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SS_readcontrol_330.tpl
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SS_readcontrol_330.tpl
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// SS_Label_file #4. **SS_readcontrol.tpl**
// SS_Label_file # * read *control_file* named in starter.ss
// SS_Label_file # * define and read needed parameters from model options selected
// SS_Label_file # * creates labels for those parameters
// SS_Label_file # * uses a function found in SS_global, <u>create_timevary()</u>, to create, index and label time-varying parameters; including autogeneration option
// SS_Label_file # * creates and labels derived quantities
// SS_Label_file # * creates covariance matrix
// SS_Label_file # * reads *wt_at_age.ss* if requested
// SS_Label_file # * finish DATA_SECTION
LOCAL_CALCS
// clang-format on
//********CONTROLS********************************
// SS_Label_Info_4.0 #Begin Reading from Control File
// /* SS_Label_Flow begin reading from control file */
ad_comm::change_datafile_name(ctlfilename);
echoinput << endl
<< " Begin reading control file " << endl;
cout << " reading from control file" << endl;
ifstream Control_Stream(ctlfilename); // even if the global_datafile name is used, there still is a different logical device created
// SS_Label_Info_4.1 #Read and store comments at top of control file
k = 0;
N_CC = 0;
while (k == 0)
{
Control_Stream >> readline; // reads the line from input stream
if (length(readline) > 2)
{
checkchar = readline(1);
k = strcmp(checkchar, "#");
checkchar = readline(1, 2);
j = strcmp(checkchar, "#C");
if (j == 0) {
N_CC++;
Control_Comments += readline;
}
}
}
// clang-format off
END_CALCS
// when a parameter is defined and its label (hence usage) is created,
// the value of its min, max, init, prior have not yet been read
// so when it gets created, need to pushback a code to indicate what special conditions affect it
// also may want to save indicator of whether the parameter is multiplier, logit, etc.
// so push_back a code to the ivector Parm_minmax
// and add a string to the adstring_array Parm_info
ivector minmax_types(1,10) // set of canned min-max types
!!// SS_Label_Info_4.2 #Read info for growth patterns, gender, settlement events, platoons
init_int WTage_rd // 0 means do not read wtatage.ss; 1 means read and use wtatage.ss and also read and use growth parameters
// future option 2 will suppress reading and use of growth
!!echoinput<<WTage_rd<<" wtatage switch "<<endl;
init_int N_GP // number of growth patterns (morphs)
!!echoinput<<N_GP<<" N growth patterns "<<endl;
init_int N_platoon // number of platoons 1, 3, 5 are best values to use
!!echoinput<<N_platoon<<" N platoons (1, 3 or 5)"<<endl;
number sd_ratio_rd; // ratio of stddev within platoon to between morphs from file
number platoon_sd_ratio; // ratio of stddev within platoon to between morphs
number sd_within_platoon;
number sd_between_platoon;
ivector ishadow(1,N_platoon);
vector shadow(1,N_platoon);
vector platoon_distr(1,N_platoon);
LOCAL_CALCS
// clang-format on
if (WTage_rd > 0)
{
// Remove unnecessary or confusing reports (issue #383)
pick_report_use(8) = "N";
pick_report_use(27) = "N";
pick_report_use(31) = "N";
pick_report_use(38) = "N";
pick_report_use(42) = "N";
// Incompatible option, fatal condition
if (nobs_mnwt > 0)
{
warnstream << "expected value for mean body-wt will be from the growth curve, not from empirical wtatage.ss";
write_message (WARN, 1);
}
}
if (N_platoon > 1)
{
*(ad_comm::global_datafile) >> sd_ratio_rd;
*(ad_comm::global_datafile) >> platoon_distr;
echoinput << sd_ratio_rd << " sd_ratio_rd" << endl;
echoinput << platoon_distr << " platoon_distr" << endl;
}
else
{
sd_ratio_rd = 1.;
platoon_distr(1) = 1.;
echoinput << " do not read sd_ratio or platoon_distr" << endl;
}
// SS_Label_Info_4.2.1 #Assign distribution among growth platoons if needed
if (platoon_distr(1) < 0.)
{
if (N_platoon == 1)
{
platoon_distr(1) = 1.;
}
else if (N_platoon == 3)
{
platoon_distr.fill("{0.15,0.70,0.15}");
}
else if (N_platoon == 5)
{
platoon_distr.fill("{0.031, 0.237, 0.464, 0.237, 0.031}");
}
}
platoon_distr /= sum(platoon_distr);
// calculate stdev values
if (sd_ratio_rd < 0)
{
platoon_sd_ratio = -sd_ratio_rd;
warnstream << "sd_ratio read is < 0, so expecting sd parameter after movement params.";
write_message (NOTE, 1);
}
else
{
platoon_sd_ratio = sd_ratio_rd;
}
if (N_platoon > 1)
{
sd_between_platoon = sqrt(1. / (1. + platoon_sd_ratio * platoon_sd_ratio));
sd_within_platoon = platoon_sd_ratio * sd_between_platoon;
}
else
{
sd_between_platoon = 0.000001;
sd_within_platoon = 1;
}
if (N_platoon == 1)
{
ishadow(1) = 0;
shadow(1) = 0.;
}
else if (N_platoon == 3)
{
ishadow.fill_seqadd(-1, 1);
shadow.fill_seqadd(-1., 1.);
}
else if (N_platoon == 5)
{
ishadow.fill_seqadd(-2, 1);
shadow.fill_seqadd(-2., 1.);
}
else
{
warnstream << "illegal N platoons: " << N_platoon << "; must be 1, 3 or 5 " ;
write_message (FATAL, 1); // EXIT!
}
// clang-format off
END_CALCS
!!// SS_Label_Info_4.2.2 #Define distribution of recruitment(settlement) among growth patterns, areas, months
int recr_dist_method // 1=like 3.24 (not used); 2=main effects for GP, Settle timing, Area; 3=each Settle entity; 4=no parms (only if GPXsettleXarea=1)
int recr_dist_area // 1=global SRR; 2=area-specific SRR
int N_settle_assignments // number of assigned settlements for GP, Settle_month, Area (>=0)
int N_settle_assignments_rd // number read, needed to distinguish between ss3.24 and SS3.30 setup
int N_settle_timings // number of recruitment settlement timings per spawning (>=1) - important for number of morphs calculation
// will be calculated from the number of unique settle_months among the settle_assignments
int settle // index to settle_assignments
int settle_time // index to setting timings
int Comp_Err_Parm_Start
int recr_dist_inx
LOCAL_CALCS
// clang-format on
* (ad_comm::global_datafile) >> recr_dist_method;
echoinput << recr_dist_method << " # Recruitment distribution method; where: 2=parms for main effects for GP, Area, Settle timing; 3=one parm for each Settle event" << endl;
*(ad_comm::global_datafile) >> recr_dist_area;
echoinput << recr_dist_area << " # future option for recr_dist_area: 1 is hardwired to do global SRR; 2 in future will do area-specific SRR" << endl;
recr_dist_area = 1; //hardwire for testing
N_settle_assignments_rd = 0;
N_settle_assignments = 1; // default
switch (recr_dist_method)
{
case 1:
{
*(ad_comm::global_datafile) >> N_settle_assignments_rd;
*(ad_comm::global_datafile) >> recr_dist_inx;
N_settle_assignments = N_settle_assignments_rd;
break;
}
case 2:
{
*(ad_comm::global_datafile) >> N_settle_assignments;
*(ad_comm::global_datafile) >> recr_dist_inx;
break;
}
case 3:
{
*(ad_comm::global_datafile) >> N_settle_assignments;
*(ad_comm::global_datafile) >> recr_dist_inx;
break;
}
case 4:
{
*(ad_comm::global_datafile) >> N_settle_assignments;
*(ad_comm::global_datafile) >> recr_dist_inx;
if (N_settle_assignments > 1)
{
warnstream << "Need to change to recr_dist_method=3 because >1 settle assignments requested";
write_message (FATAL, 0); // EXIT!
}
break;
}
}
echoinput << N_settle_assignments << " Number of settlement events: GP/area/month to read (>=0) " << endl;
if (recr_dist_method == 1)
{
warnstream << "recr_dist_method cannot be 1 in SS3.30 ";
write_message (FATAL, 0); // EXIT!
}
else if (N_settle_assignments == 1 && recr_dist_method != 4)
{
warnstream << "This model has just one settlement event. Changing to recr_dist_method 4 and removing the recruitment distribution parameters at the end of the MG parms section (below growth parameters) will produce identical results and simplify the model.";
write_message (SUGGEST, 0);
}
else if (recr_dist_method == 2)
{
warnstream << " recr_dist_method 3 is simpler and takes 1 parm for each settlement";
write_message (SUGGEST, 0);
}
echoinput << recr_dist_inx << " # unused option " << endl;
// clang-format off
END_CALCS
int birthseas; // is this still needed??
matrix settlement_pattern_rd(1,N_settle_assignments,1,4); // for each settlement event: GPat, Month, area, age
ivector settle_assignments_timing(1,N_settle_assignments); // stores the settle_timing index for each assignment
matrix settle_timings_tempvec(1,N_settle_assignments,1,2) // temporary storage for real_month and age of each settlement_timing
// dimensioned by assignments, but only uses N_settle_timings of these
LOCAL_CALCS
// clang-format on
*(ad_comm::global_datafile) >>
settlement_pattern_rd;
echoinput << " settlement pattern as read " << endl
<< "GPat Month Area Age" << endl
<< "*" << settlement_pattern_rd << "*" << endl;
echoinput << "Now calculate the number of unique settle timings, which will dictate the number of recr_dist_timing parameters " << endl;
N_settle_timings = 0;
settle_timings_tempvec.initialize();
if (N_settle_assignments == 0)
{
N_settle_timings = 1;
settle_timings_tempvec(1, 1) = 1.0;
settle_timings_tempvec(1, 2) = 0;
}
else
{
for (settle = 1; settle <= N_settle_assignments; settle++)
{
real_month = settlement_pattern_rd(settle, 2);
int settle_age_here = settlement_pattern_rd(settle, 4);
if (N_settle_timings == 0)
{
N_settle_timings++;
settle_timings_tempvec(N_settle_timings, 1) = real_month;
settle_timings_tempvec(N_settle_timings, 2) = settle_age_here;
settle_assignments_timing(settle) = N_settle_timings;
}
else
{
k = 0;
for (j = 1; j <= N_settle_timings; j++)
{
if (settle_timings_tempvec(j, 1) == real_month && settle_timings_tempvec(j, 2) == settle_age_here) // found matching settle_time
{
settle_assignments_timing(settle) = j;
k = 1;
}
}
if (k == 0)
{
N_settle_timings++;
settle_timings_tempvec(N_settle_timings, 1) = real_month;
settle_timings_tempvec(N_settle_timings, 2) = settle_age_here;
settle_assignments_timing(settle) = N_settle_timings;
}
}
}
}
echoinput << "N settle timings: " << N_settle_timings << endl
<< " unique_settle_times: " << endl
<< settle_timings_tempvec << endl;
echoinput << "settle events use these settle_times: " << settle_assignments_timing << endl;
if (recr_dist_method == 2)
{
echoinput << " Need to read N_GP * Narea * N_settletimings=" << N_GP * pop * N_settle_timings << " recruitment distribution parameters " << endl;
}
else if (recr_dist_method == 3)
{
echoinput << " Need to read N_settle_assignments=" << N_settle_assignments << " recruitment distribution parameters " << endl;
}
// SS_Label_Info_4.2.3 #Set-up arrays and indexing for growth patterns, gender, settlements, platoons
// clang-format off
END_CALCS
int g3i;
// SPAWN-RECR: define settlement timings
ivector Settle_seas(1,N_settle_timings) // calculated season in which settlement occurs
ivector Settle_seas_offset(1,N_settle_timings) // calculated number of seasons between spawning and the season in which settlement occurs
vector Settle_timing_seas(1,N_settle_timings) // calculated elapsed time (frac of year) between settlement and the begin of season in which it occurs
vector Settle_month(1,N_settle_timings) // month (real)in which settlement occurs
ivector Settle_age(1,N_settle_timings) // calculated age at which settlement occurs, with age 0 being the year in which spawning occurs
3iarray recr_dist_pattern(1,N_GP,1,N_settle_timings,0,pop); // has flag to indicate each settlement events
LOCAL_CALCS
// clang-format on
Settle_seas_offset.initialize();
Settle_timing_seas.initialize();
Settle_age.initialize();
Settle_seas.initialize();
recr_dist_pattern.initialize();
echoinput << "Calculated assignments in which settlement occurs " << endl
<< "Settle_event / Month / Seas / Seas_from_spawn / time_from_seas_start / age_at_settle" << endl;
if (N_settle_assignments > 0)
{
for (settle = 1; settle <= N_settle_assignments; settle++)
{
gp = settlement_pattern_rd(settle, 1); // growth patterns
p = settlement_pattern_rd(settle, 3); // settlement area
settle_time = settle_assignments_timing(settle);
Settle_age(settle_time) = settlement_pattern_rd(settle, 4); // settlement age as read
recr_dist_pattern(gp, settle_time, p) = 1; // indicates that settlement will occur here
recr_dist_pattern(gp, settle_time, 0) = 1; // for growth updating
Settle_month(settle_time) = settle_timings_tempvec(settle_time, 1);
}
for (settle_time = 1; settle_time <= N_settle_timings; settle_time++)
{
j = 0; // temp value for calculated settlement age
if (spawn_month > Settle_month(settle_time))
{
k = 1;
j++; // so sets season 1 as earliest possible settlement at age 1
}
else
{
k = spawn_seas; // earliest possible season for settlement at age 0
}
temp = azero_seas(k); // annual elapsed time fraction at begin of this season
Settle_timing_seas(settle_time) = (Settle_month(settle_time) - 1.0) / sumseas; // fraction of year at settlement month
while ((temp + seasdur(k)) <= Settle_timing_seas(settle_time))
{
temp += seasdur(k);
if (k == nseas)
{
k = 1;
j++;
}
else
{
k++;
}
}
if (j != Settle_age(settle_time))
{
warnstream << "settle_month is less than spawn_month, so logical age at settlement calculated to be: " << j
<< " for settle_time " << settle_time << ". Does not match read value of " << Settle_age(settle_time) << " are you sure? ";
write_message (NOTE, 0);
}
Settle_seas(settle_time) = k;
Settle_seas_offset(settle_time) = Settle_seas(settle_time) - spawn_seas + j * nseas; // number of seasons between spawning and the season in which settlement occurs
Settle_timing_seas(settle_time) -= temp; // timing from beginning of this season; needed for mortality calculation
echoinput << settle_time << " / " << Settle_month(settle_time);
echoinput << " / " << Settle_seas(settle_time) << " / " << Settle_seas_offset(settle_time) << " / "
<< Settle_timing_seas(settle_time) << " / " << Settle_age(settle_time) << endl;
if (Settle_seas_offset(settle_time) == 0 && spawn_time_seas > 0.0)
{
warnstream << "Cannot have spawn_time_seas after beginning of a season and settlements in the same season" << endl
<< "++ put spawning at beginning of the season, or move settlements to next season";
write_message (FATAL, 0); // EXIT!
}
}
}
else
{
recr_dist_pattern(1, 1, 1) = 1;
recr_dist_pattern(1, 1, 0) = 1;
Settle_month(1) = 1.;
Settle_timing_seas(1) = 0.0;
Settle_seas(1) = 1;
Settle_seas_offset(1) = 0;
Settle_age(1) = 0;
}
gmorph = gender * N_GP * N_settle_timings * N_platoon; // total potential number of biological entities, some may not get used so see use_morph(g)
// clang-format off
END_CALCS
!!// SS_Label_Info_4.2.1.1 #Define indexing vectors to keep track of characteristics of each morph
ivector sx(1,gmorph) // define sex for each growth morph
ivector GP4(1,gmorph) // index to GPat
ivector GP(1,gmorph) // index for gender*GPat; note that gp is nested inside gender
ivector GP3(1,gmorph) // index for main gender*GPat*settlement
ivector GP2(1,gmorph) // reverse pointer for platoon
imatrix g_finder(1,N_GP,1,gender) // reverse pointer to middle "g" for each main morph (used only with Growth_Std
ivector g_Start(1,N_GP*gender) // base "g" for this growth pattern
ivector Bseas(1,gmorph) // birth season
// following two containers are used to track which morphs are being used
ivector use_morph(1,gmorph)
imatrix TG_use_morph(1,N_TG2,1,gmorph)
imatrix ALK_range_g_lo(1,N_subseas*nseas*gmorph,0,nages)
imatrix ALK_range_g_hi(1,N_subseas*nseas*gmorph,0,nages)
vector azero_G(1,gmorph); // time since Jan 1 at beginning of settlement in which "g" was born
3darray real_age(1,gmorph,1,nseas*N_subseas,0,nages); // real age since settlement
3darray keep_age(1,gmorph,1,nseas*N_subseas,0,nages); // set to 0.0 if real_age<0. this allows omitting virtual young fish to be excluded from expected values
3darray calen_age(1,gmorph,1,nseas*N_subseas,0,nages); // real age since Jan 1 of spawn year
3darray lin_grow(1,gmorph,1,nseas*N_subseas,0,nages) // during linear phase has fraction of Size at Afix
ivector settle_g(1,gmorph) // settlement pattern for each platoon
int ALK_count;
LOCAL_CALCS
// clang-format on
ALK_count = 0;
use_morph.initialize();
TG_use_morph.initialize();
keep_age.initialize();
keep_age = 1.0;
for (gp = 1; gp <= N_GP * gender; gp++)
{
g_Start(gp) = (gp - 1) * N_settle_timings * N_platoon + int(N_platoon / 2) + 1 - N_platoon; // find the mid-morph being processed
}
g = 0;
g3i = 0;
echoinput << endl
<< "MORPH_INDEXING" << endl;
echoinput << "g Sex GP Settlement Birth_Seas Platoon Platoon% Sex*GP Sex*GP*settle_time Used(0/1) SettleTime_frac_yr" << endl;
for (gg = 1; gg <= gender; gg++)
for (gp = 1; gp <= N_GP; gp++)
for (settle = 1; settle <= N_settle_timings; settle++)
{
g3i++;
{
for (gp2 = 1; gp2 <= N_platoon; gp2++)
{
g++;
GP3(g) = g3i; // track counter for main morphs (gender x pattern x settlement)
Bseas(g) = Settle_seas(settle);
sx(g) = gg;
GP(g) = gp + (gg - 1) * N_GP; // counter for pattern x gender so gp is nested inside gender
GP2(g) = gp2; // reverse pointer to platoon counter
GP4(g) = gp; // counter for growth pattern
settle_g(g) = settle; // to find the settlement timing for this platoon
azero_G(g) = (Settle_month(settle) - 1.0) / sumseas; // settlement month converted to fraction of year; could be > one year
for (p = 1; p <= pop; p++)
{
if (recr_dist_pattern(gp, settle, p) == 1)
{
use_morph(g) = 1;
}
}
if (use_morph(g) == 1)
{
if ((N_platoon == 1) || (N_platoon == 3 && gp2 == 2) || (N_platoon == 5 && gp2 == 3)) g_finder(gp, gg) = g; // finds g for a given GP and gender and last birstseason
}
echoinput << g << " " << sx(g) << " " << GP4(g) << " " << settle << " " << Bseas(g) << " "
<< GP2(g) << " " << 100. * platoon_distr(GP2(g)) << " " << GP(g) << " " << GP3(g) << " " << use_morph(g) << " " << azero_G(g) << endl;
}
}
}
echoinput << "calen_age is elapsed years since beginning of year in which spawning occurred" << endl;
echoinput << "real_age is elapsed years since settlement" << endl;
echoinput << "g s subseas ALK_idx settle_time age@settle age real_age calen_age" << endl;
calen_age.initialize();
real_age.initialize();
keep_age.initialize();
for (g = 1; g <= gmorph; g++)
if (use_morph(g) == 1)
for (s = 1; s <= nseas; s++)
for (subseas = 1; subseas <= N_subseas; subseas++)
{
ALK_idx = (s - 1) * N_subseas + subseas;
settle_time = settle_g(g);
// real_age is real age since settlement and is used in growth calculations
// calen_age is real age since the beginning of the year in which spawning occurred
for (a = 0; a <= nages; a++)
{
calen_age(g, ALK_idx, a) = r_ages(a) + azero_seas(s) + double(subseas - 1) / double(N_subseas) * seasdur(s);
if (a < Settle_age(settle_time))
{
real_age(g, ALK_idx, a) = 0.;
keep_age(g, ALK_idx, a) = 0.;
}
else if (a == Settle_age(settle_time))
{
if (calen_age(g, ALK_idx, a) >= (azero_G(g) + Settle_age(settle_time)))
{
real_age(g, ALK_idx, a) = calen_age(g, ALK_idx, a) - azero_G(g) - Settle_age(settle_time);
keep_age(g, ALK_idx, a) = 1.;
}
else
{
real_age(g, ALK_idx, a) = 0.;
keep_age(g, ALK_idx, a) = 0.;
}
}
else
{
real_age(g, ALK_idx, a) = calen_age(g, ALK_idx, a) - azero_G(g) - Settle_age(settle_time);
keep_age(g, ALK_idx, a) = 1.;
}
if (a < 4) echoinput << g << " " << s << " " << subseas << " " << ALK_idx << " " << settle_time << " " << Settle_age(settle_time)
<< " " << a << " " << real_age(g, ALK_idx, a) << " " << calen_age(g, ALK_idx, a) << endl;
}
}
if (N_TG > 0)
{
for (TG = 1; TG <= N_TG; TG++)
{
for (g = 1; g <= gmorph; g++)
{
if (TG_release(TG, 6) > 2)
{
warnstream << "Gender for tag groups must be 0, 1 or 2 ";
write_message (WARN, 0);
}
if (use_morph(g) > 0 && (TG_release(TG, 6) == 0 || TG_release(TG, 6) == sx(g))) TG_use_morph(TG, g) = 1;
}
}
}
// clang-format off
END_CALCS
!!// SS_Label_Info_4.3 #Define movement between areas
int do_migration // number of explicit movements to define
number migr_firstage
matrix migr_start(1,nseas,1,N_GP)
LOCAL_CALCS
// clang-format on
migr_firstage = 0.0;
do_migration = 0;
if (pop > 1)
{
*(ad_comm::global_datafile) >> do_migration;
echoinput << do_migration << " N_migration definitions to read" << endl;
if (do_migration > 0)
{
*(ad_comm::global_datafile) >> migr_firstage;
echoinput << migr_firstage << " migr_firstage" << endl;
}
}
else
{
echoinput << " only 1 area, so no read of do_migration or migr_firstage " << endl;
}
// clang-format off
END_CALCS
init_matrix move_def(1,do_migration,1,6) // seas morph source dest minage maxage
// ivector GP3(1,gmorph) // index for main gender*GPat*settlement in that order
// plan to revise such that movement is by GP3, not GP
4iarray move_pattern(1,nseas,1,N_GP,1,pop,1,pop)
int do_migr2
ivector firstBseas(1,N_GP)
LOCAL_CALCS
// clang-format on
move_pattern.initialize();
do_migr2 = 0;
if (do_migration > 0)
{
echoinput << " migration setup " << endl
<< move_def << endl;
for (k = 1; k <= do_migration; k++)
{
s = move_def(k, 1);
gp = move_def(k, 2);
p = move_def(k, 3);
p2 = move_def(k, 4);
move_pattern(s, gp, p, p2) = k; // save index for definition of this pattern to find the right parameters
}
k = do_migration;
for (s = 1; s <= nseas; s++)
for (gp = 1; gp <= N_GP; gp++)
for (p = 1; p <= pop; p++)
{
if (move_pattern(s, gp, p, p) == 0) {
k++;
move_pattern(s, gp, p, p) = k;
} // no explicit migration for staying in this area, so create implicit
}
do_migr2 = k; // number of explicit plus implicit movement rates
migr_start.initialize();
// need to modify so it only does the calc for the first settlement used for each GP???
for (gp = 1; gp <= N_GP; gp++)
{
// use firstBseas so that the start age of migration is calculated only for the first birthseason used for each GP
firstBseas(gp) = 0;
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
if (GP4(g) == gp && firstBseas(gp) == 0) firstBseas(gp) = Bseas(g);
}
}
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0 && firstBseas(GP4(g)) == Bseas(g))
{
for (s = 1; s <= nseas; s++)
for (subseas = 1; subseas <= N_subseas; subseas++)
{
a = 0;
ALK_idx = (s - 1) * N_subseas + subseas;
while (real_age(g, ALK_idx, a) < migr_firstage) {
a++;
}
migr_start(s, GP4(g)) = a;
}
}
}
// clang-format off
END_CALCS
matrix move_def2(1,do_migr2,1,6) // movement definitions. First Do_Migration of these are explicit; rest are implicit
LOCAL_CALCS
// clang-format on
if (do_migration > 0)
{
for (k = 1; k <= do_migration; k++) {
move_def2(k) = move_def(k);
}
k = do_migration;
for (s = 1; s <= nseas; s++)
for (gp = 1; gp <= N_GP; gp++)
for (p = 1; p <= pop; p++)
{
if (move_pattern(s, gp, p, p) > do_migration)
{
k++;
move_def2(k, 1) = s;
move_def2(k, 2) = gp;
move_def2(k, 3) = p;
move_def2(k, 4) = p;
move_def2(k, 5) = 0;
move_def2(k, 6) = nages;
}
}
echoinput << "move_def " << endl
<< move_def2 << endl;
}
// clang-format off
END_CALCS
!!// SS_Label_Info_4.4 #Define the time blocks for time-varying parameters
int N_Block_Designs // read N block designs
ivector Nblk(1,1)
imatrix Block_Design(1,1,1,1)
LOCAL_CALCS
// clang-format on
* (ad_comm::global_datafile) >>
N_Block_Designs;
echoinput << N_Block_Designs << " N_Block_Designs" << endl;
if (N_Block_Designs > 0)
{
Nblk.deallocate();
Nblk.allocate(1, N_Block_Designs);
*(ad_comm::global_datafile) >> Nblk(1, N_Block_Designs);
echoinput << Nblk << " N_Blocks_per design" << endl;
ivector Nblk2; // temporary vector to create ragged array of dimensions for block matrix
Nblk2.allocate(1, N_Block_Designs);
Nblk2 = Nblk + Nblk;
Block_Design.deallocate();
Block_Design.allocate(1, N_Block_Designs, 1, Nblk2);
bool endyrChk = false;
for (j = 1; j <= N_Block_Designs; j++)
{
*(ad_comm::global_datafile) >> Block_Design(j)(1, Nblk2(j));
a = -1;
for (k = 1; k <= Nblk(j); k++)
{
a += 2;
b = a + 1;
if (Block_Design(j, b) == -1)
{
Block_Design(j, b) = endyr;
}
else if (Block_Design(j, b) == -2)
{
Block_Design(j, b) = YrMax;
}
// check block year values
if (Block_Design(j, b) > YrMax)
{
if (Block_Design(j, b) < 999) // manual suggests use of 9999, so 999 is safe choice here
{
warnstream << "Block_design:" << j << ", block: " << k << ", ends in: " << Block_Design(j, a + 1) << " reset to YrMax: " << YrMax;
write_message (ADJUST, 0);
}
Block_Design(j, b) = YrMax;
}
if (Block_Design(j, a) < styr - 1)
{
warnstream << "Block:" << j << " " << k << " starts before styr; resetting";
write_message (ADJUST, 0);
Block_Design(j, a) = styr;
}
if (Block_Design(j, b) < Block_Design(j, a))
{
warnstream << "Block:" << j << " " << k << " ends before it starts; fatal error";
write_message (FATAL, 0); // EXIT!
}
if (Block_Design(j, b) < styr - 1)
{
warnstream << "Block:" << j << " " << k << " ends before styr; fatal error";
write_message (FATAL, 1); // EXIT!
}
if (Block_Design(j, a) > retro_yr + 1)
{
warnstream << "Block:" << j << " " << k << " starts after retroyr+1; should not estimate ";
write_message (WARN, 0);
}
if (Block_Design(j, b) > retro_yr + 1)
{
warnstream << "Block:" << j << " " << k << " ends in: " << Block_Design(j, a + 1) << " after retroyr+1: " << retro_yr + 1;
write_message (WARN, 0);
}
if (Block_Design(j, a) > YrMax)
{
warnstream << "Block:" << j << " " << k << " starts in: " << Block_Design(j, a + 1) << " which is > YrMax: " << YrMax << " fatal error";
write_message (FATAL, 0); // EXIT!
}
if (Block_Design(j, b) == endyr)
{
endyrChk = true;
}
}
echoinput << " block design #: " << j << " read year pairs: " << Block_Design(j) << endl;
}
if (endyrChk == true)
{
warnstream << "At least one block pattern ends in endyr. Check the output parameter value time series to see if the values in forecast years are as intended.";
write_message (WARN, 0);
}
}
else
{
Nblk.allocate(1, 1);
Block_Design.allocate(1, 1, 1, 1);
}
// clang-format off
END_CALCS
init_int parm_adjust_method
!! echoinput<<parm_adjust_method<<" timevarying parameter constraint method"<<endl;
init_ivector autogen_timevary(1,5); // 0 means to autogenerate time-vary parameters; 1 means to read; (2) read then autogen if parm min==-12345
// first element for biology, 2nd for SRR; 3rd for Q; 4th for tag; 5th for selex
!! echoinput<<autogen_timevary<<" timevarying parameter autogenerate (0) or read (1) for each parm type or (2) read then autogen if parm min==-12345"<<endl;
ivector varparm_estimated(1,5) // flag to show what types of variance parameters are estimated
// (1) for growth
// (2) for recruitment sigmaR
// (3) for survey extraSD
!! varparm_estimated.initialize();
!!// SS_Label_Info_4.5 #Read setup and parameters for natmort, growth, biology, recruitment distribution, and migration
// read setup for natmort parameters: LO, HI, INIT, PRIOR, PR_type, CV, PHASE, use_env, use_dev, dev_minyr, dev_maxyr, dev_phase, Block, Block_type
int N_MGparm
int N_natMparms
int N_predparms
ivector predparm_pointer(1,Nfleet+1)
int N_growparms
int N_M_Grow_parms
int recr_dist_parms
int natM_type
int natM_5_opt // option selection for Maunder approach
imatrix MGparm_point(1,gender,1,N_GP)
vector NatM_break(1,1);
matrix Age_NatMort(1,1,1,1);
number natM_amin;
number natM_amax;
number fracfemale;
!!fracfemale=1.00;
number fracfemale_mult;
!!fracfemale_mult=1.0; // multiplier used in female SSB calc; gets changed to femfrac(1) if gender_rd==-1
// read natmort setup
LOCAL_CALCS
// clang-format on
N_natMparms = 0;
N_predparms = N_pred;
if (nseas > 1) N_predparms += N_pred * nseas;
natM_5_opt = 0;
MGparm_point.initialize();
// 0=1Parm; 1=segmented; 2=Lorenzen; 3=agespecific; 4=agespec with seas interpolate; 5=Maunder_M; 6=Lorenzen range
*(ad_comm::global_datafile) >> natM_type;
echoinput << natM_type << " natM_type" << endl;
switch (natM_type)
{
case 0:
{
N_natMparms = 1;
break;
}
case 1:
{
*(ad_comm::global_datafile) >> N_natMparms;
echoinput << N_natMparms << " N breakpoints " << endl;
NatM_break.deallocate();
NatM_break.allocate(1, N_natMparms);
*(ad_comm::global_datafile) >> NatM_break(1, N_natMparms);
echoinput << NatM_break << " NatM_age_segment_breaks " << endl;
break;
}
case 2:
{
N_natMparms = 1;
*(ad_comm::global_datafile) >> natM_amin;
echoinput << natM_amin << " natM_A for Lorenzen" << endl;
break;
}
case 3:
{
// same as 4
}
case 4:
{
N_natMparms = 0;
Age_NatMort.deallocate();
Age_NatMort.allocate(1, N_GP * gender, 0, nages);
for (gp = 1; gp <= N_GP * gender; gp++)
{
*(ad_comm::global_datafile) >> Age_NatMort(gp)(0, nages);
}
echoinput << " Age_NatMort empirical input: " << endl
<< Age_NatMort << endl;
break;
}
case 5:
{
// Maunder et al. age and sex specific M
// A) read in an integer for the method to do maturity Maunder_MatType = 1,2,3
*(ad_comm::global_datafile) >> natM_5_opt;
echoinput << " Maunder_NatMort option: " << natM_5_opt << endl;
N_natMparms = 4;
if (natM_5_opt == 3) N_natMparms = 6;
// Maunder_Mjuv = natMparms(1,gp);
// Maunder_lambda = natMparms(2,gp);
// Maunder_lmat = natMparms(3,gp);
// Maunder_Mmat = natMparms(4,gp);
// if(natM_5_opt==3){ //use two parameters mat50% and mat_slope.
// Maunder_L50 = natMparms(5,gp);
// Maunder_beta = natMparms(6,gp);
break;
}
case 6:
{
N_natMparms = 1;
*(ad_comm::global_datafile) >> natM_amin;
echoinput << natM_amin << " natM_minage for Lorenzen" << endl;
*(ad_comm::global_datafile) >> natM_amax;
echoinput << natM_amax << " natM_maxage for Lorenzen" << endl;
break;
}
}
// clang-format off
END_CALCS
// read growth setup
init_int Grow_type // 1=vonbert; 2=Richards; 3=age-specific K ascend; 4=age-specific K descend; 5=age-specific K; 6=read vector(not implemented); 8=growth cessation
!!echoinput<<Grow_type<<" growth model "<<endl;
!!// SS_Label_Info_4.5.1 #Create time constants for growth
number AFIX;
number AFIX2;
number AFIX2_forCV;
number AFIX_delta;
number AFIX_plus;
number Linf_decay; // decay factor to calculate mean L at maxage from Linf and the decaying abundance above maxage
// forced equal to 0.20 in 3.24 (which also assumed linear, not VBK, growth)
int do_ageK;
ivector first_grow_age(1,gmorph);
!! first_grow_age.initialize();
!! k=0;
!! do_ageK=0;
!! if(Grow_type<=2 || Grow_type==8) {k=4;} // AFIX and AFIX2
!! if (Grow_type>=3 && Grow_type<=5) {do_ageK=1; k=5;} // number of ages for age-specific K
init_vector tempvec5(1,k)
int Age_K_count;
LOCAL_CALCS
// clang-format on
Age_K_count = 0;
if (k > 0) echoinput << tempvec5 << " # growth specifications: AFIX1 AFIX2 LINF_decay placeholder age-specific_K_ages" << endl;
k1 = 0;
AFIX = 0.;
AFIX2 = 999.; // this value invokes setting Linf equal to the L2 parameter
Linf_decay = 0.0; // initialize
if (Grow_type == 1)
{
N_growparms = 5;
AFIX = tempvec5(1);
AFIX2 = tempvec5(2);
Linf_decay = tempvec5(3);
// tempvec(4) is a placeholder
}
else if (Grow_type == 2 || Grow_type == 8)
{
N_growparms = 6;
AFIX = tempvec5(1);
AFIX2 = tempvec5(2);
Linf_decay = tempvec5(3);
if (Grow_type == 8 && AFIX2 != 999)
{
warnstream << "AFIX2 set to 999 for grow_type==8 because only Linfinity allowed for growth cessation ";
write_message (ADJUST, 0);
AFIX2 = 999.;
}
if (Grow_type == 8 && AFIX != 0.0)
{
warnstream << "AFIX set to 0.0 for grow_type==8; growth cessation ";
write_message (ADJUST, 0);
AFIX2 = 0.0;
}
// tempvec(4) is a placeholder
}
else if (do_ageK == 1)
{
AFIX = tempvec5(1);
AFIX2 = tempvec5(2);
Linf_decay = tempvec5(3);
// tempvec(4) is a placeholder
Age_K_count = tempvec5(5);
echoinput << " read this number of ages for age-specific K " << Age_K_count << endl;
N_growparms = 5 + Age_K_count;
}
else if (Grow_type == 6) // not implemented
{
N_growparms = 2; // for the two CV parameters
k1 = N_GP * gender; // for reading empirical length_at_age
}
echoinput << " N_growparms " << N_growparms << endl;
AFIX2_forCV = AFIX2;
if (AFIX2_forCV > nages) AFIX2_forCV = nages;
AFIX_delta = AFIX2 - AFIX;
if (AFIX != 0.0)
{
AFIX_plus = AFIX;
}
else
{
AFIX_plus = 1.0e-06;
}
N_M_Grow_parms = N_natMparms + N_growparms;
lin_grow.initialize();
echoinput << "g a seas subseas ALK_idx real_age calen_age lin_grow first_grow_age" << endl;
for (g = 1; g <= gmorph; g++)
if (use_morph(g) > 0)
{
for (a = 0; a <= nages; a++)
{
for (s = 1; s <= nseas; s++)
for (subseas = 1; subseas <= N_subseas; subseas++)
{
ALK_idx = (s - 1) * N_subseas + subseas;
// if(a==0 && s<Bseas(g))
// {lin_grow(g,ALK_idx,a)=0.0;} // so fish are not yet born so will get zero length
if (real_age(g, ALK_idx, a) < AFIX)
{
lin_grow(g, ALK_idx, a) = real_age(g, ALK_idx, a) / AFIX_plus;
} // on linear portion of the growth
else if (real_age(g, ALK_idx, a) == AFIX)
{
lin_grow(g, ALK_idx, a) = 1.0; // at the transition from linear to VBK growth
}
else if (first_grow_age(g) == 0)
{
lin_grow(g, ALK_idx, a) = -1.0; // flag for first age on growth curve beyond AFIX
if (subseas == N_subseas) {
first_grow_age(g) = a;
} // so that lingrow will be -1 for rest of this season
}
else
{
lin_grow(g, ALK_idx, a) = -2.0;
} // flag for being in growth curve
if (a < 4) echoinput << g << " " << a << " " << s << " " << subseas << " " << ALK_idx << " " << real_age(g, ALK_idx, a)