 << "#_use negative fleet value to fill for all higher numbered fleets (recommended!)" << endl;
report1 << "#_must enter in fleet, partition order; but only need to enter for used combos" << endl;
report1 << "#_fleet = -9999 to terminate list" << endl;
report1 << "#_fleet partition mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (int i = 0; i <= comp_control_L_count; i++)
report1 << comp_control_L[i] << endl;
}
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: (0=combined; 1=discard; 2=retained" << endl;
report1 << nlen_bin << " #_N_LengthBins" << endl
<< len_bins_dat << endl;
// report1<<sum(Nobs_l)<<" #_N_Length_obs"<<endl;
report1 << "#_year month fleet sex part Nsamp datavector(female-male)" << endl;
for (f = 1; f <= Nfleet; f++)
{
if (Nobs_l(f) > 0)
{
for (i = 1; i <= Nobs_l(f); i++)
{
k = 1000;
if (nsamp_l(f, i) < k)
k = nsamp_l(f, i);
exp_l_temp_dat = nsamp_l(f, i) * value(exp_l(f, i) / sum(exp_l(f, i)));
report1 << header_l_rd(f, i)(1, 3) << " " << gen_l(f, i) << " " << header_l_rd(f, i)(5) << " " << nsamp_l(f, i) << " " << exp_l_temp_dat << endl;
}
}
}
report1 << -9999. << " ";
for (j = 2; j <= 6 + nlen_bin2; j++)
report1 << "0 ";
report1 << endl;
}
else
{
report1 << "# see manual for format of length composition data " << endl;
}
report1 << "#" << endl
<< n_abins << " #_N_age_bins" << endl;
if (n_abins > 0)
{
report1 << age_bins1 << endl;
}
else
{
report1 << "# ";
}
report1 << N_ageerr << " #_N_ageerror_definitions" << endl;
if (N_ageerr > 0)
report1 << age_err_rd << endl;
report1 << "#_mintailcomp: upper and lower distribution for females and males separately are accumulated until exceeding this level." << endl;
report1 << "#_addtocomp: after accumulation of tails; this value added to all bins" << endl;
report1 << "#_combM+F: males and females treated as combined sex below this bin number " << endl;
report1 << "#_compressbins: accumulate upper tail by this number of bins; acts simultaneous with mintailcomp; set=0 for no forced accumulation" << endl;
report1 << "#_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << "#_ParmSelect: parm number for dirichlet or MV_Tweedie" << endl;
report1 << "#_minsamplesize: minimum sample size; set to 1 to match 3.24, minimum value is 0.001" << endl;
report1 << "#" << endl;
report1 << "#_mintailcomp addtocomp combM+F CompressBins CompError ParmSelect minsamplesize" << endl;
for (f = 1; f <= Nfleet; f++)
{
if (n_abins <= 0)
report1 << "# ";
report1 << min_tail_A(f) << " " << min_comp_A(f) << " " << CombGender_A(f) << " " << AccumBin_A(f) << " " << Comp_Err_A(f) << " " << Comp_Err_A2(f) << " " << min_sample_size_A(f) << " #_fleet:" << f << "_" << fleetname(f) << endl;
}
if (n_abins <= 0)
report1 << "# ";
report1 << Lbin_method << " #_Lbin_method_for_Age_Data: 1=poplenbins; 2=datalenbins; 3=lengths" << endl;
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: (0=combined; 1=discard; 2=retained" << endl;
report1 << "#_year month fleet sex part ageerr Lbin_lo Lbin_hi Nsamp datavector(female-male)" << endl;
if (Nobs_a_tot > 0)
for (f = 1; f <= Nfleet; f++)
{
if (Nobs_a(f) >= 1)
{
for (i = 1; i <= Nobs_a(f); i++)
{
k = 1000;
if (nsamp_a(f, i) < k)
k = nsamp_a(f, i); // note that nsamp is adjusted by var_adjust, so var_adjust
// should be reset to 1.0 in control files that read the nudata.dat files
exp_a_temp = nsamp_a(f, i) * value(exp_a(f, i) / sum(exp_a(f, i)));
report1 << header_a(f, i)(1) << " " << header_a_rd(f, i)(2, 3) << " " << header_a(f, i)(4, 8) << " " << nsamp_a(f, i) << " " << exp_a_temp << endl;
}
}
}
f = exp_a_temp.size() + 8;
if (n_abins <= 0)
report1 << "# ";
report1 << "-9999 ";
for (i = 1; i <= f; i++)
report1 << " 0";
report1 << endl;
report1 << "#" << endl
<< use_meansizedata << " #_Use_MeanSize-at-Age_obs (0/1)" << endl;
if (use_meansizedata > 0)
{
report1 << "# sex codes: 0=combined; 1=use female only; 2=use male only; 3=use both as joint sex*length distribution" << endl;
report1 << "# partition codes: 0=combined; 1=discard; 2=retained" << endl;
report1 << "# ageerr codes: positive means mean length-at-age; negative means mean bodywt_at_age" << endl;
report1 << "#_year month fleet sex part ageerr ignore datavector(female-male)" << endl;
report1 << "# samplesize(female-male)" << endl;
for (f = 1; f <= Nfleet; f++)
{
if (Nobs_ms(f) > 0)
{
for (i = 1; i <= Nobs_ms(f); i++)
{
report1 << header_ms(f, i)(1) << " " << header_ms_rd(f, i)(2, 3) << " " << header_ms(f, i)(4, 7);
for (a = 1; a <= n_abins2; a++)
{
report1 << " ";
temp = exp_ms(f, i, a);
if (temp <= 0.)
{
temp = 0.0001;
}
report1 << temp;
}
report1 << endl
<< obs_ms_n_read(f, i) << endl;
}
}
}
report1 << "-9999 ";
for (j = 1; j <= 6 + n_abins2; j++)
report1 << " 0";
report1 << endl;
for (j = 1; j <= n_abins2; j++)
report1 << " 0";
report1 << endl;
}
report1 << "#" << endl
<< N_envvar << " #_N_environ_variables" << endl;
report1 << "# -2 in year will subtract mean for that env_var; -1 will subtract mean and divide by stddev (e.g. Z-score)" << endl;
report1 << "#_year variable value" << endl;
if (N_envvar > 0)
{
for (i = 0; i <= N_envdata - 1; i++)
report1 << env_temp[i] << endl;
report1 << "-9999 0 0" << endl;
}
report1 << "#" << endl << "# Sizefreq data. Defined by method because a fleet can use multiple methods" << endl;
report1 << SzFreq_Nmeth_rd << " # N sizefreq methods to read (or -1 for expanded options)" << endl;
if (SzFreq_Nmeth_rd < 0) {
report1 << SzFreq_Nmeth << " # N sizefreq methods to read" << endl;
}
if (SzFreq_Nmeth != 0)
{
report1 << "# each row below has entry for each sizefreq method " << endl;
report1 << "#_ ";
for (int j = 1; j <= SzFreq_Nmeth; j++ )
{ report1 << j << " ";}
report1 << " # Method" << endl;
report1 << SzFreq_Nbins << " #_Sizefreq N bins" << endl;
report1 << SzFreq_units << " #_Sizefreq units(1=bio/2=num)" << endl;
report1 << SzFreq_scale << " #_Sizefreq scale(1=kg/2=lbs/3=cm/4=inches)" << endl;
report1 << SzFreq_mincomp << " #_Sizefreq: small constant to add to comps" << endl;
report1 << SzFreq_nobs << " #_Sizefreq number of obs per method" << endl;
if (SzFreq_Nmeth_rd < 0) {
report1 << Comp_Err_Sz << " #_Comp_Error: 0=multinomial, 1=dirichlet using Theta*n, 2=dirichlet using beta, 3=MV_Tweedie" << endl;
report1 << Comp_Err_Sz2 << " #_ParmSelect: consecutive index for dirichlet or MV_Tweedie comp_error" << endl;
}
report1 << "#_Sizefreq bins. one row for each method" << endl
<< "#Note: negative value for first bin makes it accumulate all smaller fish vs. truncate small fish" << endl;
for (i = 1; i <= SzFreq_Nmeth; i++)
{ report1 << SzFreq_Omit_Small(i) * SzFreq_bins1(i, 1) << SzFreq_bins1(i)(2, SzFreq_Nbins(i)) << endl; }
report1 << "#_method year month fleet sex part Nsamp <data> " << endl;
for (iobs = 1; iobs <= SzFreq_totobs; iobs++) {
report1 << SzFreq_obs1(iobs)(1, 7) << " " << SzFreq_exp(iobs) << endl;
}
}
// begin tagging data section #2 (expected values)
report1 << "#" << endl
<< Do_TG << " # do tags (0/1)" << endl;
if (Do_TG > 0)
{
// info on dimensions of tagging data
report1 << N_TG << " # N tag groups" << endl;
report1 << N_TG_recap << " # N recap events" << endl;
report1 << TG_mixperiod << " # mixing latency period: N periods to delay before comparing observed to expected recoveries (0 = release period)" << endl;
report1 << TG_maxperiods << " # max periods (seasons) to track recoveries, after which tags enter accumulator" << endl;
// tag releases
report1 << "# Release data for each tag group. Tags are considered to be released at the beginning of a season (period)" << endl;
report1 << "#<TG> area year seas <tfill> sex age Nrelease (note that the TG and tfill values are placeholders and are replaced by program generated values)" << endl;
report1 << TG_release << endl;
// tag recaptures
report1 << "#_Note: Expected values for tag recaptures are reported only for the same combinations of" << endl;
report1 << "# group, year, area, and fleet that had observed recaptures. " << endl;
report1 << "#_TG year seas fleet Nrecap" << endl;
for (j = 1; j <= N_TG_recap; j++)
{
// fill in first 4 columns:
for (k = 1; k <= 4; k++)
report1 << TG_recap_data(j, k) << " ";
// fill in 5th column with bootstrap values
TG = TG_recap_data(j, 1);
overdisp = TG_parm(2 * N_TG + TG);
t = styr + int((TG_recap_data(j, 2) - styr) * nseas + TG_recap_data(j, 3) - 1) - TG_release(TG, 5); // find elapsed time in terms of number of seasons
if (t > TG_maxperiods)
t = TG_maxperiods;
report1 << value(TG_recap_exp(TG, t, 0)) << " #_overdisp: " << value(overdisp) << endl;
}
}
// end tagging data section #2 (expected values)
report1 << "#" << endl
<< Do_Morphcomp << " # morphcomp data(0/1) " << endl;
if (Do_Morphcomp > 0)
{
report1 << "# note that raw data, not bootstrap are reported here " << endl;
report1 << Morphcomp_nobs << " # Nobs" << endl;
report1 << Morphcomp_nmorph << " # Nmorphs" << endl;
report1 << Morphcomp_mincomp << " # add_to_comp" << endl;
report1 << "#_year, month, fleet, null, Nsamp, datavector_by_Nmorphs" << endl;
for (i = 1; i <= Morphcomp_nobs; i++)
{
report1 << Morphcomp_obs(i)(1, 5) << " " << Morphcomp_exp(i) << endl;
}
}
else
{
report1 << "# Nobs, Nmorphs, mincomp" << endl;
report1 << "#_year, seas, type, partition, Nsamp, datavector_by_Nmorphs" << endl;
}
report1 << "#" << endl
<< Do_SelexData << " # Do dataread for selectivity priors(0/1)" << endl;
report1 << "#_year, seas, fleet, age/size, bin, selex_prior, prior_sd" << endl;
report1 << "# feature not yet implemented" << endl;
report1 << "#" << endl
<< "999" << endl
<< endl;
}
else // create bootstrap data
{
report1 << "#_Catch data: year, seas, fleet, catch, catch_se" << endl;
report1 << "#_catch_se: standard error of log(catch)" << endl;
report1 << "#_NOTE: catch data is ignored for survey fleets" << endl;
k = 0;
for (f = 1; f <= Nfleet; f++)
{
if (fleet_type(f) <= 2)
{
for (y = styr - 1; y <= endyr; y++)
{
for (s = 1; s <= nseas; s++)
{
k++;
t = styr + (y - styr) * nseas + s - 1;
if (y == styr - 1)
{ report1 << -999 << " "; }
else
{ report1 << y << " "; }
report1 << s << " " << f << " ";
if (fleet_type(f) == 2 && catch_ret_obs(f, t) > 0.0)
{
report1 << 0.1 << " " << catch_se(t, f) << endl; // for bycatch only fleet
}
else if (catchunits(f) == 1)
{
report1 << catch_fleet(t, f, 3) * mfexp(randn(radm) * catch_se(t, f) - 0.5 * catch_se(t, f) * catch_se(t, f))
<< " " << catch_se(t, f) << endl;
}
else
{
report1 << catch_fleet(t, f, 6) * mfexp(randn(radm) * catch_se(t, f) - 0.5 * catch_se(t, f) * catch_se(t, f))
<< " " << catch_se(t, f) << endl;
}
}
}
}
}
report1 << "-9999 0 0 0 0" << endl
<< "#" << endl;
report1 << "#_CPUE_and_surveyabundance_and_index_observations" << endl;
report1 << "#_units: 0=numbers; 1=biomass; 2=F; 30=spawnbio; 31=exp(recdev); 36=recdev; 32=spawnbio*recdev; 33=recruitment; 34=depletion(&see Qsetup); 35=parm_dev(&see Qsetup)" << endl;
report1 << "#_errtype: -1=normal; 0=lognormal; 1=lognormal with bias correction; >1=df for T-dist" << endl;
report1 << "#_SD_report: 0=not; 1=include survey expected value with se" << endl;
report1 << "#_note that link functions are specified in Q_setup section of control file" << endl;
report1 << "#_dataunits = 36 and 35 should use Q_type 5 to provide offset parameter" <<endl;
report1 << "#_fleet units errtype SD_report" << endl;
for (f = 1; f <= Nfleet; f++)
report1 << f << " " << Svy_units(f) << " " << Svy_errtype(f) << " " << Svy_sdreport(f) << " # " << fleetname(f) << endl;
report1 << "#_year month index obs err" << endl;
if (Svy_N > 0)
for (f = 1; f <= Nfleet; f++)
for (i = 1; i <= Svy_N_fleet(f); i++)
{
t = Svy_time_t(f, i);
ALK_time = Svy_ALK_time(f, i);
double newobs = 0.0;
report1 << Show_Time(t, 1) << " " << Svy_super(f, i) * data_time(ALK_time, f, 1) << " " << f * Svy_use(f, i) << " ";
if (Svy_errtype(f) == -1) // normal error
{
newobs = value(Svy_est(f, i) + randn(radm) * Svy_se_use(f, i)); // uses Svy_se_use, not Svy_se_rd to include both effect of input var_adjust and extra_sd
}
if (Svy_errtype(f) == 0) // lognormal
{
newobs = value(mfexp(Svy_est(f, i) + randn(radm) * Svy_se_use(f, i))); // uses Svy_se_use, not Svy_se_rd to include both effect of input var_adjust and extra_sd
}
else if (Svy_errtype(f) > 1000) // T-dist
{
dvariable df = Svy_errtype(f) - 1000.;
temp = sqrt((df + 1.) / df);
newobs = value(mfexp(Svy_est(f, i) + randn(radm) * Svy_se_use(f, i) * temp)); // adjusts the sd by the df sample size
}
if (Svy_minval(f) >= 0.0 && Svy_errtype(f) != 0) // this logic may need adjustment
newobs = max(newobs, 0.5 * Svy_minval(f));
report1 << newobs << " " << Svy_se_rd(f, i) << " #_orig_obs: " << Svy_obs(f, i) << " " << fleetname(f) << endl;
}
report1 << "-9999 1 1 1 1 # terminator for survey observations " << endl;
report1 << "#" << endl
<< Ndisc_fleets << " #_N_fleets_with_discard" << endl;
report1 << "#_discard_units (1=same_as_catchunits(bio/num); 2=fraction; 3=numbers)" << endl;
report1 << "#_discard_errtype: >0 for DF of T-dist(read CV below); 0 for normal with CV; -1 for normal with se; -2 for lognormal; -3 for trunc normal with CV" << endl;
report1 << "# note: only enter units and errtype for fleets with discard " << endl;
report1 << "# note: discard data is the total for an entire season, so input of month here must be to a month in that season" << endl;
report1 << "#_Fleet units errtype" << endl;
if (Ndisc_fleets > 0)
{
for (f = 1; f <= Nfleet; f++)
if (disc_units(f) > 0)
report1 << f << " " << disc_units(f) << " " << disc_errtype(f) << " # " << fleetname(f) << endl;
report1 << "#_year month fleet obs stderr" << endl;
for (f = 1; f <= Nfleet; f++)
for (i = 1; i <= disc_N_fleet(f); i++)
{
ALK_time = disc_time_ALK(f, i);
report1 << Show_Time(disc_time_t(f, i), 1) << " " << yr_disc_super(f, i) * data_time(ALK_time, f, 1) << " " << f * yr_disc_use(f, i) << " ";
if (disc_errtype(f) >= 1)
{
temp = exp_disc(f, i) + randn(radm) * sd_disc(f, i) * sqrt((disc_errtype(f) + 1.) / disc_errtype(f)) * exp_disc(f, i);
if (temp < 0.001)
temp = 0.001;
}
else if (disc_errtype(f) == 0)
{
temp = exp_disc(f, i) + randn(radm) * sd_disc(f, i);
if (temp < 0.001)
temp = 0.001;
}
else if (disc_errtype(f) == -1)