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SS_readdata_330.tpl
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SS_readdata_330.tpl
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// SS_Label_file #3. **SS_readdata.tpl**
// SS_Label_file # * read *data_file* named in starter.ss
// SS_Label_file # * create arrays for data with dimensioning defined dynamically
// SS_Label_file # * creates link from each data element to area/time/fleet that datum occur, and other arrays with specification of which data types occur in each area/time
// SS_Label_file # * uses function found in SS_global: <u>get_data_timing()</u>
// SS_Label_file # * read *forecast.ss*
// SS_Label_file # * note that this extends the time dimension of some arrays, so is read before readcontrol
// SS_Label_Flow read data file named in starter.ss file
// SS_Label_Info_2.0 #READ DATA FILE
// SS_Label_Info_2.1 #Read comments and dimension info
// SS_Label_Info_2.1.1 #Read and save comments at top of data file
number fif // end of file marker
LOCAL_CALCS
// clang-format on
//
ad_comm::change_datafile_name(datfilename);
if (finish_starter == 999)
{
warnstream << "finish_starter=999, so probably used a 3.24 starter.ss; please update";
write_warning(N_warn, 0, 0);
finish_starter = 3.30;
}
cout << " reading from data file" << endl;
ifstream Data_Stream(datfilename); // even if the global_datafile name is used, there still is a different logical device created
k = 0;
N_DC = 0;
while (k == 0)
{
Data_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_DC++;
Data_Comments += readline;
}
}
}
// clang-format off
END_CALCS
!!// SS_Label_Info_2.1.2 #Read model time dimensions
int read_seas_mo; // 1=read integer season; 2=read real months
LOCAL_CALCS
// clang-format on
read_seas_mo = 2;
// clang-format off
END_CALCS
int N_subseas; // number of subseasons within season; must be even number to get one to be mid_season
ivector timing_constants(1,6);
LOCAL_CALCS
// clang-format on
*(ad_comm::global_datafile) >> styr; //start year of the model
echoinput << styr << " start year " << endl;
*(ad_comm::global_datafile) >> endyr; // end year of the model
echoinput << endyr << " end year " << endl;
*(ad_comm::global_datafile) >> nseas; // number of seasons
echoinput << nseas << " N seasons " << endl;
// clang-format off
END_CALCS
init_vector seasdur(1,nseas); // season duration; enter in units of months, fractions OK; will be rescaled to sum to 1.0 if total is greater than 11.9
LOCAL_CALCS
// clang-format on
echoinput << seasdur << " months/seas (fractions OK) " << endl;
*(ad_comm::global_datafile) >> N_subseas;
echoinput << N_subseas << " Number of subseasons (even number only; min 2) for calculation of ALK " << endl;
mid_subseas = N_subseas / 2 + 1;
timing_constants(1) = read_seas_mo;
timing_constants(2) = nseas;
timing_constants(3) = N_subseas;
timing_constants(4) = mid_subseas;
timing_constants(5) = styr;
timing_constants(6) = endyr;
// clang-format off
END_CALCS
int TimeMax;
int TimeMax_Fcast_std;
int ALK_time_max;
int eq_yr;
int bio_yr;
number sumseas;
// SS_Label_Info_2.1.3 #Set up seasons
vector seasdur_half(1,nseas); // half a season
matrix subseasdur(1,nseas,1,N_subseas); // cumulative time, within season, for each subseas
vector subseasdur_delta(1,nseas); // length of each subseason
vector azero_seas(1,nseas); // cumulative time, within year, up until begin of this season
LOCAL_CALCS
// clang-format on
sumseas = sum(seasdur);
if (sumseas >= 11.9)
{
seasdur /= sumseas;
seas_as_year = 0;
sumseas = 12.0; // to be sure it is exactly 12.
}
else
{
seasdur /= 12.;
seas_as_year = 1;
// sumseas will now be used as the duration of the pseudo-year, rather than assuming year has 12 months;
if (nseas > 1)
{
warnstream << "Error. Can only have 1 season when during seasons as psuedo-years.";
write_warning(N_warn, 0, 1);
}
}
seasdur_half = seasdur * 0.5; // half a season
subseasdur_delta = seasdur / double(N_subseas);
TimeMax = styr + (endyr + 50 - styr) * nseas + nseas - 1;
retro_yr = endyr + retro_yr;
ALK_time_max = (endyr - styr + 51) * nseas * N_subseas; // sets maximum size for data array indexing 50 years into forecast
// ALK_time_max will be redefined after reading forecast's YrMax to accomodate forecasts longer than the 50 year data limit
azero_seas(1) = 0.;
if (nseas > 1)
{
for (s = 2; s <= nseas; s++) /* SS_loop: calculate azero_seas from cumulative sum of seasdur(s) */
{
azero_seas(s) = sum(seasdur(1, s - 1));
}
}
subseasdur.initialize();
for (s = 1; s <= nseas; s++) /* SS_loop: for each season */
{
for (subseas = 2; subseas <= N_subseas; subseas++) /* SS_loop: calculate cumulative time within season to start of each subseas */
{
subseasdur(s, subseas) = subseasdur(s, subseas - 1) + seasdur(s) / double(N_subseas);
}
}
echoinput << seasdur << " processed season duration (frac. of year) " << endl;
echoinput << subseasdur_delta << " processed subseason duration (frac. of year) " << endl;
echoinput << " processed subseason cumulative annual time within season " << endl
<< subseasdur << endl;
if (seas_as_year == 1)
{
warnstream << "Season durations sum to <11.9, so SS3 assumes you are doing years as pseudo-seasons." << endl
<< "There can be only 1 season in this timestep and SS3 will ignore month input and assume all observation occur at middle of this pseudo-year" << endl
<< "mortality, growth and movement rates are per annum, so will get multiplied by the duration of this timestep as they are used." << endl
<< "What gets reported as age is now age in timesteps; and input of age-specific M or K requires one entry per timestep" << endl
<< "Similarly, output of age-specific quantities is in terms of number of timesteps, not real years" << endl
<< "spawn_month and settlement_month in control file are best set to 1.0 when doing years as pseudo-seasons" << endl;
write_warning(N_warn, 1, 0);
}
// clang-format off
END_CALCS
// SPAWN-RECR: define spawning season
init_number spawn_rd;
number spawn_month; // month that spawning occurs
int spawn_seas; // spawning occurs in this season
int spawn_subseas; //
number spawn_time_seas; // real time within season for mortality calculation
LOCAL_CALCS
// clang-format on
if (read_seas_mo == 1) // so reading values of integer season
{
spawn_seas = spawn_rd;
spawn_month = 1.0 + azero_seas(spawn_seas) / sumseas;
spawn_subseas = 1;
spawn_time_seas = 0.0;
}
else // reading values of month
{
spawn_month = spawn_rd;
temp1 = (spawn_month - 1.0) / sumseas; // spawn_month as fraction of year
if (spawn_month >= 13.0)
{
warnstream << "Fatal error. spawn_month must be <13.0, end of year is 12.99, value read is: " << spawn_month;
write_warning(N_warn, 0, 1);
}
spawn_seas = 1; // earlist possible spawn_seas;
spawn_subseas = 1; // earliest possible subseas in spawn_seas
temp = azero_seas(spawn_seas) + subseasdur_delta(spawn_seas); // starting value
while (temp <= temp1 + 1.0e-9)
{
if (spawn_subseas == N_subseas)
{
spawn_seas++;
spawn_subseas = 1;
}
else
{
spawn_subseas++;
}
temp += subseasdur_delta(spawn_seas);
}
spawn_time_seas = (temp1 - azero_seas(spawn_seas)) / seasdur(spawn_seas); // remaining fraction of year converted to fraction of season
}
echoinput << "SPAWN month: " << spawn_month << "; seas: " << spawn_seas << "; subseas_for_ALK: " << spawn_subseas << "; timing_in_season: " << spawn_time_seas << endl;
if (spawn_seas > nseas)
{
warnstream << " spawn_seas index must be <= nseas ";
write_warning(N_warn, 0, 0);
}
// clang-format off
END_CALCS
int pop; // number of areas
int gender_rd;
int gender; // number of sexes
int nages; // maxage as accumulator
int nages2; // doubled vector to store males after females = gender*nages+gender-1
int Nsurvey;
int Nfleet;
int Nfleet1; // used with 3.24 for number of fishing fleets
LOCAL_CALCS
// clang-format on
{
*(ad_comm::global_datafile) >> gender_rd;
gender = abs(gender_rd);
if (gender_rd < 0)
echoinput << "gender read is negative, so total spawnbiomass will be multiplied by frac_female parameter" << endl;
*(ad_comm::global_datafile) >> nages;
echoinput << gender << " N sexes " << endl
<< "Accumulator age " << nages << endl;
*(ad_comm::global_datafile) >> pop;
echoinput << pop << " N_areas " << endl;
*(ad_comm::global_datafile) >> Nfleet;
Nfleet1 = 0;
Nsurvey = 0;
nages2 = gender * nages + gender - 1;
echoinput << Nfleet << " total number of fishing fleets and surveys " << endl;
}
// clang-format off
END_CALCS
// SS_Label_Info_2.1.5 #Define fleets, surveys, predators and areas
imatrix pfleetname(1,Nfleet,1,2);
ivector fleet_type(1,Nfleet); // 1=fleet with catch; 2=discard only fleet with F; 3=survey(ignore catch); 4=M2=predator
int N_bycatch; // number of bycatch only fleets
int N_pred; // number of predator fleets
ivector N_catchfleets(0,pop); // number of bycatch plus landed catch fleets by area
imatrix fish_fleet_area(0,pop,0,Nfleet); // list of catch_fleets that are type 1 or 2, so have a F
ivector predator(1,Nfleet); // list of "fleets" that are type 4
ivector predator_rev(1,Nfleet); // predator ID given f
imatrix predator_area(0,pop,0,Nfleet); // list of predators by area
ivector need_catch_mult(1,Nfleet); // 0=no, 1=need catch_multiplier parameter
vector surveytime(1,Nfleet); // (-1, 1) code for fisheries to indicate use of season-wide observations, or specifically timed observations
ivector fleet_area(1,Nfleet); // areas in which each fleet/survey/predator operates
vector catchunits1(1,Nfleet); // 1=biomass; 2=numbers
// vector catch_se_rd1(1,Nfleet) // units are se of log(catch); use -1 to ignore input catch values for discard only fleets
vector catchunits(1,Nfleet);
// vector catch_se_rd(1,Nfleet)
matrix catch_se(styr-nseas,TimeMax,1,Nfleet);
matrix fleet_setup(1,Nfleet,1,5); // type, timing, area, units, need_catch_mult
matrix bycatch_setup(1,Nfleet,1,6);
// 1: fleet number; must match fleet definitions"<<endl;
// 2: 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;
// 3: 1=Fmult scales with other fleets; 2=bycatch F constant at input value; 3=mean bycatch F from range of years"<<endl;
// 4: F or first year of range"<<endl;
// 5: last year of range"<<endl;
// 6: not used"<<endl;
ivector YPR_mask(1,Nfleet);
ivector retParmLoc(1,1);
int N_retParm;
LOCAL_CALCS
// clang-format on
bycatch_setup.initialize();
YPR_mask.initialize();
catch_se = 0.01; // initialize to a small value
{
N_bycatch = 0;
N_catchfleets.initialize();
fish_fleet_area.initialize();
predator_area.initialize();
N_pred = 0;
predator.initialize();
echoinput << "rows are fleets; columns are: Fleet_#, fleet_type, timing, area, units, need_catch_mult" << endl;
for (f = 1; f <= Nfleet; f++)
{
*(ad_comm::global_datafile) >> fleet_setup(f)(1, 5);
*(ad_comm::global_datafile) >> anystring;
fleetname += anystring;
fleet_type(f) = int(fleet_setup(f, 1));
if (fleet_type(f) == 2)
N_bycatch++;
surveytime(f) = fleet_setup(f, 2) / fabs(fleet_setup(f, 2));
fleet_setup(f, 2) = surveytime(f);
p = int(fleet_setup(f, 3)); //area
fleet_area(f) = p;
catchunits(f) = int(fleet_setup(f, 4));
need_catch_mult(f) = int(fleet_setup(f, 5));
if (fleet_type(f) <= 2)
{
N_catchfleets(0)++; // overall N
N_catchfleets(p)++; // count by area
fish_fleet_area(0, N_catchfleets(0)) = f; // to find the "f" index for a catchfleet when not within an area loop
fish_fleet_area(p, N_catchfleets(p)) = f; // to find the index when in an area loop
YPR_mask(f) = 1;
if (surveytime(f) != -1.)
{
warnstream << "fishing fleet: " << f << " surveytime read as: " << surveytime(f) << " normally is -1 for fishing fleet; can override for indiv. obs. using 1000+month";
write_warning(N_warn, 0, 0);
}
}
else if (fleet_type(f) == 3)
{
if (surveytime(f) == -1.)
{
warnstream << "survey fleet: " << f << " surveytime read as: " << surveytime(f) << " SS3 resets to 1 for all survey fleets, and always overridden by indiv. obs. month";
write_warning(N_warn, 0, 0);
surveytime(f) = 1.;
}
}
else if (fleet_type(f) == 4) // predator, e.g. red tide
{
N_pred++;
predator(N_pred) = f;
predator_rev(f) = N_pred;
predator_area(0, N_pred) = f; // to find the "f" index for a predator when not within an area loop
predator_area(p, N_pred) = f; // to find the index when in an area loop
surveytime(f) = -1.;
}
if (fleet_type(f) > 1 && need_catch_mult(f) > 0)
{
warnstream << "Need_catch_mult can be used only for fleet_type=1 fleet= " << f;
write_warning(N_warn, 0, 1);
}
echoinput << f << " # " << fleet_setup(f) << " # " << fleetname(f) << endl;
if (f > 1) { // check for duplicate fleet names, which will break r4ss
for (int f1 = 1; f1 < f; f1++)
{
if (fleetname(f1) == fleetname(f))
{
warnstream << "duplicate fleet names for fleets: " << f1 << " and " << f << "; " << fleetname(f) << "; SS3 will exit";
write_warning(N_warn, 0, 1);
}
}
}
}
if (N_bycatch > 0)
{
echoinput << "Now read bycatch fleet characteristics for " << N_bycatch << " fleets" << endl;
echoinput << "1: fleet number; must match fleet definitions" << endl;
echoinput << "2: 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;
echoinput << "3: 1=Fmult scales with other fleets; 2=bycatch F constant at input value; 3=mean bycatch F from range of years" << endl;
echoinput << "4: F or first year of range" << endl;
echoinput << "5: last year of range" << endl;
echoinput << "6: not used" << endl;
for (j = 1; j <= N_bycatch; j++)
{
*(ad_comm::global_datafile) >> f;
bycatch_setup(f, 1) = f;
*(ad_comm::global_datafile) >> bycatch_setup(f)(2, 6);
if (fleet_type(f) == 2)
{
echoinput << f << " " << fleetname(f) << " bycatch_setup: " << bycatch_setup(f) << endl;
if (bycatch_setup(f, 2) == 2) // omit bycatch fleet catch from YPR optimize
{
YPR_mask(f) = 0;
}
if (bycatch_setup(f, 3) == 3) // check year range
{
if (bycatch_setup(f, 4) < styr)
bycatch_setup(f, 4) = styr;
if (bycatch_setup(f, 5) > retro_yr)
bycatch_setup(f, 5) = retro_yr;
}
}
else
{
warnstream << "fleet " << f << " is in bycatch list but not designated as bycatch fleet";
write_warning(N_warn, 0, 1);
}
}
}
echoinput << "YPR_optimize_mask: " << YPR_mask << endl;
Nfleet1 = N_catchfleets(0);
N_retParm = 0;
}
// clang-format off
END_CALCS
// ProgLabel_2.1.5 define genders and max age
ivector age_vector(0,nages);
vector r_ages(0,nages);
vector frac_ages(0,nages);
ivector years(styr,endyr); // vector of the years of the model
vector r_years(styr,endyr);
ivector ALK_subseas_update(1,nseas*N_subseas); // 0 means ALK is OK for this subseas, 1 means that recalc is needed
ivector F_reporting_ages(1,2);
LOCAL_CALCS
// clang-format on
for (a = 0; a <= nages; a++) // SS_loop: fill ivector age vector
age_vector(a) = a;
for (a = 0; a <= nages; a++) // SS_loop: fill real vector r_ages
r_ages(a) = double(a);
frac_ages = r_ages / r_ages(nages);
for (y = styr; y <= endyr; y++)
{ //year vector
years(y) = y;
r_years(y) = y;
}
if (F_reporting == 4 || F_reporting == 5)
{
F_reporting_ages = F_reporting_ages_R;
if (F_reporting_ages(1) > (nages - 2) || F_reporting_ages(1) < 0)
{
warnstream << "reset lower end of F_reporting_ages to be nages-2 ";
write_warning(N_warn, 0, 0);
F_reporting_ages(1) = nages - 2;
}
if (F_reporting_ages(2) > (nages - 2) || F_reporting_ages(2) < 0)
{
warnstream << "reset upper end of F_reporting_ages to be nages-2 ";
write_warning(N_warn, 0, 0);
F_reporting_ages(2) = nages - 2;
}
}
else
{
F_reporting_ages(1) = nages / 2;
F_reporting_ages(2) = F_reporting_ages(1);
}
// clang-format off
END_CALCS
// SS_Label_Info_2.1.6 #Indexes for data timing. "have_data" and "data_time" hold pointers for data occurrence, timing, and ALK need
int data_type;
number data_timing;
4iarray have_data(1,ALK_time_max,0,Nfleet,0,9,0,100);
imatrix have_data_yr(styr,endyr+50,0,Nfleet);
// have_data stores the data index of each datum occurring at time ALK_time, for fleet f of observation type k. Up to 150 data are allowed due to CAAL data
// have_data(ALK_idx,0,0,0) is overall indicator that some datum requires ALK update in this ALK_time
// have_data() 3rd element: 0=any; 1=survey/CPUE/effort; 2=discard; 3=mnwt; 4=length; 5=age; 6=SizeFreq; 7=sizeage; 8=morphcomp; 9=tags
// have_data() 4th element; zero'th element contains N obs for this subseas; allows for 150 observations per datatype per fleet per subseason
3darray data_time(1,ALK_time_max,1,Nfleet,1,3);
// data_time(): first value will hold real month; 2nd is timing within season; 3rd is year.fraction
// for a given fleet x subseas, all observations must have the same specific timing (month.fraction)
// a warning will be given if subsequent observations have a different month.fraction
// an observation's real_month is used to assign it to a season and a subseas within that seas, and it is used to calculate the data_timing within the season for mortality
// where ALK_idx=(y-styr)*nseas*N_subseas+(s-1)*N_subseas+subseas This is index to subseas and used to indicate which ALK is being referenced
// 3darray data_ALK_time(1,Nfleet,0,9,1,<nobsperkind/fleet>) stores ALK_time
// ProgLabel_2.2 Read CATCH amount by fleet
matrix obs_equ_catch(1,nseas,1,Nfleet); // initial, equilibrium catch. now seasonal
LOCAL_CALCS
// clang-format on
have_data.initialize();
have_data_yr.initialize();
obs_equ_catch.initialize();
for (y = 1; y <= ALK_time_max; y++)
for (f = 1; f <= Nfleet; f++)
{
data_time(y, f, 1) = -1.0; // set to illegal value since 0.0 is valid
}
// clang-format off
END_CALCS
!!// SS_Label_Info_2.2 #Read CATCH amount by fleet
int N_ReadCatch;
// int Catch_read;
vector tempvec(1,6); // vector used for temporary reads
LOCAL_CALCS
// clang-format on
ender = 0;
do
{
dvector tempvec(1, 5);
*(ad_comm::global_datafile) >> tempvec(1, 5);
if (tempvec(1) == -9999.)
ender = 1;
catch_read.push_back(tempvec(1, 5));
} while (ender == 0);
N_ReadCatch = catch_read.size() - 1;
echoinput << N_ReadCatch << " records" << endl;
// clang-format off
END_CALCS
matrix catch_ret_obs(1,Nfleet,styr-nseas,TimeMax+nseas);
imatrix do_Fparm(1,Nfleet,styr-nseas,TimeMax+nseas);
imatrix catch_record_count(1,Nfleet,styr-nseas,TimeMax+nseas);
3iarray catch_seas_area(styr,TimeMax,1,pop,0,Nfleet);
matrix totcatch_byarea(styr,TimeMax,1,pop);
vector totcat(styr-1,endyr); // by year, not by t
int first_catch_yr;
vector catch_by_fleet(1,Nfleet);
ivector disc_fleet_list(1,Nfleet);
int N_retain_fleets;
int catch_warn;
LOCAL_CALCS
// clang-format on
catch_ret_obs.initialize();
catch_record_count.initialize();
catch_warn = 0;
tempvec.initialize();
for (k = 0; k <= N_ReadCatch - 1; k++)
{
// do read in list format y, s, f, catch, catch_se
tempvec(1, 5) = catch_read[k];
g = tempvec(1);
s = tempvec(2);
f = tempvec(3);
if (g == -999)
{ // designates initial equilibrium
y = styr - 1;
}
else
{
y = g;
}
if (k == 0)
echoinput << "first catch record: " << tempvec(1, 5) << endl;
if (k == (N_ReadCatch - 1))
echoinput << "last catch record: " << tempvec(1, 5) << endl;
if (y >= (styr - 1) && y <= endyr && (g == -999 || g >= styr)) // observation is in date range
{
if (s > nseas)
{
catch_warn++;
s = nseas;
// allows for collapsing multiple season catch data down into fewer seasons
// typically to collapse to annual because accumulation will all be in the index "nseas"
}
if (s > 0)
{
t = styr + (y - styr) * nseas + s - 1;
{
catch_ret_obs(f, t) += tempvec(4);
catch_record_count(f, t)++;
catch_se(t, f) = tempvec(5);
}
}
else // distribute catch equally across seasons
{
for (s = 1; s <= nseas; s++)
{
t = styr + (y - styr) * nseas + s - 1;
{
catch_ret_obs(f, t) += tempvec(4) / nseas;
catch_record_count(f, t)++;
}
}
}
}
}
if (catch_warn > 0) {
if (catch_warn > 1)
warnstream << catch_warn << " catch records have ";
else
warnstream << "one catch record has ";
warnstream << "seas>nseas; perhaps erroneous entry of month rather than season; changed to nseas";
write_warning(N_warn, 0, 0);
}
// warn on duplicate catch records
for (y = styr - 1; y <= endyr; y++)
for (s = 1; s <= nseas; s++)
for (f = 1; f <= Nfleet; f++) {
t = styr + (y - styr) * nseas + s - 1;
if (catch_record_count(f, t) > 1)
{
warnstream << catch_record_count(f, t) << " catch records have been accumulated into yr, seas, fleet " << y << " " << s << " " << f << "; total catch= " << catch_ret_obs(f, t);
write_warning(N_warn, 0, 0);
}
}
obs_equ_catch.initialize();
for (s = 1; s <= nseas; s++)
{
for (f = 1; f <= Nfleet; f++)
if (fleet_type(f) <= 2)
{
obs_equ_catch(s, f) = catch_ret_obs(f, styr - nseas - 1 + s);
}
echoinput << " equ, seas: -1 " << s << " catches: " << obs_equ_catch(s) << endl;
}
for (y = styr; y <= endyr; y++)
for (s = 1; s <= nseas; s++)
{
t = styr + (y - styr) * nseas + s - 1;
echoinput << "year, seas: " << y << " " << s << " catches: " << trans(catch_ret_obs)(t) << endl;
}
// calc total catch by year so can calculate the first year with catch and to omit zero catch years from sdreport
totcat.initialize();
catch_seas_area.initialize();
totcatch_byarea.initialize();
totcat(styr - 1) = sum(obs_equ_catch); // sums over all seasons and fleets
first_catch_yr = 0;
if (totcat(styr - 1) > 0.0)
first_catch_yr = styr - 1;
for (y = styr; y <= endyr; y++)
{
for (s = 1; s <= nseas; s++)
{
t = styr + (y - styr) * nseas + s - 1;
for (p = 1; p <= pop; p++)
for (f = 1; f <= Nfleet; f++)
if (fleet_area(f) == p && catch_ret_obs(f, t) > 0.0 && fleet_type(f) <= 2) // excludes survey and predator fleets
{
catch_seas_area(t, p, f) = 1;
catch_seas_area(t, p, 0) = 1;
if (fleet_type(f) == 1)
totcat(y) += catch_ret_obs(f, t);
if (fleet_type(f) == 1)
totcatch_byarea(t, p) += catch_ret_obs(f, t);
}
}
if (totcat(y) > 0.0 && first_catch_yr == 0)
first_catch_yr = y;
if (y == endyr && totcat(y) == 0.0)
{
warnstream << "catch is 0.0 in endyr; this can cause problem in the benchmark and forecast calculations. ";
write_warning(N_warn, 0, 0);
}
}
echoinput << endl
<< "#_show_total_catch_by_fleet" << endl;
catch_by_fleet = rowsum(catch_ret_obs);
for (f = 1; f <= Nfleet; f++)
{
echoinput << f << " type: " << fleet_type(f) << " " << fleetname(f) << " catch: " << catch_by_fleet(f);
if (fleet_type(f) == 3 && catch_by_fleet(f) > 0.0)
{
warnstream << " Catch by survey fleet will be ignored " << fleet_type(f);
write_warning(N_warn, 1, 0);
}
echoinput << endl;
}
// clang-format off
END_CALCS
// SS_Label_Info_2.3 #Read fishery CPUE, effort, and Survey index or abundance
!!echoinput<<endl<<"#_ now read survey characteristics: fleet_#, svyunits, svyerrtype for each fleet "<<endl;
int Svy_N_rd;
int Svy_N;
init_imatrix Svy_units_rd(1,Nfleet,1,4);
ivector Svy_units(1,Nfleet); //0=num; 1=bio; 2=F; >=30 for special patterns
ivector Svy_errtype(1,Nfleet); // -1=normal / 0=lognormal / >0=T
ivector Svy_sdreport(1,Nfleet); // 0=no sdreport; 1=enable sdreport
int Svy_N_sdreport;
LOCAL_CALCS
// clang-format on
data_type = 1; // for surveys
echoinput << "Units: 0=numbers; 1=biomass; 2=F; >=30 for special patterns" << endl;
echoinput << "Errtype: -1=normal; 0=lognormal; >0=T" << endl;
echoinput << "SD_Report: 0=no sdreport; 1=enable sdreport" << endl;
echoinput << "Fleet Units Err_Type SD_Report" << endl;
echoinput << Svy_units_rd << endl;
Svy_units = column(Svy_units_rd, 2);
Svy_errtype = column(Svy_units_rd, 3);
Svy_sdreport = column(Svy_units_rd, 4);
ender = 0;
do
{
dvector tempvec(1, 5);
*(ad_comm::global_datafile) >> tempvec(1, 5);
if (tempvec(1) == -9999.)
ender = 1;
Svy_data.push_back(tempvec(1, 5));
} while (ender == 0);
Svy_N_rd = Svy_data.size() - 1;
echoinput << Svy_N_rd << " nobs_survey " << endl;
// clang-format off
END_CALCS
// init_matrix Svy_data(1,Svy_N_rd,1,5)
// !!if(Svy_N_rd>0) echoinput<<" Svy_data "<<endl<<Svy_data<<endl;
ivector Svy_N_fleet(1,Nfleet); // total N
ivector Svy_N_fleet_use(1,Nfleet); // N in likelihood
int in_superperiod;
ivector Svy_super_N(1,Nfleet); // N super_yrs per fleet
LOCAL_CALCS
// clang-format on
// count the number of observations, exclude those outside the specified year range, count the number of superperiods
Svy_N = 0;
Svy_N_fleet = 0;
Svy_N_fleet_use = 0;
Svy_super_N = 0;
if (Svy_N_rd > 0)
{
for (i = 0; i <= Svy_N_rd - 1; i++)
{
echoinput << Svy_data[i] << endl;
y = Svy_data[i](1);
if (y >= styr)
{
f = abs(Svy_data[i](3)); // negative f turns off observation
Svy_N_fleet(f)++;
if (Svy_data[i](5) < 0)
{
warnstream << "cannot use negative se to indicate superperiods in survey data";
write_warning(N_warn, 0, 1);
}
if (Svy_data[i](2) < 0)
Svy_super_N(f)++; // count the super-periods if seas<0
}
}
Svy_N = sum(Svy_N_fleet);
for (f = 1; f <= Nfleet; f++)
if (Svy_super_N(f) > 0)
{
j = Svy_super_N(f) / 2; // because we counted the begin and end
if (2 * j != Svy_super_N(f))
{
warnstream << "unequal number of starts and ends of survey superperiods ";
write_warning(N_warn, 0, 1);
}
else
{
Svy_super_N(f) = j;
}
}
}
// check if there are observations for the index before enabling sdreport
for (f = 1; f <= Nfleet; ++f)
{
if (Svy_N_fleet(f) == 0) Svy_sdreport(f) = 0;
}
// clang-format off
END_CALCS
imatrix Svy_time_t(1,Nfleet,1,Svy_N_fleet); // stores the continuous season index (t) for each obs
imatrix Svy_ALK_time(1,Nfleet,1,Svy_N_fleet); // stores the continuous subseas index (ALK_time) for each obs
imatrix Svy_use(1,Nfleet,1,Svy_N_fleet);
matrix Svy_obs(1,Nfleet,1,Svy_N_fleet);
matrix Svy_obs_log(1,Nfleet,1,Svy_N_fleet);
matrix Svy_se_rd(1,Nfleet,1,Svy_N_fleet);
matrix Svy_se(1,Nfleet,1,Svy_N_fleet);
matrix Svy_selec_abund(1,Nfleet,1,Svy_N_fleet); // Vulnerable biomass
// arrays for Super-years
imatrix Svy_super(1,Nfleet,1,Svy_N_fleet); // indicator used to display start/stop in reports
imatrix Svy_super_start(1,Nfleet,1,Svy_super_N); // where Svy_super_N is a vector
imatrix Svy_super_end(1,Nfleet,1,Svy_super_N);
matrix Svy_super_weight(1,Nfleet,1,Svy_N_fleet);
ivector Svy_styr(1,Nfleet);
ivector Svy_endyr(1,Nfleet);
imatrix Svy_yr(1,Nfleet,1,Svy_N_fleet);
number real_month;
vector timing_input(1,3);
vector timing_r_result(1,3);
vector Svy_minval(1,Nfleet);
vector Svy_maxval(1,Nfleet);
ivector timing_i_result(1,6);
// r_result(1,3) will contain: real_month, data_timing_seas, data_timing_yr,
// i_result(1,6) will contain y, t, s, f, ALK_time, use_midseas
LOCAL_CALCS
// clang-format on
// SS_Label_Info_2.3.1 #Process survey observations, move info into working arrays,create super-periods as needed
Svy_super_N.initialize();
Svy_N_fleet.initialize();
Svy_styr.initialize();
Svy_endyr.initialize();
Svy_yr.initialize();
Svy_minval.initialize();
Svy_minval = 999999999.;
Svy_maxval.initialize();
Svy_maxval = -999999999.;
in_superperiod = 0;
if (Svy_N > 0)
{
for (i = 0; i <= Svy_N_rd - 1; i++) // loop all, including those out of yr range
{
y = Svy_data[i](1);
if (y > endyr + 50)
{
warnstream << "forecast observations cannot be beyond endyr +50";
write_warning(N_warn, 0, 1);
}
if (y >= styr)
{
// call a global function to calculate data timing and create various indexes
// function will return: data_timing, ALK_time, real_month, use_midseas
timing_input(1, 3) = Svy_data[i](1, 3);
get_data_timing(timing_input, timing_constants, timing_i_result, timing_r_result, seasdur, subseasdur_delta, azero_seas, surveytime);
f = abs(Svy_data[i](3));
if (y > retro_yr)
Svy_data[i](3) = -f;
Svy_N_fleet(f)++; // count obs by fleet again
j = Svy_N_fleet(f); // index of observation as stored in working array
t = timing_i_result(2);
ALK_time = timing_i_result(5);
// some fleet specific indexes and working versions of the data and se
Svy_time_t(f, j) = t;
Svy_ALK_time(f, j) = ALK_time; // continuous subseas counter in which jth obs from fleet f occurs
Svy_se_rd(f, j) = Svy_data[i](5); // later adjust with varadjust, copy to se_cr_use, then adjust with extra se parameter
if (Svy_data[i](3) < 0)
{
Svy_use(f, j) = -1;
}
else
{
Svy_use(f, j) = 1;
Svy_N_fleet_use(f)++;
}
Svy_obs(f, j) = Svy_data[i](4);
Svy_yr(f, j) = y;
if (Svy_styr(f) == 0 || (y >= styr && y < Svy_styr(f)))
Svy_styr(f) = y; // for dimensioning survey q devs
if (Svy_endyr(f) == 0 || (y <= endyr && y > Svy_endyr(f)))
Svy_endyr(f) = y; // for dimensioning survey q devs
if (y >= styr && Svy_data[i](3) > 0)
{
Svy_minval(f) = min(Svy_minval(f), Svy_obs(f, j));
Svy_maxval(f) = max(Svy_maxval(f), Svy_obs(f, j));
}
// some all fleet indexes
if (data_time(ALK_time, f, 1) < 0.0) // so first occurrence of data at ALK_time,f
{ // real_month,fraction of season, year.fraction
data_time(ALK_time, f)(1, 3) = timing_r_result(1, 3);
}
else if (timing_r_result(1) == data_time(ALK_time, f, 1))
{
warnstream << "SURVEY: duplicate survey obs for this time-fleet: y,s,f: " << y << " " << s << " " << f << " SS3 will exit ";
write_warning(N_warn, 0, 1);
}
have_data(ALK_time, 0, 0, 0) = 1;
have_data(ALK_time, f, 0, 0) = 1; // so have data of some type in this subseas, for this fleet
have_data(ALK_time, f, data_type, 0)++; // count the number of observations in this subseas
p = have_data(ALK_time, f, data_type, 0); // current number of observations
have_data(ALK_time, f, data_type, p) = j; // store data index for the p'th observation in this subseas
have_data_yr(y, f) = 1; // survey or comp data exist this year
have_data_yr(y, 0) = 1;
// create super_year indexes
if (Svy_data[i](2) < 0) // start or stop a super-period; ALL observations must be continguous in the file
{
Svy_super(f, j) = -1;
if (in_superperiod == 0) // start superperiod
{
Svy_super_N(f)++;
Svy_super_start(f, Svy_super_N(f)) = j;
in_superperiod = 1;
}
else
{
if (in_superperiod == 1) // end superperiod
{
Svy_super_end(f, Svy_super_N(f)) = j;
in_superperiod = 0;
}
else
{
}
}
}
else
{
Svy_super(f, j) = 1;
}
}
}
echoinput << "Successful read of survey data; total N: " << Svy_N << endl;
echoinput << "Index Survey_name N Super_Per Min_val max_val // Observations:" << endl;
for (f = 1; f <= Nfleet; f++)
{
if (Svy_N_fleet(f) > 0)
{
echoinput << f << " " << fleetname(f) << " " << Svy_N_fleet(f) << " " << Svy_super_N(f) << " " << Svy_minval(f) << " " << Svy_maxval(f) << " // " << Svy_obs(f) << endl;
if (Svy_errtype(f) == 0 && Svy_minval(f) <= 0.)
{
warnstream << "error, SS3 has exited. A fleet uses lognormal error and has an observation <=0.0; fleet: " << f;
write_warning(N_warn, 0, 1);
}
}
}
}
Svy_N_sdreport = 0;
for (f = 1; f <= Nfleet; ++f)
{
if (Svy_sdreport(f) > 0)
{
Svy_N_sdreport += Svy_N_fleet(f);
}
}
if (Svy_N_sdreport < 0)
Svy_N_sdreport = 0;
echoinput << "Number of sdreport index values: " << Svy_N_sdreport << endl;
// clang-format off
END_CALCS
init_int Ndisc_fleets;
int nobs_disc; // number of discard records kept in active array
int disc_N_read; // number of records read
ivector disc_N_fleet(1,Nfleet); // kept obs per fleet
ivector disc_N_fleet_use(1,Nfleet); // kept obs per fleet
ivector N_suprper_disc(1,Nfleet); // N super_yrs per obs
LOCAL_CALCS
// clang-format on
// SS_Label_Info_2.4 #read Discard data
echoinput << " note order of discard read is now: N fleets with disc, then if Ndisc_fleets>0 read: fleet, disc_units, disc_error(for 1,Ndisc_fleets), then read obs " << endl;
echoinput << Ndisc_fleets << " N fleets with discard " << endl;
if (Ndisc_fleets > 0)
{
j = Nfleet;
}
else
{
j = 0;
}
data_type = 2; // for discard
// clang-format off
END_CALCS
init_imatrix disc_units_rd(1,Ndisc_fleets,1,3);
ivector disc_units(1,j); // formerly scalar disc_type
ivector disc_errtype(1,j); // formerly scalar DF_disc
vector disc_errtype_r(1,j); // real version for T-dist
vector disc_minval(1,j);
vector disc_maxval(1,j);
LOCAL_CALCS
// clang-format on
disc_units.initialize();
disc_errtype.initialize();
disc_minval.initialize();
disc_minval = 999999999.;
disc_maxval.initialize();
disc_maxval = -999999999.;
nobs_disc = 0;
disc_N_fleet = 0;
disc_N_fleet_use = 0;
N_suprper_disc = 0;
if (Ndisc_fleets > 0)
{
echoinput << "#_discard_units (1=same_as_catchunits(bio/num);2=fraction; 3=numbers)" << endl;
echoinput << "#_discard_error: >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;
echoinput << "#Fleet Units Err_Type" << endl;
echoinput << disc_units_rd << endl;
for (j = 1; j <= Ndisc_fleets; j++)
{
f = disc_units_rd(j, 1);
disc_units(f) = disc_units_rd(j, 2);
disc_errtype(f) = disc_units_rd(j, 3);
disc_errtype_r(f) = float(disc_errtype(f));
}
ender = 0;
do
{
dvector tempvec(1, 5);
*(ad_comm::global_datafile) >> tempvec(1, 5);
if (tempvec(1) == -9999.)
ender = 1;
discdata.push_back(tempvec(1, 5));
} while (ender == 0);
disc_N_read = discdata.size() - 1;
echoinput << disc_N_read << " N discard obs " << endl;
if (disc_N_read > 0)
{
for (i = 0; i <= disc_N_read - 1; i++) // get count of observations in date range
{
echoinput << discdata[i] << endl;
y = discdata[i](1);
if (y >= styr)
{
f = abs(discdata[i](3));
disc_N_fleet(f)++;
if (discdata[i](5) < 0)
{
warnstream << "Cannot use negative se as indicator of superperiod in discard data";
write_warning(N_warn, 0, 1);
}
if (discdata[i](2) < 0)
N_suprper_disc(f)++; // count the super-periods if seas<0 or se<0
}
}
nobs_disc = sum(disc_N_fleet); // sum of obs in the date range
for (f = 1; f <= Nfleet; f++)
if (N_suprper_disc(f) > 0)
{
j = N_suprper_disc(f) / 2; // because we counted the begin and end
if (2 * j != N_suprper_disc(f))
{