diff --git a/assessments/nrs/2018/fm.cpp b/assessments/nrs/2018/fm.cpp index 074a60b..1a89156 100644 --- a/assessments/nrs/2018/fm.cpp +++ b/assessments/nrs/2018/fm.cpp @@ -4,116 +4,152 @@ #include #endif #endif - # include "admodel.h" // Include AD class definitions - // logs input for checking - /** - \def log_input(object) - Prints name and value of \a object on ADMB report %ofstream file. - */ - #undef log_input - #define log_input(object) writeinput << "# " #object "\n" << object << endl; - // Shorter way to write to R_report - /** - \def REPORT(object) - Prints name and value of \a object on ADMB report %ofstream file. - */ - #undef REPORT - #define REPORT(object) R_report << "$" #object "\n" << object << endl; - #undef WriteData - #define WriteData(object) SimDat << "#" #object "\n" << object << endl; - ofstream writeinput("writeinput.log"); - ofstream R_report("fm_R.rep"); - ofstream report_sex_ratio("sex_ratio.rep"); - ofstream SimDat("sim.dat"); - adstring model_name; - adstring datafile; - adstring projfile_name; - adstring cntrlfile_name; - adstring tmpstring; - adstring repstring; - ofstream evalout("evalout.rep"); - ofstream srecpar("srecpar.rep"); // To write srec-parameters for projection model - // ofstream ssb_retro("ssb_retro.rep",ios::app); // To write srec-parameters for projection model - + // Include AD class definitions + #include + // logs input for checking + /** + \def log_input(object) + Prints name and value of \a object on ADMB report %ofstream file. + */ + #undef log_input + #define log_input(object) writeinput << "# " #object "\n" << object << endl; + // Shorter way to write to R_report + /** + \def REPORT(object) + Prints name and value of \a object on ADMB report %ofstream file. + */ + #undef REPORT + #define REPORT(object) R_report << #object "\n" << object << endl; + #undef WriteData + #define WriteData(object) SimDat << "#" #object "\n" << object << endl; + ofstream writeinput("writeinput.log"); + ofstream R_report("fm.rep"); + ofstream L_report("fm_legacy.rep"); + ofstream report_sex_ratio("sex_ratio.rep"); + ofstream SimDat("sim.dat"); + adstring model_name; + adstring datafile; + adstring projfile_name; + adstring cntrlfile_name; + adstring tmpstring; + adstring repstring; + ofstream evalout("evalout.rep"); + ofstream srecpar("srecpar.rep"); // To write srec-parameters for projection model + // ofstream ssb_retro("ssb_retro.rep",ios::app); // To write srec-parameters for projection model + +#ifdef DEBUG + #include +#endif #include +#ifdef USE_ADMB_CONTRIBS #include +#include +#endif extern "C" { void ad_boundf(int i); } -#include - #include model_data::model_data(int argc,char * argv[]) : ad_comm(argc,argv) { - oper_mod = 0; - mcmcmode = 0; - mcflag = 1; + adstring tmpstring; tmpstring=adprogram_name + adstring(".dat"); if (argc > 1) { int on=0; if ( (on=option_match(argc,argv,"-ind"))>-1) { - if (on>argc-2 | argv[on+1][0] == '-') - { + if (on>argc-2 || argv[on+1][0] == '-') + { cerr << "Invalid input data command line option" - " -- ignored" << endl; + " -- ignored" << endl; } else { - cntrlfile_name = adstring(argv[on+1]); + tmpstring = adstring(argv[on+1]); } } - if ( (on=option_match(argc,argv,"-om"))>-1) - { - oper_mod = 1; - cout<<"Got to operating model option "<-1) - { - mcmcmode = 1; - } } - global_datafile= new cifstream(cntrlfile_name); + global_datafile = new cifstream(tmpstring); if (!global_datafile) { + cerr << "Error: Unable to allocate global_datafile in model_data constructor."; + ad_exit(1); } - else + if (!(*global_datafile)) { - if (!(*global_datafile)) - { - delete global_datafile; - global_datafile=NULL; - } + delete global_datafile; + global_datafile=NULL; } -ad_comm::change_datafile_name("mod.ctl"); // GRID *(ad_comm::global_datafile) >> model_name; *(ad_comm::global_datafile) >> datafile; + oper_mod = 0; + mcmcmode = 0; + mcflag = 1; + tmpstring=adprogram_name + adstring(".dat"); + if (argc > 1) + { + int on=0; + if ( (on=option_match(argc,argv,"-ind"))>-1) + { + if (on>argc-2 | argv[on+1][0] == '-') + { + cerr << "Invalid input data command line option" + " -- ignored" << endl; + } + else + { + cntrlfile_name = adstring(argv[on+1]); + } + } + if ( (on=option_match(argc,argv,"-om"))>-1) + { + oper_mod = 1; + cout<<"Got to operating model option "<-1) + { + mcmcmode = 1; + } + } + global_datafile= new cifstream(cntrlfile_name); + if (!global_datafile) + { + } + else + { + if (!(*global_datafile)) + { + delete global_datafile; + global_datafile=NULL; + } + } + cout<0&&init_age_comp > 0) - { - styr_rec = styr ; // Change in two places (see below) - phase_init_age_comp = 2; - } - else - { - styr_rec = styr - nages+1; // Extend recruitment devs back in time to estimate init_age from rec_dev - phase_init_age_comp = -2; // Don't estimate initial age comp parameters - } + rec_lag=1; //Lag between year-class and recruitment + if (phase_init_age_comp>0&&init_age_comp > 0) + { + styr_rec = styr ; // Change in two places (see below) + phase_init_age_comp = 2; + } + else + { + styr_rec = styr - nages+1; // Extend recruitment devs back in time to estimate init_age from rec_dev + phase_init_age_comp = -2; // Don't estimate initial age comp parameters + } spawnmo.allocate("spawnmo"); spmo_frac =(spawnmo-1)/12.; log_input(spawnmo); @@ -321,85 +365,157 @@ log_input(srv_mo); log_input(n_wts); growth_cov.allocate(styr,endyr,"growth_cov"); log_input(growth_cov); + Check.allocate("Check"); + log_input(Check); + cout << Check << endl; + if (Check != 123456) { cout << "Invalid data file " << Check << endl; exit(1); } num_proj_Fs = 5; offset_srv.allocate(1,nsrv); offset_fsh.allocate(1,nfsh); - offset_fsh.initialize(); - offset_srv.initialize(); - for (int k=1;k<=nfsh;k++) - { - for (i=1;i<=nyrs_fsh_age_c(k);i++) - { - oac_fsh_c(k,i) /= sum(oac_fsh_c(k,i)); - offset_fsh(k) -= nsmpl_fsh_c(k,i)*(oac_fsh_c(k,i) + 0.001) * log(oac_fsh_c(k,i) + 0.001); - } - for (i=1;i<=nyrs_fsh_age_s(k);i++) - { - oac_fsh_s(k,i) /= sum(oac_fsh_s(k,i)); - offset_fsh(k) -= nsmpl_fsh_s(k,i)*(oac_fsh_s(k,i) + 0.001) * log(oac_fsh_s(k,i) + 0.001); - } - } - for (int k=1;k<=nsrv;k++) - { - for (i=1;i<=nyrs_srv_age_c(k);i++) - { - oac_srv_c(k,i) /= sum(oac_srv_c(k,i)); - offset_srv(k)-= nsmpl_srv_c(k,i)*(oac_srv_c(k,i) + 0.001) * log(oac_srv_c(k,i) + 0.001); - } - for (int i=1;i<=nyrs_srv_age_s(k);i++) - { - oac_srv_s(k,i) /= sum(oac_srv_s(k,i)); - offset_srv(k)-= nsmpl_srv_s(k,i)*(oac_srv_s(k,i) + 0.001) * log(oac_srv_s(k,i) + 0.001); - } + offset_fsh.initialize(); + offset_srv.initialize(); + double btmp=0.; + double ctmp=0.; + dvector ntmp(1,nages); + ntmp(1) = 1.; + for (int a=2;a<=nages;a++) + ntmp(a) = ntmp(a-1)*exp(-m_exp-.05); + btmp = wt_pop_f_in(endyr)(1,nages) * ntmp; + ctmp = mean(obs_catch); + log_input( ctmp ); + R_guess = log((ctmp/.02 )/btmp) ; + log_input( R_guess ); + // Now that everything is read in, can change the "endyr" to reflect retrospective year + endyr = endyr - n_retro; + // Lag between weights and years + if (endyr <= endyr_wt) endyr_wt = endyr - (endyr_in-endyr_wt ); + if (endyr <= endyr_wt) endyr_wt = endyr - (endyr_in-endyr_wt ); + endyr_sr = endyr - (endyr_in-endyr_sr ); + styr_fut=endyr+1; + endyr_fut=endyr+nyrs_fut; + //Modified retro..................................................................... + int nyrs_srv_tmp; + + for (int isrv=1;isrv<=nsrv;isrv++) + { + //survey biomass + for(int iyr=1; iyr<=nyrs_srv(isrv);iyr++) + { + if(yrs_srv(isrv,iyr)<=endyr) nyrs_srv_tmp=iyr; + if(surv_dwnwt==1 & yrs_srv(isrv,iyr)>= endyr) obs_lse_srv(isrv,iyr)=cv_inc; + } + nyrs_srv(isrv)=nyrs_srv_tmp; + //reset temporary variable + nyrs_srv_tmp=0; + for (int iyr=1;iyr<=nyrs_srv_age_c(isrv);iyr++) + { + if (yrs_srv_age_c(isrv,iyr)<= endyr) nyrs_srv_tmp=iyr; + if(surv_dwnwt==1 & yrs_srv_age_c(isrv,iyr)>= endyr) nsmpl_srv_c(isrv,iyr)=n_comp; + } + nyrs_srv_age_c(isrv)=nyrs_srv_tmp; + //reset temporary variable + nyrs_srv_tmp=0; + for (int iyr=1;iyr<=nyrs_srv_age_s(isrv);iyr++) + { + if (yrs_srv_age_s(isrv,iyr)<= endyr) nyrs_srv_tmp=iyr; + if(surv_dwnwt==1 & yrs_srv_age_s(isrv,iyr)>= endyr) nsmpl_srv_s(isrv,iyr)=n_comp; + } + nyrs_srv_age_s(isrv)=nyrs_srv_tmp; + } + + for (int ifsh=1;ifsh<=nfsh;ifsh++) + { + for (int iyr=1;iyr<=nyrs_fsh_age_s(ifsh);iyr++) + if (endyr <= yrs_fsh_age_s(ifsh,iyr)) + nyrs_fsh_age_s(ifsh) = min(nyrs_fsh_age_s(ifsh),iyr); + + for (int iyr=1;iyr<=nyrs_fsh_age_c(ifsh);iyr++) + if (endyr <= yrs_fsh_age_c(ifsh,iyr)) + nyrs_fsh_age_c(ifsh) = min(nyrs_fsh_age_c(ifsh),iyr); + } + + //retained from original + for (int k=1;k<=nfsh;k++) + { + for (i=1;i<=nyrs_fsh_age_c(k);i++) + { + oac_fsh_c(k,i) /= sum(oac_fsh_c(k,i)); + offset_fsh(k) -= nsmpl_fsh_c(k,i)*(oac_fsh_c(k,i) + 0.001) * log(oac_fsh_c(k,i) + 0.001); + } + for (i=1;i<=nyrs_fsh_age_s(k);i++) + { + + oac_fsh_s(k,i) /= sum(oac_fsh_s(k,i)); + offset_fsh(k) -= nsmpl_fsh_s(k,i)*(oac_fsh_s(k,i) + 0.001) * log(oac_fsh_s(k,i) + 0.001); + // cout<<"i="<0) - { - wt_fsh_fut_f= wt_fsh_mn_f; // initializes estimates to correct values... - wt_fsh_fut_m= wt_fsh_mn_m; // initializes estimates to correct values... - wt_pop_fut_f= wt_pop_mn_f; // initializes estimates to correct values... - wt_pop_fut_m= wt_pop_mn_m; // initializes estimates to correct values... - } - else - { - wt_fsh_fut_f = wt_fsh_f_in(1,endyr) ; // initializes estimates to correct values... - wt_fsh_fut_m = wt_fsh_m_in(1,endyr) ; - wt_pop_fut_f = wt_pop_f(endyr) ; // initializes estimates to correct values... - wt_pop_fut_m = wt_pop_m(endyr) ; // initializes estimates to correct values... - } - for (int j=1;j<=nages;j++) - { - wt_vbg_f(j) = value(a_lw_f * pow(Linf_f*(1.-exp(-K_f*(double(j)-t0_f))),b_lw_f)); - wt_vbg_m(j) = value(a_lw_m * pow(Linf_m*(1.-exp(-K_m*(double(j)-t0_m))),b_lw_m)); - } - base_incr_f(2,nages) = wt_vbg_f(2,nages) - ++wt_vbg_f(1,nages-1); - base_incr_m(2,nages) = wt_vbg_m(2,nages) - ++wt_vbg_m(1,nages-1); - // cout <0) + { + wt_fsh_fut_f= wt_fsh_mn_f; // initializes estimates to correct values... + wt_fsh_fut_m= wt_fsh_mn_m; // initializes estimates to correct values... + wt_pop_fut_f= wt_pop_mn_f; // initializes estimates to correct values... + wt_pop_fut_m= wt_pop_mn_m; // initializes estimates to correct values... + } + else + { + wt_fsh_fut_f = wt_fsh_f_in(1,endyr) ; // initializes estimates to correct values... + wt_fsh_fut_m = wt_fsh_m_in(1,endyr) ; + wt_pop_fut_f = wt_pop_f(endyr) ; // initializes estimates to correct values... + wt_pop_fut_m = wt_pop_m(endyr) ; // initializes estimates to correct values... + } + for (int j=1;j<=nages;j++) + { + wt_vbg_f(j) = value(a_lw_f * pow(Linf_f*(1.-exp(-K_f*(double(j)-t0_f))),b_lw_f)); + wt_vbg_m(j) = value(a_lw_m * pow(Linf_m*(1.-exp(-K_m*(double(j)-t0_m))),b_lw_m)); + } + base_incr_f(2,nages) = wt_vbg_f(2,nages) - ++wt_vbg_f(1,nages-1); + base_incr_m(2,nages) = wt_vbg_m(2,nages) - ++wt_vbg_m(1,nages-1); + // cout <1&&(current_phase()<=1)) - if (Growth_Option>1 && (last_phase()||current_phase()<=phase_wt)) - Get_wt_age(); - if(!do_wt_only) - { - get_selectivity(); - get_mortality(); - get_numbers_at_age(); - //if(active(R_logalpha)) - compute_sr_fit(); - if (sd_phase() || mceval_phase()) - { - get_msy(); - dvariable maxspawn=max(SSB)*1.2; - for (i=0;i<=30;i++) - { - SRR_SSB(i) = double(i+.001)*maxspawn/30; - rechat(i) = R_alpha*SRR_SSB(i)*(mfexp(-R_beta*SRR_SSB(i))); - } - Future_projections(); - for (i=styr;i<=endyr;i++) - pred_rec(i) = 2.*natage_f(i,1); - } - catch_at_age(); - } - evaluate_the_objective_function(); - // next part returns the Byesian posterior for the listed parameters - if (mceval_phase()) - { - // if (oper_mod) - // Oper_Model(); - // else - { - // compute_spr_rates(); - // write_mceval(); - } - // inf 0 0 0 inf 0.0814782 13.984 1.64572 8.52093 0 32.6187 30.3609 0 0.00937666 90.4879 586.823 539.73 0.846482 0.93861 0.861563 0.874594 0.822898 0.948608 0.870741 0.929537 0.887822 0.921366 0.841266 0.939439 0.807067 0.819997 0.964657 0.898865 0.970638 0.741473 0.857768 0.890177 0.962105 1.0011 0.968926 0.974933 0.821446 0.819997 0.781815 0.786663 0.783197 0.880017 0.762049 0.828732 0.960408 0.964657 1.10127 0.901082 0.108481 0.125338 0.123776 2632.62 2541.99 495.109 441.419 2316.82 2297.56 2273.5 2244.68 2231.11 2214.01 2063.31 1643.45 1145.61 793.073 833.721 829.768 875.837 862.19 791.983 824.822 792.25 838.237 904.882 1148.06 1380.96 1709.52 2009.46 2315.49 2608.21 2768.31 2952.35 3121.75 3236.7 3229.15 3448.95 3467.12 3193.03 3159.11 3057.89 3100.9 2971.87 3087 3290.59 3314.14 3346.24 3133.91 3044.85 3058.49 2791.15 2621.02 2668.73 2599.82 2643.57 2849.5 3060.22 3170.87 3163.42 3178.93 3055.94 2894.21 2962.15 2996.96 2993.04 2952.77 2742.2 2761.32 2915.27 2940.14 901.167 920.002 921.81 908.759 883.521 817.961 640.2 342.496 40.5581 8.5617 19.2127 39.7057 66.8238 90.8636 115.809 123.692 93.8937 67.3402 55.344 58.6771 65.6652 106.58 162.363 251.184 368.564 493.526 636.116 771.942 853.952 970.539 1064.57 1123.49 1117.1 1116.88 1059.53 1031.97 1044.92 1132.33 1219.69 1258.41 1264.11 1264.75 1197.41 1158.19 1088.47 1080.12 1068.13 1063.64 1063.77 1073.22 1106.35 1125.56 1150.04 1158.91 1135.78 1101.19 1079.63 1059.48 1045.84 1042.59 1005.04 1009.94 1029.02 1038.32 0.807464 0.0837012 0.188333 0.359539 0.565576 0.749304 0.873568 1.58871 5.05441 0.0245567 -0.00616844 - evalout <1&&(current_phase()<=1)) + if (Growth_Option>1 && (last_phase()||current_phase()<=phase_wt)) + Get_wt_age(); + if(!do_wt_only) + { + get_selectivity(); + get_mortality(); + get_numbers_at_age(); + //if(active(R_logalpha)) + compute_sr_fit(); + if (sd_phase() || mceval_phase()) + { + get_msy(); + dvariable maxspawn=max(SSB)*1.2; + for (i=0;i<=30;i++) + { + SRR_SSB(i) = double(i+.001)*maxspawn/30; + rechat(i) = R_alpha*SRR_SSB(i)*(mfexp(-R_beta*SRR_SSB(i))); + } + Future_projections(); + for (i=styr;i<=endyr;i++) + pred_rec(i) = 2.*natage_f(i,1); + } + catch_at_age(); + } + evaluate_the_objective_function(); + // next part returns the Byesian posterior for the listed parameters + if (mceval_phase()) + { + // if (oper_mod) + // Oper_Model(); + // else + { + // compute_spr_rates(); + // write_mceval(); + } + // inf 0 0 0 inf 0.0814782 13.984 1.64572 8.52093 0 32.6187 30.3609 0 0.00937666 90.4879 586.823 539.73 0.846482 0.93861 0.861563 0.874594 0.822898 0.948608 0.870741 0.929537 0.887822 0.921366 0.841266 0.939439 0.807067 0.819997 0.964657 0.898865 0.970638 0.741473 0.857768 0.890177 0.962105 1.0011 0.968926 0.974933 0.821446 0.819997 0.781815 0.786663 0.783197 0.880017 0.762049 0.828732 0.960408 0.964657 1.10127 0.901082 0.108481 0.125338 0.123776 2632.62 2541.99 495.109 441.419 2316.82 2297.56 2273.5 2244.68 2231.11 2214.01 2063.31 1643.45 1145.61 793.073 833.721 829.768 875.837 862.19 791.983 824.822 792.25 838.237 904.882 1148.06 1380.96 1709.52 2009.46 2315.49 2608.21 2768.31 2952.35 3121.75 3236.7 3229.15 3448.95 3467.12 3193.03 3159.11 3057.89 3100.9 2971.87 3087 3290.59 3314.14 3346.24 3133.91 3044.85 3058.49 2791.15 2621.02 2668.73 2599.82 2643.57 2849.5 3060.22 3170.87 3163.42 3178.93 3055.94 2894.21 2962.15 2996.96 2993.04 2952.77 2742.2 2761.32 2915.27 2940.14 901.167 920.002 921.81 908.759 883.521 817.961 640.2 342.496 40.5581 8.5617 19.2127 39.7057 66.8238 90.8636 115.809 123.692 93.8937 67.3402 55.344 58.6771 65.6652 106.58 162.363 251.184 368.564 493.526 636.116 771.942 853.952 970.539 1064.57 1123.49 1117.1 1116.88 1059.53 1031.97 1044.92 1132.33 1219.69 1258.41 1264.11 1264.75 1197.41 1158.19 1088.47 1080.12 1068.13 1063.64 1063.77 1073.22 1106.35 1125.56 1150.04 1158.91 1135.78 1101.19 1079.63 1059.48 1045.84 1042.59 1005.04 1009.94 1029.02 1038.32 0.807464 0.0837012 0.188333 0.359539 0.565576 0.749304 0.873568 1.58871 5.05441 0.0245567 -0.00616844 + evalout <phase_wt) - { - Age_Like(); - Srv_Like(); - if (phase_fmort>0) - { - catch_like = 0.; - for (int ifsh=1;ifsh<=nfsh;ifsh++) - catch_like += norm2(log(obs_catch(ifsh)(styr,endyr)+.000001)-log(pred_catch(ifsh)+.000001)); - obj_fun += lambda(3) * catch_like; - } - Fmort_Pen(); - obj_fun +=fpen; - } - if(active(wt_fsh_fut_f)) - { - wt_fut_like=0.; - for (int j=1;j<=nages;j++) - { - dvariable res = wt_fsh_mn_f(j)-wt_fsh_fut_f(j); - wt_fut_like += res*res / (2.*wt_fsh_sigma_f(j)*wt_fsh_sigma_f(j)); - res = wt_fsh_mn_m(j)-wt_fsh_fut_m(j); - wt_fut_like += res*res / (2.*wt_fsh_sigma_m(j)*wt_fsh_sigma_m(j)); - res = wt_pop_mn_f(j)-wt_pop_fut_f(j); - wt_fut_like += res*res / (2.*wt_pop_sigma_f(j)*wt_pop_sigma_f(j)); - res = wt_pop_mn_m(j)-wt_pop_fut_m(j); - wt_fut_like += res*res / (2.*wt_pop_sigma_m(j)*wt_pop_sigma_m(j)); - } - obj_fun += wt_fut_like; - } - if(active(log_msy_sel_f)) - { - wt_msy_like=0.; - // dvar_vector pf_tmp = log(F(1,endyr)/F(1,endyr,nages)); // NOTE: For one fishery only!!! - // obj_fun += 0.5*norm2(pf_tmp - log_sel_coff)/(pf_sigma*pf_sigma); - dvar_vector log_sel_mean(1,nages); - log_sel_mean = log_sel_fsh_f(1,endyr) ; - log_sel_mean += log_sel_fsh_f(1,endyr-1) ; - log_sel_mean += log_sel_fsh_f(1,endyr-2) ; - log_sel_mean /= 3. ; - wt_msy_like += 0.5*norm2(log_sel_mean - log_msy_sel_f)/(pf_sigma*pf_sigma); - log_sel_mean = log_sel_fsh_m(1,endyr) ; - log_sel_mean += log_sel_fsh_m(1,endyr-1) ; - log_sel_mean += log_sel_fsh_m(1,endyr-2) ; - log_sel_mean /= 3. ; - wt_msy_like += 0.5*norm2(log_sel_mean - log_msy_sel_m)/(pf_sigma*pf_sigma); - obj_fun += wt_msy_like; - } - // small penalty to initialize stock to have similar values (unless data suggest otherwise) - if(active(init_dev_m)) - { - init_like = norm2(init_dev_m-init_dev_f); - obj_fun += init_like; - } - } + if (active(F40)) + { + compute_spr_rates(); + dvar_vector incr_dev_tmp(2,nages); + // two degree increase in temperature + incr_dev_tmp(5,nages-5) = growth_alpha * 2.0 + age_incr; + incr_dev_tmp(nages-4,nages) = incr_dev_tmp(nages-5) ; + incr_dev_tmp(2,4) = incr_dev_tmp(5) ; + wt_pop_fut_f(1) = wt_vbg_f(1); + wt_pop_fut_m(1) = wt_vbg_m(1); + wt_pop_fut_f(2,nages) = ++wt_vbg_f(1,nages-1) + elem_prod(base_incr_f,mfexp(incr_dev_tmp)) ; // initializes estimates to correct values... + wt_pop_fut_m(2,nages) = ++wt_vbg_m(1,nages-1) + elem_prod(base_incr_m,mfexp(incr_dev_tmp)) ; // initializes estimates to correct values... + } + fpen.initialize(); + wt_like.initialize(); + q_prior.initialize(); + if(active(yr_incr)||active(age_incr)||active(growth_alpha)) + { + // cout <0) - { - R_report << "$yrs_fsh_age_c" <0) - { - R_report << "$yrs_fsh_age_s" <0) - { - R_report << "$yrs_srv_age_c" <0) - { - R_report << "$yrs_srv_age_s" <0) - { - report << "alpha= " << alpha << endl; - report << "beta= " << beta << endl; - report << endl<<"Environmental_effect_q " << endl; - for (i=1;i<=nyrs_srv(1);i++) - for (k=1;k<=n_env_cov(1);k++) - report <0) report << " survey_q= " << mean(exp(-alpha+q_beta*env_cov(1)))<0) + { + R_report << "yrs_fsh_age_c" <0) + { + R_report << "yrs_fsh_age_s" <0) + { + R_report << "yrs_srv_age_c" <0) + { + R_report << "yrs_srv_age_s" <0) + { + // L_report << "alpha= " << q_alpha << endl; + // L_report << "beta= " << q_beta << endl; + // L_report << endl<<"Environmental_effect_q " << endl; + // init_ivector n_env_cov(1,nsrv) + // !!log_input(n_env_cov); + // init_3darray env_cov(1,nsrv,1,n_env_cov,1,nyrs_srv) + // !! for (int j=1;j<=nsrv;j++) for (int k=1;k<=n_env_cov(j);k++) { env_cov(j,k) -= mean(env_cov(j,k)); } + // for (i=1;i<=nyrs_srv(1);i++) + // for (k=1;k<=n_env_cov(1);k++); + // L_report <0) L_report << " survey_q= " << mean(exp(-q_alpha+q_beta*env_cov(1)))< 1e-5) - { - icount++; - ftmp += (TACin-cc) / btmp; - Fatmp_f = ftmp * partial_F_f; - Z_tmp_f = Fatmp_f + natmort_f; - S_tmp_f = mfexp( -Z_tmp_f ); - Fatmp_m = ftmp * partial_F_m; - Z_tmp_m = Fatmp_m + natmort_m; - S_tmp_m = mfexp( -Z_tmp_m ); - cc = (wttmp_f * elem_prod(elem_div(Fatmp_f, Z_tmp_f),elem_prod(1.-S_tmp_f,N_tmp_f))); // Catch equation (vectors) - cc += (wttmp_m * elem_prod(elem_div(Fatmp_m, Z_tmp_m),elem_prod(1.-S_tmp_m,N_tmp_m))); // Catch equation (vectors) - dd = cc / TACin - 1.; - //cout << ispp<<" "<< ftmp << " "<< cc << " "<100) dd=1e-6; - } - return(ftmp); - /* FUNCTION dvariable SolveF2(const dvar_vector& N_tmp, double TACin) - dvariable dd = 10.; - dvariable cc = TACin; - dvar_vector wttmp = wt_pop_fut_f; - dvariable btmp = N_tmp * wttmp ; - dvariable ftmp; - ftmp = TACin/btmp; - dvar_vector Fatmp = ftmp * partial_F; - dvar_vector Z_tmp = Fatmp+ natmort; - dvar_vector S_tmp = exp(-Z_tmp); - int icount; - icount=0; - while (dd > 1e-5) - { - icount++; - ftmp += (TACin-cc) / btmp; - Fatmp = ftmp * partial_F; - Z_tmp = Fatmp + natmort; - S_tmp = mfexp( -Z_tmp ); - cc = (wttmp * elem_prod(elem_div(Fatmp, Z_tmp),elem_prod(1.-S_tmp,N_tmp))); // Catch equation (vectors) - dd = cc / TACin - 1.; - //cout << ispp<<" "<< ftmp << " "<< cc << " "<100) dd=1e-6; - } - return(ftmp); - */ + dvariable dd = 10.; + dvariable cc = TACin; + dvar_vector wttmp_f = wt_pop_fut_f; + dvar_vector wttmp_m = wt_pop_fut_m; + dvariable btmp = N_tmp_f * wttmp_f ; + dvariable ftmp; + ftmp = TACin/btmp; + dvar_vector Fatmp_f = ftmp * partial_F_f; + dvar_vector Fatmp_m = ftmp * partial_F_m; + dvar_vector Z_tmp_f = Fatmp_f + natmort_f; + dvar_vector Z_tmp_m = Fatmp_m + natmort_m; + dvar_vector S_tmp_f = exp(-Z_tmp_f); + dvar_vector S_tmp_m = exp(-Z_tmp_m); + int icount; + icount=0; + while (dd > 1e-5) + { + icount++; + ftmp += (TACin-cc) / btmp; + Fatmp_f = ftmp * partial_F_f; + Z_tmp_f = Fatmp_f + natmort_f; + S_tmp_f = mfexp( -Z_tmp_f ); + Fatmp_m = ftmp * partial_F_m; + Z_tmp_m = Fatmp_m + natmort_m; + S_tmp_m = mfexp( -Z_tmp_m ); + cc = (wttmp_f * elem_prod(elem_div(Fatmp_f, Z_tmp_f),elem_prod(1.-S_tmp_f,N_tmp_f))); // Catch equation (vectors) + cc += (wttmp_m * elem_prod(elem_div(Fatmp_m, Z_tmp_m),elem_prod(1.-S_tmp_m,N_tmp_m))); // Catch equation (vectors) + dd = cc / TACin - 1.; + //cout << ispp<<" "<< ftmp << " "<< cc << " "<100) dd=1e-6; + } + return(ftmp); + /* FUNCTION dvariable SolveF2(const dvar_vector& N_tmp, double TACin) + dvariable dd = 10.; + dvariable cc = TACin; + dvar_vector wttmp = wt_pop_fut_f; + dvariable btmp = N_tmp * wttmp ; + dvariable ftmp; + ftmp = TACin/btmp; + dvar_vector Fatmp = ftmp * partial_F; + dvar_vector Z_tmp = Fatmp+ natmort; + dvar_vector S_tmp = exp(-Z_tmp); + int icount; + icount=0; + while (dd > 1e-5) + { + icount++; + ftmp += (TACin-cc) / btmp; + Fatmp = ftmp * partial_F; + Z_tmp = Fatmp + natmort; + S_tmp = mfexp( -Z_tmp ); + cc = (wttmp * elem_prod(elem_div(Fatmp, Z_tmp),elem_prod(1.-S_tmp,N_tmp))); // Catch equation (vectors) + dd = cc / TACin - 1.; + //cout << ispp<<" "<< ftmp << " "<< cc << " "<100) dd=1e-6; + } + return(ftmp); + */ + } void model_parameters::Write_sd(void) { - ofstream sdreport("extra_sd.rep"); - sdreport << "Year HM_Fmsyr AM_Fmsyr GM_Biom Catch_Assump ABC_HM OFL_AM Bmsy SSB Adjust "<> nsims; sim_in.close(); - dvector ran_srv_vect(1,nsrv); - ofstream SaveOM("Om_Out.dat",ios::app); - double C_tmp; - dvariable Fnow; - dvariable meanrec; - meanrec=mean(recruits); - dvector new_srv(1,nsrv); - new_srv.initialize(); - dvariable mean5plus; - mean5plus.initialize(); - for (i=1975;i<=1999;i++) - mean5plus += natage(i)(5,nages)*wt_fsh(1,i)(5,nages); - mean5plus /= 25.; - system("cls"); cout<<"Number of replicates: "<> C_tmp; CatchNext.close(); - Fnow = SolveF2(endyr,nage_future(i), C_tmp); - F_future(1,i) = sel_fsh(1,endyr) * Fnow; - Z_future(i) = F_future(1,i) + natmort; - S_future(i) = mfexp(-Z_future(i)); - // nage_future(i,1) = SRecruit( Sp_Biom_future(i-rec_age) ) * mfexp(rec_dev_future(i)) ; - nage_future(i,1) = meanrec; - Sp_Biom_future(i) = wt_mature * elem_prod(nage_future(i),pow(S_future(i),spmo_frac)) ; - // Now graduate for the next year.... - if (i> nsims; sim_in.close(); + dvector ran_srv_vect(1,nsrv); + ofstream SaveOM("Om_Out.dat",ios::app); + double C_tmp; + dvariable Fnow; + dvariable meanrec; + meanrec=mean(recruits); + dvector new_srv(1,nsrv); + new_srv.initialize(); + dvariable mean5plus; + mean5plus.initialize(); + for (i=1975;i<=1999;i++) + mean5plus += natage(i)(5,nages)*wt_fsh(1,i)(5,nages); + mean5plus /= 25.; + system("cls"); cout<<"Number of replicates: "<> C_tmp; CatchNext.close(); + Fnow = SolveF2(endyr,nage_future(i), C_tmp); + F_future(1,i) = sel_fsh(1,endyr) * Fnow; + Z_future(i) = F_future(1,i) + natmort; + S_future(i) = mfexp(-Z_future(i)); + // nage_future(i,1) = SRecruit( Sp_Biom_future(i-rec_age) ) * mfexp(rec_dev_future(i)) ; + nage_future(i,1) = meanrec; + Sp_Biom_future(i) = wt_mature * elem_prod(nage_future(i),pow(S_future(i),spmo_frac)) ; + // Now graduate for the next year.... + if (i=1982) - incr_dev(i)(5,nages-5) = growth_alpha * growth_cov(i) ; // + age_incr; vestigial - // else - // incr_dev(i)(5,nages-5) = 0.; - incr_dev(i)(nages-4,nages) = incr_dev(i,nages-5) ; - incr_dev(i)(2,4) = incr_dev(i,5) ; - wt_srv_f(1,i,1) = wt_srv_f(1,i-1,1); - wt_srv_m(1,i,1) = wt_srv_m(1,i-1,1); - wt_srv_f(1,i)(2,nages) = ++wt_srv_f(1,i-1)(1,nages-1) + elem_prod(base_incr_f,mfexp(incr_dev(i))) ; - wt_srv_m(1,i)(2,nages) = ++wt_srv_m(1,i-1)(1,nages-1) + elem_prod(base_incr_m,mfexp(incr_dev(i))) ; - wt_pop_f(i) = wt_srv_f(1,i); - wt_pop_m(i) = wt_srv_m(1,i); - } - Get_Pred_wt(); - } - break; - } - } + incr_dev.initialize(); + if (active(yr_incr)||active(age_incr)||active(growth_alpha)) + { + switch (Growth_Option) + { + case 0 : // Use constant time-invariant growth (from base growth parameters) + // No need to do anything since they are initialized at these values... + break; + case 1 : // Use empirical (values in data file) mean wts at age + // No need to do anything since they are initialized at these values... + break; + case 2 : // Use base growth values (not estimated) and deviations decomposed by year and age + { + // Do it once for all years then apply to each fishery and survey... + // initialize survey "1" and first year of growth to mean + Initial_wt(); + for (i=styr+1;i<=endyr;i++) + { + // Age component estimated from 5-15 + incr_dev(i)(5,nages-5) = yr_incr(i) + age_incr; + incr_dev(i)(nages-4,nages) = incr_dev(i,nages-5) ; + incr_dev(i)(2,4) = incr_dev(i,5) ; + wt_srv_f(1,i,1) = wt_srv_f(1,i-1,1); + wt_srv_m(1,i,1) = wt_srv_m(1,i-1,1); + wt_srv_f(1,i)(2,nages) = ++wt_srv_f(1,i-1)(1,nages-1) + elem_prod(base_incr_f,mfexp(incr_dev(i))) ; + wt_srv_m(1,i)(2,nages) = ++wt_srv_m(1,i-1)(1,nages-1) + elem_prod(base_incr_m,mfexp(incr_dev(i))) ; + wt_pop_f(i) = wt_srv_f(1,i); + wt_pop_m(i) = wt_srv_m(1,i); + } + Get_Pred_wt(); + } + break; + case 3 : // Use base growth values (not estimated) and deviations as fn of temperature and // decomposed by year and age + { + Initial_wt(); + for (i=styr+1;i<=endyr;i++) + { + // Age component estimated from 5-15 + // if (i >=1982) + incr_dev(i)(5,nages-5) = growth_alpha * growth_cov(i) ; // + age_incr; vestigial + // else + // incr_dev(i)(5,nages-5) = 0.; + incr_dev(i)(nages-4,nages) = incr_dev(i,nages-5) ; + incr_dev(i)(2,4) = incr_dev(i,5) ; + wt_srv_f(1,i,1) = wt_srv_f(1,i-1,1); + wt_srv_m(1,i,1) = wt_srv_m(1,i-1,1); + wt_srv_f(1,i)(2,nages) = ++wt_srv_f(1,i-1)(1,nages-1) + elem_prod(base_incr_f,mfexp(incr_dev(i))) ; + wt_srv_m(1,i)(2,nages) = ++wt_srv_m(1,i-1)(1,nages-1) + elem_prod(base_incr_m,mfexp(incr_dev(i))) ; + wt_pop_f(i) = wt_srv_f(1,i); + wt_pop_m(i) = wt_srv_m(1,i); + } + Get_Pred_wt(); + } + break; + } + } + } void model_parameters::Initial_wt(void) { - wt_srv_f(1,styr) = wt_vbg_f; - wt_srv_m(1,styr) = wt_vbg_m; - wt_pop_f(styr) = wt_vbg_f; - wt_pop_m(styr) = wt_vbg_m; + wt_srv_f(1,styr) = wt_vbg_f; + wt_srv_m(1,styr) = wt_vbg_m; + wt_pop_f(styr) = wt_vbg_f; + wt_pop_m(styr) = wt_vbg_m; } void model_parameters::Get_Pred_wt(void) { - // Get predicted weights - for (i=styr_wt;i<=endyr_wt;i++) - { - wt_pred_f(i) = wt_srv_f(1,i); - wt_pred_m(i) = wt_srv_m(1,i); - } - // for other surveys set equal to survey 1... - for (k=2;k<=nsrv;k++) - for (i=styr;i<=endyr;i++) - { - wt_srv_f(k,i) = wt_srv_f(1,i) ; - wt_srv_m(k,i) = wt_srv_m(1,i) ; - } - // set fisheries equal to surveys - for (k=1;k<=nfsh;k++) - for (i=styr;i<=endyr;i++) - { - wt_fsh_f(k,i) = wt_srv_f(1,i) ; - wt_fsh_m(k,i) = wt_srv_m(1,i) ; - } + // Get predicted weights + for (i=styr_wt;i<=endyr_wt;i++) + { + wt_pred_f(i) = wt_srv_f(1,i); + wt_pred_m(i) = wt_srv_m(1,i); + } + // for other surveys set equal to survey 1... + for (k=2;k<=nsrv;k++) + for (i=styr;i<=endyr;i++) + { + wt_srv_f(k,i) = wt_srv_f(1,i) ; + wt_srv_m(k,i) = wt_srv_m(1,i) ; + } + // set fisheries equal to surveys + for (k=1;k<=nfsh;k++) + for (i=styr;i<=endyr;i++) + { + wt_fsh_f(k,i) = wt_srv_f(1,i) ; + wt_fsh_m(k,i) = wt_srv_m(1,i) ; + } } void model_parameters::Write_R_wts(void) { - R_report<<"$Yr"<0) - { - R_report << "$pobs_fsh_"<< (k) <<""<< endl; - for (i=1;i<=nyrs_fsh_age(k);i++) - R_report << yrs_fsh_age(k,i)<< " "<< oac_fsh(k,i) << endl; - R_report << endl; - } - } - for (int k=1;k<=nfsh;k++) - { - if (nyrs_fsh_age(k)>0) - { - R_report << "$phat_fsh_"<< (k) <<""<< endl; - for (i=1;i<=nyrs_fsh_age(k);i++) - R_report << yrs_fsh_age(k,i)<< " "<< eac_fsh(k,i) << endl; - R_report << endl; - } - } - for (int k=1;k<=nsrv;k++) - { - if (nyrs_srv_age(k)>0) - { - R_report << "$pobs_srv_"<<(k)<<""<< endl; - for (i=1;i<=nyrs_srv_age(k);i++) - R_report << yrs_srv_age(k,i)<< " "<< oac_srv(k,i) << endl; - R_report << endl; - } - } - for (int k=1;k<=nsrv;k++) - { - if (nyrs_srv_age(k)>0) - { - R_report << "$phat_srv_"<<(k)<<""<< endl; - for (i=1;i<=nyrs_srv_age(k);i++) - R_report << yrs_srv_age(k,i)<< " "<< eac_srv(k,i) << endl; - R_report << endl; - } - } - for (int k=1;k<=nfsh;k++) - { - R_report << endl<< "$Obs_catch_"<<(k) << endl; - R_report << obs_catch(k)(styr,endyr)<< endl; - R_report << endl; - R_report << "$Pred_catch_" <<(k) << endl; - R_report << pred_catch(k) << endl; - R_report << endl; - } - for (int k=1;k<=nfsh;k++) - { - R_report << "$F_fsh_"<<(k)<<" "<0) - { - R_report <<"$EffN_Fsh_"<<(k)<<""<0) - { - R_report <<"$EffN_Survey_"<<(k)<<""<(std::chrono::high_resolution_clock::now() - start).count() << " microseconds." << endl; #ifndef __SUNPRO_C bool failedtest = false; if (std::fetestexcept(FE_DIVBYZERO)) diff --git a/assessments/nrs/2018/fm.htp b/assessments/nrs/2018/fm.htp index 1fac69a..fa3dc53 100644 --- a/assessments/nrs/2018/fm.htp +++ b/assessments/nrs/2018/fm.htp @@ -52,6 +52,11 @@ class model_data : public ad_comm{ data_number yr1_futcat; data_number yr2_futcat; data_number n_retro; + data_number surv_dwnwt; + data_number cv_inc; + data_number n_comp; + data_number eof_check; + int phase_male_sel_offset; data_int nyrs_fut; data_vector fut_temp; data_int styr; @@ -130,6 +135,7 @@ class model_data : public ad_comm{ dvector srv_mo_frac; data_matrix n_wts; data_vector growth_cov; + data_int Check; int styr_fut; int endyr_fut; int num_proj_Fs; @@ -137,6 +143,7 @@ class model_data : public ad_comm{ dvector offset_srv; dvector offset_fsh; double R_guess; + data_matrix future_ABC; ~model_data(); model_data(int argc,char * argv[]); friend class model_parameters; @@ -149,7 +156,6 @@ public: ~model_parameters(); void preliminary_calculations(void); void set_runtime(void); - virtual void * mycast(void) {return (void*)this;} static int mc_phase(void) { return initial_params::mc_phase; @@ -176,6 +182,12 @@ public: return *objective_function_value::pobjfun; } private: + dvariable adromb(dvariable(model_parameters::*f)(const dvariable&), double a, double b, int ns) + { + using namespace std::placeholders; + _func func = std::bind(f, this, _1); + return function_minimizer::adromb(func, a, b, ns); + } ivector integer_control_flags; dvector double_control_flags; param_init_vector ln_q_srv; @@ -217,6 +229,7 @@ private: param_number slope_tmp; param_number sel50_tmp; param_init_vector sel_slope_fsh_m; + param_init_bounded_number male_sel_offset; param_init_bounded_matrix sel_slope_fsh_devs_m; param_init_vector sel50_fsh_m; param_init_bounded_matrix sel50_fsh_devs_m; @@ -343,6 +356,7 @@ private: param_stddev_number endbiom; param_stddev_number depletion; param_stddev_matrix future_catch; + param_stddev_vector future_Fs; param_stddev_matrix future_SSB; param_stddev_matrix future_TotBiom; public: diff --git a/assessments/nrs/2018/mod.ctl b/assessments/nrs/2018/mod.ctl index 711b8fd..42197dc 100644 --- a/assessments/nrs/2018/mod.ctl +++ b/assessments/nrs/2018/mod.ctl @@ -1,91 +1,92 @@ #Growth_Option -1 +0 #ABC_age_lb 6 -# +#phase_age_incr -1 -# +#phase_init_age_comp 2 -# +#phase_mn_rec 1 -# +#phase_rec_dev 2 -# +#phase_mn_f 2 -# --6 -# +#phase_F40 +8 +#phase_fmort 3 -# -7 -# +#phase_proj +6 +#phase_logist_sel 4 -# +#phase_logist_sel_devs 4 -# +#phase_male_sel 5 -# +#phase_q 5 -# --0.136 -# +#q_alpha_prior +-0.336 +#phase_q_alpha -4 -# -0.05 -# --5 -# +#q_beta_prior +0.01 +#phase_q_beta_in +-4 +#phase_m_f -6 -# +#phase_m_m -7 -# -6 -# +#phase_sr +-33 +#phase_env_cov -4 -# +#phase_sigmaR -5 -# +#phase_wtfmsy -4 -# +#pf_sigma 0.05 -# +#a50_sigma 0.35 -# +#slp_sigma 0.2 -# -1.5 -# -0.05 -# +#q_exp +1.0 +#q_sigma +0.056 +#m_exp 0.15 -# +#m_sigma 0.2 -# +#sigmaR_exp 0.6 -# +#sigmaR_sigma 0.6 -# +#nselages 17 -1 -# -1 -# -300 --1 -1 -1 -1 -1 -1 -1 +#lambda +1 1 200 1 1 1 1 1 1 1 +#styr_sr 1978 +#endyr_sr 2012 +#styr_wt 1982 +#endyr_wt 2012 +#yr1_futcat 65 +#yr2_futcat 65 +#n_retro 0 -1 +#surv_dwnwt +0 +#cv_inc 10 +#n_comp 1 +#eof_check 123456 diff --git a/assessments/nrs/2018/sim.dat b/assessments/nrs/2018/sim.dat index 56dd42d..e69de29 100644 --- a/assessments/nrs/2018/sim.dat +++ b/assessments/nrs/2018/sim.dat @@ -1,450 +0,0 @@ -#endyr_in -2018 -#nages -20 -#a_lw_f -0.00618 -#b_lw_f -3.1765 -#a_lw_m -0.00505 -#b_lw_m -3.2243 -#nfsh -1 -#obs_catch - 12.014 9.964 5.319 7.038 5.874 8.798 9.021 11.843 13.619 37.679 18.75 19.611 40.822 86.366 68.912 35.253 60.587 56.998 63.953 59.606 58.87 46.928 67.564 33.642 40.51 49.264 29.255 41.331 35.395 47.637 35.546 36.411 36.768 51.275 48.649 53.221 60.401 76.099 59.773 51.946 45.466 45.101 35.272 26 -#nyrs_fsh_age_c - 0 -#nyrs_fsh_age_s - 39 -#yrs_fsh_age_c - -#yrs_fsh_age_s - 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 -#oac_fsh_c - -#oac_fsh_s - 0 0 0 0.000209215 0.000164187 0.00105274 0.00855397 0.0430108 0.16303 0.165336 0.0530752 0.0546635 0.0552296 0.0440693 0.0226745 0.0156178 0.000257722 0 0.000109669 0 0 0 0 8.34e-05 0.000490169 0.00071514 0.0105632 0.0220274 0.0504313 0.0891616 0.0634365 0.0741637 0.0421945 0.0171758 0 0.00250299 0 0 0 0 - 0 0 0.0083923 0.0426667 0.0619307 0.0339029 0.069585 0.0435024 0.0345273 0.108745 0.0818106 0.0306045 0.0370014 0.0252498 0.0207391 0.00746879 0 0 0 0 0 0.00412853 0.0402993 0.0201805 0.0871304 0.0456849 0.0250792 0.0244199 0.0326448 0.0612131 0.0242412 0.0149257 0.0046968 0.00772301 0.00150626 0 0 0 0 0 - 0 9.56e-05 0.0247216 0.0443374 0.0170981 0.135341 0.044579 0.0232841 0.0221222 0.0351523 0.103036 0.0432597 0.0373161 0.0124538 0.0230018 0.0108101 0.00200773 0.000948094 0 0 0 0.00248542 0.0436621 0.0666117 0.036742 0.170666 0.0218895 0.0124747 0.01907 0.0310787 0.0132297 0.000801575 0.00057788 0.000216239 0.000654309 0.000208782 6.71e-05 0 0 0 - 0 0 0.0228433 0.0232455 0.02486 0.102162 0.120397 0.103473 0.043176 0.0521799 0.036704 0.0310351 0.0305334 0.0175662 0.00289661 0.00559083 0.00364145 0 0.000893811 0 0 0.00266761 0.0139902 0.0321786 0.0267495 0.0297795 0.08528 0.0483209 0.0167171 0.0211927 0.0189697 0.0525051 0.0229909 0.00745944 0 0 0 0 0 0 - 0 0 0.000588229 0.00996645 0.0288763 0.0259604 0.0783695 0.102075 0.0809289 0.0778122 0.0435105 0.0550334 0.110537 0.0526074 0.0392626 0.0393162 0.0075649 0.00464746 0.00150149 0 0 0 0.000159053 0.0085962 0.024337 0.0145772 0.028159 0.046841 0.0145069 0.0192653 0.00306176 0.0114916 0.0311677 0.0187086 0.0161173 0.00445347 0 0 0 0 - 0 0 0.00118123 0.0120689 0.0220672 0.0250627 0.0428066 0.0503348 0.0871745 0.0688083 0.0395793 0.0437519 0.0728678 0.0449348 0.041574 0.0319648 0.0090742 0 0.0090742 0 0 0.00221028 0.0103237 0.0670165 0.0413492 0.0176607 0.0650918 0.0318807 0.0603858 0.015145 0.0113024 0.0145822 0.00354485 0.0166578 0.0118675 0.0128456 0.00354485 0 0 0.0122657 - 0 0.00161257 0.00765731 0.0503106 0.102398 0.0602491 0.0635485 0.0608005 0.0319531 0.0525167 0.0132678 0.00646384 0.00275998 0.0057615 0.0137919 0.0172102 0.00225967 0.00218053 0.00154366 0.00409828 0 0.00735846 0.0284209 0.0918442 0.149259 0.0956978 0.0417413 0.0305614 0.0243179 0.0145571 0.00274121 0.000177466 0.00153442 0.007084 0.000539536 0.00153566 0.00224608 0 0 0 - 0 0 0 0.00216573 0.0338487 0.0705868 0.085543 0.0652861 0.0934052 0.0353335 0.0917138 0.0146466 0.0146426 0.0135543 0.00455297 0.0130549 0.0128471 0.000433488 0 0.0123717 0 0 0.00615786 0.0263261 0.0798486 0.151453 0.0731684 0.0406468 0.0303352 0 0.0280773 0 0 0 0 0 0 0 0 0 - 0 0 0.0117429 0.0363151 0.0282694 0.074118 0.145732 0.0443389 0.0267349 0.0307078 0.0249669 0.046963 0.0104157 0.00294368 0.00357015 0.00179279 0.00344148 0.00262337 0.000828639 0.00513328 0 0.000453553 0.0206048 0.0348645 0.0855514 0.0818842 0.127711 0.0414543 0.0510153 0.0249067 0 0.0278926 0 0 0 0 0.00302369 0 0 0 - 0 0 0.00369231 0.00753921 0.0980767 0.0476505 0.0784407 0.0760005 0.0495462 0.0164351 0.0375632 0.0133538 0.0204531 0.0153377 0 0.00217492 0.0032546 0.0117845 0.00382722 0.00461344 0 0.000727802 0.00343509 0.0234886 0.0834618 0.12815 0.136874 0.0479537 0.038455 0.00226799 0.0147268 0.0133213 0 0.00464416 0 0 0 0.00797763 0.00477258 0 - 0 6.74e-05 0.000900255 0.00781905 0.0320034 0.104736 0.0720494 0.0943765 0.0774478 0.0269036 0.0195251 0.0287651 0.0155577 0.0237553 0.0142206 0.00405958 0.00124015 0.00124015 0.0129599 0.00985688 0 0.000145763 0.00228764 0.0206002 0.0735003 0.109794 0.0810777 0.0462145 0.0423843 0.0235376 0.012929 0.00560115 0.00604701 0.0139579 0 0.0121412 0 0 0 0.00229791 - 0 0 0.00271205 0.0247631 0.0312153 0.050564 0.0669836 0.105965 0.0506072 0.027975 0.0257767 0.00359777 0.0207874 0.00782112 0.00985425 0.00595594 0.00373396 0 0 0.00599972 0 0 0.00648194 0.0604748 0.0567778 0.137462 0.108774 0.0787842 0.0355074 0.0274438 0.0220183 0.00363704 0.00828412 0.00588432 0.00207944 0 0 0.00207944 0 0 - 0 0 0.00389178 0.0190039 0.0125506 0.0194178 0.02342 0.0835602 0.0546366 0.0621456 0.0525464 0.0225517 0.0132746 0.0122757 0.0055364 0.0105467 0.000295804 0.00126835 0.000440628 0.00661304 0 0 0.00824389 0.0256207 0.0149657 0.0604514 0.0829786 0.154994 0.100687 0.0517644 0.0273773 0.0212026 0.0116407 0.00550966 0.0129874 0.00636405 0.00529517 0.0020802 0 0.00386101 - 0 0 0 0 0.0113467 0.0172252 0.0274425 0.0643971 0.0759103 0.0223691 0.069391 0.0455036 0.0190627 0.0189944 0.00703125 0.00127457 0.0104522 0.00317641 0.00305735 0.00525321 0 0 0.00117262 0.0059989 0.0407389 0.0372864 0.0589041 0.143365 0.114067 0.0588708 0.0636033 0.0213943 0.00740546 0.0129071 0.00734022 0 0.0250582 0 0 0 - 0 0 0.000191393 0.00119848 0.00580836 0.0171574 0.0490742 0.0464917 0.0678907 0.089414 0.02084 0.0416217 0.0336099 0.0199412 0.0131945 0.00324043 0 0 0.00292163 0.00292163 0 0.000168875 0.00198662 0.00444646 0.00820066 0.064668 0.11302 0.0630514 0.175778 0.0611359 0.0387964 0.0128835 0.0160976 0.0141038 0.00665559 0 0 0 0 0.00348918 - 0 0 0 0.000113603 0 0.0017924 0.0272155 0.044905 0.0584113 0.072605 0.0632355 0.0209212 0.0325375 0.0266759 0.00935679 0.00801341 0.0028284 0.000833089 0.00516263 0.00321781 0 0 0 0.00203077 0 0.00920701 0.0761423 0.174238 0.0780704 0.0881597 0.113501 0.0202647 0.0281619 0.0116294 0.00825383 0.00714249 0 0 0.00537321 0 - 0 0 0 0.00124409 0.0048206 0.00653413 0.00861229 0.0911706 0.0838905 0.0729401 0.0880909 0.0997974 0.0320127 0.0177618 0.0618317 0.00187602 0.00438011 0.0015414 0 0 0 0 0 0.0010817 0.00380235 0.00329652 0.0275104 0.0770279 0.101115 0.0560199 0.0544758 0.0464806 0.022951 0.0265801 0.00158425 0 0 0.0015702 0 0 - 0 0 0 0 6.1e-05 0.00404799 0.00296792 0.0240966 0.0832414 0.126572 0.0682683 0.0447842 0.0652933 0.0275654 0.0287515 0.0278799 0.00754735 0.00458888 0.00111759 0.00502915 0 0 0.000262131 0.000467131 0.00205 0.0187078 0.015223 0.0393537 0.11608 0.0795345 0.0545407 0.0204045 0.0212576 0.0175376 0.00572152 0.0435995 0.03382 0.00962828 0 0 - 0 0 0 0.00394245 0.00172021 0.00660511 0.046166 0.021658 0.0201258 0.121161 0.0689188 0.0401053 0.0722178 0.0317518 0.0248647 0.0239982 0.0137624 0.00905319 0 0 0 3.61208e-05 0.000500196 0.00500746 0.00511937 0.0105704 0.0538614 0.00643882 0.0744974 0.148755 0.0613702 0.0625155 0.0236541 0.0293054 0.0123185 0 0 0 0 0 - 0 0 0 0 0.000404221 0.00215593 0.00900707 0.0200852 0.0155733 0.0287624 0.115414 0.0673366 0.0535379 0.04623 0.0132943 0.00841338 0.0149203 0.00680645 0.000858621 0.00315014 0 0 0 0 0.00315667 0.00190288 0.00549893 0.0341562 0.0336215 0.0827791 0.228998 0.101039 0.0304191 0.0292039 0.0170037 0.00401437 0.0101047 0.0121521 0 0 - 0 0 0 0 0.00762444 0.0103979 0.0171583 0.00934154 0.0330866 0.0292881 0.055995 0.238225 0.0880103 0.0570559 0.0479814 0.00963996 0.00451749 0.00600735 0.000994222 0.0077425 0 0 0 0 0.00407855 0.00218994 0.011235 0.00675317 0.0715033 0.0272926 0.0586741 0.129199 0.0349307 0.0102926 0.0178064 0.002978 0 0 0 0 - 0 0 0 0 0.0028016 0.00582979 0.00350907 0.0144162 0.0395131 0.0906444 0.0255952 0.0656581 0.183834 0.0740764 0.0328868 0.0248465 0.0206922 0.00237586 0.00709364 0 0 0 0 0 0 0.00234402 0.0103962 0.0120066 0.0288337 0.113522 0.0454004 0.0337542 0.0860428 0.0348374 0.0230881 0.00939491 0.00219822 0.00168503 0.00162313 0.0011005 - 0 0 0 0 0.00254955 0.0191673 0.0218705 0.0218923 0.0235753 0.0348696 0.0995653 0.0557413 0.06927 0.130316 0.079011 0.0219259 0.0265666 0.00751362 0.00333481 0.00444566 0 0 0 0 0.00927867 0.00895288 0.0138651 0.0256718 0.0239647 0.0542235 0.102671 0.0355784 0.0350097 0.0428152 0.0191822 0.0059043 0.00126828 0 0 0 - 0 0 0 0 0 0.00673543 0.020208 0.019271 0.0520628 0.0235024 0.0490902 0.0907803 0.0396241 0.0496672 0.10301 0.0487587 0.0203235 0.0288612 0.00718687 0.00277151 0 0 0 0.00208509 0.00555371 0.0340092 0.0172138 0.0156466 0.0444586 0.0534309 0.0562523 0.0923949 0.0318505 0.00690971 0.0527337 0.0210865 0.00452126 0 0 0 - 0 0 0 0.00456645 0.0119869 0.0066927 0.0243429 0.0138096 0.0208966 0.0453143 0.0214064 0.0730885 0.0916565 0.0378122 0.0538652 0.0646978 0.0472894 0.0145757 0.00745243 0.00903411 0 0 0 0.0107803 0.00414017 0.0292823 0.0319235 0.0361982 0.0390092 0.0403284 0.03066 0.0418553 0.0655992 0.0290255 0.0258356 0.0301093 0.0162452 0.00718473 0.00461231 0.00872302 - 0 0 0.000102882 0 0.00137176 0.0203589 0.00949618 0.0200484 0.0286265 0.0103494 0.0589801 0.0356514 0.0546039 0.0989318 0.0361148 0.00989203 0.0863514 0.0342022 0.0193036 0.0235644 0 0 0 0 0.0219836 0.0287936 0.0156773 0.0349907 0.0448007 0.0293302 0.0626338 0.0227674 0.0266496 0.0745695 0.0230401 0.0122476 0.0296768 0.0130726 0.0046635 0.00715347 - 0 0 0 0.00427641 0.00994926 0.0132086 0.0224564 0.0103463 0.0309214 0.0358562 0.0277101 0.0397985 0.03389 0.0481268 0.0824458 0.0397153 0.0433512 0.0506222 0.0243639 0.0355045 0 0 0.00429513 0.0175782 0.0384589 0.0255993 0.0421998 0.0189927 0.034274 0.0677263 0.029514 0.0325391 0.0190757 0.0293912 0.0260284 0.0193956 0.00828614 0.0228644 0.00603703 0.00520112 - 0 0 0 0 0.0135261 0.0351757 0.0265878 0.0258676 0.0264343 0.0408308 0.033962 0.0303067 0.0338979 0.0219898 0.0335609 0.0862245 0.0319467 0.0199246 0.0473002 0.0448864 0 0 0 0.0077973 0.0329148 0.0311303 0.0254349 0.0367602 0.0334884 0.0201068 0.0159405 0.018616 0.0387067 0.0229723 0.0346962 0.0563463 0.0115446 0.0194403 0.0255537 0.0161284 - 0 0 0 0 0.00461514 0.0319124 0.0509754 0.0207718 0.0457091 0.0300192 0.0678651 0.0288239 0.0297545 0.0163925 0.024578 0.0246696 0.0536726 0.0274284 0.0354316 0.10415 0 0 0 0.00219295 0.0489091 0.0616013 0.0457276 0.0471027 0.0392894 0.0225999 0.0218819 0.013179 0.0214707 0.012428 0.00682181 0.0192458 0.00646716 0.00465221 0.00964486 0.0200163 - 0 0 0 0.00254438 0.00328758 0.0241433 0.0461077 0.0575415 0.0381076 0.0719285 0.0335698 0.0431453 0.0346646 0.0181855 0.0324452 0.0354558 0.0427599 0.0483071 0.0198888 0.0762425 0 0 0 0 0.0156822 0.0161188 0.0616933 0.0545556 0.0412083 0.0524256 0.00587774 0.0133467 0.0207518 0.0190803 0.0109462 0.0057654 0.0155284 0.0153352 0.00350106 0.0198583 - 0 0 0 0 0 0.0134678 0.0626294 0.0798865 0.0865447 0.0397955 0.0525764 0.0359911 0.0381688 0.0238973 0.0219595 0.0184452 0.0137499 0.0162076 0.0438791 0.0309595 0 0 0 0.00195108 0.00493452 0.0336605 0.0755461 0.0771787 0.0738458 0.025547 0.0360509 0.0155426 0.00391261 0.00871987 0.00969799 0.0153969 0.00659064 0.0102854 0.0137161 0.0092648 - 0 0 0 0 0 0.0182967 0.0193974 0.0438386 0.0746966 0.0448749 0.0317971 0.0679609 0.0394949 0.0240919 0.0216965 0.0138601 0.0177312 0.0234862 0.0268101 0.0967101 0 0 0 0 0.0143716 0.0208353 0.0675384 0.0801121 0.0904879 0.0586092 0.0244027 0.0200396 0.00319587 0.0219624 0.00101477 0.0031847 0.00606413 0.00317495 0.00865711 0.0116061 - 0 0 0 0 0 0.00218866 0.00899318 0.0658079 0.0763396 0.0815507 0.0930838 0.0311299 0.0179593 0.0133253 0.0240685 0.0138611 0.0251693 0.00334249 0.0159221 0.0893305 0 0 0 0 0 0.0301622 0.0314632 0.0742228 0.108755 0.0653051 0.0461235 0.0146859 0.0231762 0.00760265 0.00622811 0.0061392 0.00206038 0.00244167 0 0.0195614 - 0 0 0 0 0 0.00204335 0.0339487 0.0428834 0.0591194 0.0839946 0.12909 0.0511244 0.0273471 0.0289142 0.0194603 0.0156864 0.0161131 0.00933419 0.0101765 0.0844918 0 0 0 0 0.0075542 0.0118757 0.0512766 0.0579088 0.0480799 0.0843517 0.071364 0.0127663 0.00949661 0.00549968 0.00652555 0.00355688 0.008531 0.00165541 0.00128165 0.00454851 - 0 0 0 0 0 0.00850217 0.0314259 0.0669044 0.0896089 0.0852831 0.100881 0.0478996 0.0308871 0.0186144 0.00558733 0.00651887 0.00924856 0.00670507 0.00345932 0.0230908 0 0 0 0 0 0.000875836 0.0154808 0.126627 0.0646012 0.060901 0.0582949 0.0602042 0.0231268 0.0109947 0.00619487 0.00251026 0.011586 0.00494121 0.00142197 0.0176229 - 0 0 0 0 0 0 0 0.0069314 0.0407978 0.0495177 0.0935422 0.10596 0.0876375 0.0326854 0.0037103 0.020378 0.00231143 0.00558353 0.0065569 0.052624 0 0 0 0.0072622 0 0 0 0.0145588 0.111946 0.0842119 0.0421142 0.110467 0.0410414 0.0326292 0.0053719 0.0114816 0.00442166 0.0109834 0.0053719 0.00990293 - 0 0 0 0 0 0 0.00322748 0 0.0201301 0.074059 0.0471345 0.0729992 0.0909283 0.0742929 0.0345602 0.00615809 0.00683573 0.00439392 0.00850349 0.0230862 0 0 0 0 0 0.00621989 0.0136802 0.00984401 0.0212052 0.160066 0.0866254 0.0792098 0.0677748 0.0458944 0.0105174 0.0121106 0.00220859 0.00284462 0.00688638 0.00860331 - 0 8.52e-05 0.00111637 0.00295828 0.00212196 0.00830385 0.00492015 0 0.00251538 0.0258598 0.103176 0.093661 0.0906992 0.0967025 0.0582983 0.0194127 0.00265717 0.0110956 0.00406645 0.0263255 0 0 0.00661212 0.00902683 0.0170501 0.0267106 0.00825443 0.00733281 0.012687 0.035996 0.0934907 0.0863119 0.049382 0.027081 0.0373648 0.00729178 0.0027214 0.00688718 0.00221626 0.00960792 - 0 0 0 0.00301258 0.00895511 0.00933809 0.00237349 0 0.00620094 0.0016724 0.0196087 0.138407 0.08863 0.0808274 0.0917003 0.0602884 0.0203689 0.00715664 0.00174856 0.0228512 0 0 0.00147482 0.0035027 0.00352114 0.0393088 0.00407683 0.0217805 0.0155544 0.0109207 0.0336675 0.0780778 0.0715744 0.0722696 0.0242059 0.0321593 0.0176497 0 0.00103237 0.00608415 -#wt_fsh_in - 0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 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0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 - 0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -#nsmpl_fsh_c - -#nsmpl_fsh_s - 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 -#nsrv -1 -#nyrs_srv - 37 -#yrs_srv - 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 2018 -#mo_srv - 7 -#obs_srv - 600.63 759.588 850.355 695.465 1086.29 1273.49 1480.56 1326.69 1384.45 1585.65 1549.54 1995.6 2724.85 2180.56 2070.26 2623.16 2196.17 1648.1 2080.73 2344.16 1883.59 2111.31 2196.17 2121.08 2216.43 2034.3 2031.89 1539 2065.7 1977.3 1920.42 1752.97 1857.45 1411.83 1461.27 1331.78 1051.5 -#obs_se_srv - 74.082 81.8512 81.8245 58.7762 83.7444 91.228 101.509 91.0905 89.0219 95.9685 112.279 122.047 223.254 130.541 121.985 190.492 123.659 162.403 317.094 259.021 171.437 196.192 183.573 150.26 149.968 278.942 300.653 159 203.358 164.582 185.891 136.588 129.331 130.437 130.966 99.607 115.323 -#nyrs_srv_age_c - 0 -#nyrs_srv_age_s - 39 -#yrs_srv_age_c - -#yrs_srv_age_s - 1979 1980 1981 1982 1983 1984 1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 2009 2010 2011 2012 2013 2014 2015 2016 2017 -#nsmpl_srv_c - -#nsmpl_srv_s - 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 -#oac_srv_c - -#oac_srv_s - 0 0 0.0136616 0.0516972 0.0368 0.0828869 0.034087 0.0294129 0.0581352 0.0429907 0.0128967 0.0155924 0.0168259 0.0132449 0.00832478 0.00405219 0.000167022 0 0.000133788 0 0 0 0.0251897 0.0902536 0.0742152 0.100657 0.0619607 0.0452871 0.0755302 0.054815 0.0203411 0.018297 0.00410428 0.00817312 0 0.000266648 0 0 0 0 - 0 0 0.0467893 0.0681502 0.0836813 0.0467646 0.0438567 0.023393 0.0197666 0.0668525 0.0496389 0.0191993 0.0147037 0.0092504 0.00724254 0.00341622 0 0 0 0 0 0.0147965 0.0815959 0.0343737 0.124348 0.0565548 0.0293991 0.0240078 0.0345528 0.0571921 0.0197381 0.0109692 0.00283703 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0.528 0.539 0.554 0.622 0.629 0.69 0.525 0.606 - 0.004 0.013 0.031 0.066 0.103 0.193 0.169 0.13 0.316 0.33 0.376 0.459 0.536 0.57 0.573 0.617 0.681 0.698 0.483 0.573 - 0.004 0.016 0.033 0.092 0.138 0.267 0.273 0.308 0.322 0.394 0.455 0.504 0.509 0.565 0.578 0.628 0.715 0.742 0.535 0.605 - 0 0.024 0.069 0.071 0.194 0.184 0.252 0.216 0.393 0.414 0.46 0.484 0.494 0.528 0.588 0.603 0.702 0.696 0.609 0.644 - 0.004 0.035 0.102 0.172 0.276 0.287 0.318 0.371 0.5 0.462 0.486 0.527 0.509 0.555 0.585 0.63 0.709 0.79 0.681 0.716 - 0.004 0.035 0.102 0.172 0.276 0.287 0.318 0.371 0.5 0.462 0.486 0.527 0.509 0.555 0.585 0.63 0.709 0.79 0.681 0.716 -#wt_pop_m_in - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 - 0.002 0.014 0.047 0.078 0.088 0.145 0.176 0.205 0.208 0.282 0.339 0.239 0.273 0.352 0.31 0.582 0.373 0.325 0.36 0.399 - 0.002 0.014 0.047 0.078 0.088 0.145 0.176 0.205 0.208 0.282 0.339 0.239 0.273 0.352 0.31 0.582 0.373 0.325 0.36 0.399 - 0.002 0.015 0.029 0.093 0.132 0.149 0.191 0.219 0.201 0.24 0.208 0.255 0.297 0.306 0.306 0.49 0.373 0.325 0.36 0.399 - 0.002 0.018 0.023 0.053 0.12 0.13 0.198 0.216 0.228 0.284 0.256 0.251 0.292 0.293 0.294 0.447 0.346 0.325 0.36 0.399 - 0.002 0.018 0.034 0.061 0.135 0.206 0.228 0.256 0.252 0.327 0.335 0.327 0.575 0.369 0.298 0.481 0.353 0.325 0.36 0.399 - 0.002 0.018 0.027 0.037 0.092 0.168 0.261 0.252 0.253 0.26 0.299 0.327 0.575 0.369 0.3 0.501 0.357 0.325 0.36 0.399 - 0.002 0.012 0.029 0.065 0.101 0.176 0.257 0.303 0.277 0.26 0.299 0.327 0.575 0.369 0.3 0.501 0.354 0.325 0.36 0.399 - 0.002 0.014 0.022 0.049 0.11 0.172 0.233 0.301 0.337 0.438 0.324 0.278 0.345 0.458 0.302 0.538 0.352 0.342 0.36 0.399 - 0.002 0.012 0.022 0.048 0.097 0.156 0.208 0.293 0.286 0.368 0.313 0.356 0.345 0.341 0.31 0.562 0.365 0.358 0.36 0.372 - 0.002 0.006 0.014 0.033 0.066 0.125 0.203 0.29 0.305 0.292 0.314 0.377 0.336 0.398 0.32 0.542 0.363 0.374 0.36 0.35 - 0.002 0.012 0.011 0.03 0.062 0.105 0.174 0.225 0.243 0.312 0.322 0.425 0.351 0.422 0.34 0.521 0.36 0.391 0.36 0.35 - 0.002 0.008 0.013 0.031 0.053 0.089 0.166 0.202 0.244 0.234 0.323 0.311 0.345 0.318 0.347 0.477 0.376 0.407 0.36 0.35 - 0.002 0.007 0.019 0.035 0.069 0.096 0.149 0.166 0.263 0.309 0.353 0.34 0.471 0.355 0.369 0.432 0.391 0.407 0.36 0.35 - 0.002 0.011 0.02 0.041 0.066 0.093 0.143 0.216 0.216 0.242 0.286 0.317 0.361 0.362 0.383 0.42 0.399 0.407 0.368 0.377 - 0.002 0.011 0.029 0.039 0.069 0.093 0.153 0.175 0.218 0.247 0.281 0.303 0.379 0.306 0.387 0.408 0.406 0.407 0.375 0.399 - 0.002 0.006 0.02 0.045 0.07 0.113 0.152 0.205 0.205 0.232 0.302 0.294 0.245 0.359 0.352 0.391 0.42 0.422 0.383 0.399 - 0.002 0.006 0.018 0.04 0.071 0.112 0.147 0.208 0.215 0.219 0.272 0.263 0.323 0.255 0.362 0.398 0.419 0.437 0.39 0.399 - 0.002 0.006 0.023 0.041 0.072 0.083 0.148 0.174 0.225 0.225 0.232 0.257 0.245 0.325 0.356 0.407 0.417 0.478 0.398 0.399 - 0.002 0.006 0.015 0.031 0.041 0.092 0.142 0.155 0.19 0.2 0.239 0.255 0.229 0.262 0.338 0.404 0.425 0.505 0.398 0.399 - 0.002 0.006 0.015 0.038 0.034 0.068 0.12 0.163 0.205 0.205 0.23 0.26 0.277 0.269 0.318 0.382 0.406 0.52 0.406 0.399 - 0.002 0.018 0.028 0.053 0.066 0.095 0.147 0.194 0.227 0.229 0.221 0.263 0.286 0.257 0.339 0.365 0.396 0.484 0.434 0.399 - 0.002 0.015 0.037 0.067 0.093 0.112 0.173 0.195 0.224 0.219 0.247 0.258 0.256 0.285 0.317 0.349 0.389 0.467 0.415 0.407 - 0.002 0.012 0.035 0.064 0.104 0.107 0.166 0.161 0.218 0.227 0.291 0.266 0.261 0.26 0.294 0.326 0.369 0.415 0.396 0.415 - 0.002 0.024 0.036 0.099 0.195 0.148 0.186 0.244 0.228 0.227 0.272 0.292 0.297 0.278 0.295 0.341 0.346 0.367 0.384 0.392 - 0.002 0.012 0.021 0.054 0.15 0.175 0.226 0.238 0.256 0.306 0.356 0.329 0.398 0.272 0.295 0.34 0.344 0.332 0.363 0.371 - 0.002 0.009 0.018 0.037 0.083 0.149 0.208 0.209 0.23 0.246 0.245 0.3 0.287 0.352 0.285 0.343 0.332 0.348 0.316 0.357 - 0.002 0.005 0.015 0.03 0.063 0.126 0.166 0.246 0.25 0.243 0.253 0.312 0.273 0.325 0.292 0.346 0.322 0.349 0.32 0.355 - 0.002 0.01 0.019 0.029 0.047 0.111 0.146 0.234 0.243 0.234 0.324 0.279 0.36 0.337 0.299 0.394 0.318 0.35 0.32 0.34 - 0.002 0.01 0.015 0.031 0.054 0.091 0.153 0.206 0.232 0.292 0.285 0.368 0.303 0.285 0.305 0.363 0.334 0.36 0.313 0.341 - 0.002 0.01 0.027 0.039 0.065 0.103 0.136 0.187 0.24 0.292 0.253 0.315 0.29 0.306 0.329 0.355 0.348 0.364 0.314 0.344 - 0.002 0.01 0.023 0.056 0.078 0.11 0.163 0.192 0.254 0.223 0.264 0.275 0.36 0.341 0.339 0.363 0.353 0.355 0.331 0.353 - 0.002 0.01 0.016 0.038 0.114 0.148 0.182 0.188 0.267 0.269 0.287 0.303 0.379 0.303 0.347 0.354 0.355 0.34 0.347 0.329 - 0.002 0.008 0.038 0.046 0.088 0.185 0.177 0.195 0.228 0.265 0.272 0.309 0.344 0.306 0.355 0.329 0.374 0.354 0.382 0.326 - 0.002 0.016 0.036 0.074 0.108 0.119 0.176 0.186 0.234 0.247 0.262 0.293 0.278 0.375 0.368 0.332 0.374 0.37 0.383 0.339 - 0.002 0.02 0.036 0.089 0.137 0.158 0.234 0.238 0.257 0.283 0.281 0.312 0.329 0.333 0.355 0.359 0.373 0.383 0.388 0.361 - 0.004 0.022 0.056 0.078 0.175 0.197 0.22 0.262 0.278 0.251 0.303 0.303 0.295 0.305 0.356 0.358 0.373 0.427 0.373 0.392 - 0.005 0.014 0.036 0.091 0.167 0.212 0.208 0.234 0.272 0.292 0.256 0.294 0.303 0.331 0.346 0.368 0.378 0.46 0.395 0.434 - 0.005 0.014 0.036 0.091 0.167 0.212 0.208 0.234 0.272 0.292 0.256 0.294 0.303 0.331 0.346 0.368 0.378 0.46 0.395 0.434 -#maturity - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 - 0 0 0 0 0.001 0.008 0.061 0.2 0.505 0.75 0.888 0.929 0.955 0.979 0.983 0.991 0.996 0.997 0.997 0.997 -#init_age_comp -1 -#n_env_cov - 0 -#env_cov - -#spawnmo -2 -#srv_mo - 7 -#n_wts - 2 24 40 49 87 77 57 79 39 44 42 53 53 41 19 16 12 4 4 16 - 0 1 3 29 43 94 95 45 60 45 38 61 55 43 51 20 13 10 0 20 - 0 0 11 55 82 79 79 61 53 56 58 38 42 43 53 34 21 12 5 34 - 0 0 5 33 89 125 60 80 67 38 45 41 37 40 44 42 24 20 3 42 - 0 0 2 9 40 86 162 53 66 48 46 34 39 30 35 27 32 11 12 27 - 0 0 1 20 26 173 89 122 45 39 42 31 34 22 24 29 24 23 25 29 - 0 0 2 3 52 7 146 69 51 12 19 15 18 31 19 10 12 12 16 10 - 0 0 1 6 27 121 31 199 89 59 13 16 27 19 28 17 10 8 22 17 - 0 0 2 18 27 62 151 31 187 58 56 12 13 17 9 26 21 13 14 26 - 0 0 1 20 44 19 45 134 15 170 38 57 11 17 12 19 24 18 7 19 - 0 0 1 31 57 54 23 26 91 11 98 14 32 11 14 19 12 18 12 19 - 0 0 3 11 36 58 32 21 21 111 8 93 15 17 8 9 13 16 8 9 - 0 2 6 9 17 45 78 45 32 21 94 1 61 5 25 10 5 8 16 10 - 0 0 3 35 33 26 79 67 22 21 7 85 3 96 13 12 18 11 14 12 - 0 0 5 16 122 36 28 44 43 28 17 21 71 14 89 15 12 16 15 15 - 0 0 10 40 51 84 21 18 37 18 11 16 12 46 6 30 7 11 8 30 - 0 0 7 15 41 49 101 31 27 32 35 33 15 16 21 9 40 20 14 9 - 0 0 2 32 48 55 57 176 33 25 57 42 26 12 16 32 20 41 21 32 - 0 0 1 4 29 23 28 63 92 20 30 25 21 12 15 16 24 24 30 16 - 0 2 1 15 31 80 42 59 64 88 34 11 21 13 11 17 11 21 8 17 - 0 0 11 22 28 45 120 56 55 43 75 32 15 32 19 20 14 15 23 20 - 0 0 6 24 43 42 41 158 35 44 24 36 17 9 20 18 13 11 14 18 - 1 13 24 42 89 81 42 40 112 24 15 20 24 12 5 20 19 12 9 20 - 0 6 27 48 31 71 59 26 47 94 15 12 15 20 10 7 16 11 12 7 - 0 1 20 40 44 28 48 34 18 22 41 9 10 9 8 9 3 8 12 9 - 0 1 13 105 73 79 47 83 39 19 32 57 15 19 16 12 14 18 16 12 - 0 0 4 16 119 102 99 68 75 34 21 35 53 16 11 11 20 11 13 11 - 0 1 7 18 27 144 90 95 48 39 38 18 17 35 13 9 7 10 14 9 - 0 0 9 45 70 66 149 82 80 32 35 21 15 16 23 14 8 14 21 11 - 0 0 9 45 70 66 149 82 80 32 35 21 15 16 23 14 8 14 21 11 - 0 0 9 45 70 66 149 82 80 32 35 21 15 16 23 14 8 14 21 11 -#growth_cov - 0.468534 0.477176 0.056903 -0.286957 1.40687 1.44508 0.489911 0.897448 0.69368 0.57906 0.0951096 0.438969 0.426234 0.337085 1.49602 0.642738 0.910184 0.566324 -1.3058 -0.796378 -0.427047 0.515382 -0.719965 -1.50957 0.680944 1.40687 1.49602 1.19037 1.9545 -1.01288 0.540853 -1.01288 -1.28033 -1.19118 0.388027 -0.337899 -0.146866 -0.325163 -0.490725 -0.834585 0.846506 -0.669023 -1.03835 0.413498 diff --git a/assessments/nrs/data/nrs_2018.dat b/assessments/nrs/data/nrs_2018.dat index a8653df..07b08d4 100644 --- a/assessments/nrs/data/nrs_2018.dat +++ b/assessments/nrs/data/nrs_2018.dat @@ -66,50 +66,51 @@ # wt_fsh (begin year to end year) # Female Female Female Female Female Female Female Female Female Female Female Female Female Female Female Female Female Female Female Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male Male # 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.015 0.03 0.059 0.112 0.183 0.267 0.363 0.439 0.489 0.577 0.57 0.612 0.667 0.714 0.79 0.862 0.939 0.889 0.815 0.007 0.011 0.013 0.026 0.055 0.1 0.153 0.213 0.256 0.259 0.311 0.301 0.314 0.353 0.367 0.33 0.455 0.342 0.366 0.36 -0.009 0.014 0.029 0.056 0.101 0.159 0.233 0.312 0.386 0.441 0.517 0.531 0.573 0.634 0.666 0.73 0.81 0.862 0.844 0.817 0.007 0.011 0.016 0.032 0.059 0.099 0.152 0.203 0.244 0.25 0.299 0.295 0.311 0.336 0.355 0.339 0.435 0.379 0.384 0.386 -0.009 0.012 0.027 0.053 0.09 0.134 0.199 0.261 0.332 0.393 0.457 0.491 0.535 0.6 0.619 0.67 0.758 0.785 0.799 0.819 0.007 0.011 0.02 0.038 0.063 0.097 0.151 0.194 0.233 0.241 0.286 0.289 0.309 0.318 0.343 0.348 0.414 0.416 0.402 0.412 -0.009 0.011 0.026 0.05 0.078 0.11 0.165 0.211 0.278 0.346 0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 -0.009 0.011 0.026 0.05 0.078 0.11 0.165 0.211 0.278 0.346 0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 -0.009 0.011 0.026 0.05 0.078 0.11 0.165 0.211 0.278 0.346 0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 -0.009 0.011 0.026 0.05 0.078 0.11 0.165 0.211 0.278 0.346 0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 -0.009 0.011 0.026 0.05 0.078 0.11 0.165 0.211 0.278 0.346 0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 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0.397 0.452 0.496 0.566 0.571 0.61 0.707 0.709 0.753 0.821 0.007 0.01 0.023 0.044 0.067 0.096 0.151 0.185 0.221 0.232 0.273 0.282 0.307 0.301 0.33 0.357 0.393 0.453 0.42 0.438 -0.009 0.013 0.026 0.051 0.09 0.134 0.201 0.23 0.294 0.359 0.405 0.461 0.485 0.545 0.552 0.581 0.659 0.651 0.711 0.758 0.007 0.011 0.023 0.047 0.086 0.114 0.166 0.201 0.228 0.243 0.276 0.291 0.309 0.303 0.319 0.358 0.369 0.418 0.387 0.403 -0.009 0.015 0.026 0.053 0.102 0.158 0.236 0.249 0.311 0.373 0.413 0.47 0.473 0.524 0.533 0.552 0.611 0.594 0.668 0.695 0.007 0.012 0.023 0.051 0.104 0.132 0.181 0.218 0.234 0.254 0.279 0.3 0.311 0.305 0.308 0.359 0.345 0.383 0.354 0.369 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 0.055 0.123 0.149 0.196 0.234 0.241 0.265 0.282 0.308 0.314 0.307 0.297 0.36 0.321 0.348 0.321 0.335 -0.009 0.017 0.025 0.054 0.114 0.181 0.272 0.269 0.327 0.387 0.421 0.479 0.462 0.504 0.514 0.523 0.562 0.537 0.626 0.632 0.007 0.013 0.023 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311 301 314 353 367 330 455 342 366 360 +9 15 30 59 112 183 267 363 439 489 577 570 612 667 714 790 862 939 889 815 7 11 13 26 55 100 153 213 256 259 311 301 314 353 367 330 455 342 366 360 +9 15 30 59 112 183 267 363 439 489 577 570 612 667 714 790 862 939 889 815 7 11 13 26 55 100 153 213 256 259 311 301 314 353 367 330 455 342 366 360 +9 14 29 56 101 159 233 312 386 441 517 531 573 634 666 730 810 862 844 817 7 11 16 32 59 99 152 203 244 250 299 295 311 336 355 339 435 379 384 386 +9 12 27 53 90 134 199 261 332 393 457 491 535 600 619 670 758 785 799 819 7 11 20 38 63 97 151 194 233 241 286 289 309 318 343 348 414 416 402 412 +9 11 26 50 78 110 165 211 278 346 397 452 496 566 571 610 707 709 753 821 7 10 23 44 67 96 151 185 221 232 273 282 307 301 330 357 393 453 420 438 +9 11 26 50 78 110 165 211 278 346 397 452 496 566 571 610 707 709 753 821 7 10 23 44 67 96 151 185 221 232 273 282 307 301 330 357 393 453 420 438 +9 11 26 50 78 110 165 211 278 346 397 452 496 566 571 610 707 709 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346 397 452 496 566 571 610 707 709 753 821 7 10 23 44 67 96 151 185 221 232 273 282 307 301 330 357 393 453 420 438 +9 13 26 51 90 134 201 230 294 359 405 461 485 545 552 581 659 651 711 758 7 11 23 47 86 114 166 201 228 243 276 291 309 303 319 358 369 418 387 403 +9 15 26 53 102 158 236 249 311 373 413 470 473 524 533 552 611 594 668 695 7 12 23 51 104 132 181 218 234 254 279 300 311 305 308 359 345 383 354 369 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 +9 17 25 54 114 181 272 269 327 387 421 479 462 504 514 523 562 537 626 632 7 13 23 55 123 149 196 234 241 265 282 308 314 307 297 360 321 348 321 335 # nsmpl_fsh_age(1 nfsh 1 nyrs_fish_age) 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 200 # nsrv diff --git a/assessments/yfs/runs/surveyloss/orig/Makefile b/assessments/yfs/runs/surveyloss/orig/Makefile index aff2b96..c76b22e 100644 --- a/assessments/yfs/runs/surveyloss/orig/Makefile +++ b/assessments/yfs/runs/surveyloss/orig/Makefile @@ -1,7 +1,6 @@ EXEC = fm DIST = ../../../../../../src/ ARGS = -nox -iprint 50 -ARGS = -nox -iprint 50 -hbf 1 ts := $(shell /bin/date "+%Y-%m-%d---%H-%M-%S") pn = fmpl_$(ts) diff --git a/assessments/yfs/runs/surveyloss/orig/mod.ctl b/assessments/yfs/runs/surveyloss/orig/mod.ctl index 6ea49d8..bdc989f 100644 --- a/assessments/yfs/runs/surveyloss/orig/mod.ctl +++ b/assessments/yfs/runs/surveyloss/orig/mod.ctl @@ -13,11 +13,11 @@ #phase_mn_f 2 #phase_F40 - 6 + 4 #phase_fmort 3 #phase_proj - 7 + 8 #phase_logist_sel 5 #phase_logist_sel_devs @@ -49,9 +49,9 @@ #pf_sigma 0.05 #a50_sigma - 0.2 + 0.1 #slp_sigma - 0.4 + 0.2 #q_exp 1 #q_sigma @@ -67,7 +67,7 @@ #nselages 17 #lambda -1 1 300 -1 1 1 1 1 1 1 +1 1 200 -1 1 1 1 1 1 1 #styr_sr 1978 #endyr_sr diff --git a/assessments/yfs/runs/surveyloss/yfs_red.R b/assessments/yfs/runs/surveyloss/yfs_red.R index a9117ae..e6ec122 100644 --- a/assessments/yfs/runs/surveyloss/yfs_red.R +++ b/assessments/yfs/runs/surveyloss/yfs_red.R @@ -64,25 +64,33 @@ spp="yfs" #6.3. Get projection results ############################################################################################################################################################ #files to copy to retrospective subfolders -j=1 +j=2 +i=10 #retro_sub = "retro" or "survRed_retro" #6.1. Run for full time series #Create main retrospective subfolder +do_run <- FALSE df_res <- NULL for(j in 1:length(retros_sub)) { + setwd(master) cpto <- paste0(main_dir,"/",retros_sub[j],"0" ) fc <- paste0("mkdir -p ",cpto," ; cp orig/* ",cpto) system("fc") #IS added "fc" #Command line to run assessment model *.exe setwd(file.path(main_dir,paste0(retros_sub[j],"0"))) - system("make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED + if (do_run) system("rm fm.std; make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED #6.2 Get tier one projections dftmp <- data.frame(read.table("ABC_OFL.rep",header=TRUE)) dftmp$peel <- 0 dftmp$retros <- retros_sub[j] df_res <- rbind(df_res,dftmp) +<<<<<<< HEAD setwd(master) for(i in 0:length(endyrvec)){ +======= + for(i in 1:length(endyrvec)){ + setwd(master) +>>>>>>> 85e590bda024c8467c4a2fe9a16e3e9e3af480cc cpto <- paste0(main_dir,"/",retros_sub[j],i ) fc <- paste0("mkdir -p ",cpto," ; cp orig/* ",cpto) system(fc) @@ -91,18 +99,17 @@ for(j in 1:length(retros_sub)) { ctl$n_retro <- i ctl$surv_dwnwt <- j-1 write_dat(ctl,"mod.ctl") - system("make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED + if (do_run) system("rm fm.std; make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED dftmp <- data.frame(read.table("ABC_OFL.rep",header=TRUE)) dftmp$peel <- -i dftmp$retros <- retros_sub[j] df_res <- rbind(df_res,dftmp) - setwd(master) } } setwd(master) -6. Summarize results +#6. Summarize results write.csv(df_res,"yfs_results.csv") names(df_res) # Some dumb figure---------- @@ -111,10 +118,11 @@ ggplot(aes(x=Endyr,y=SSB,color=retros)) + geom_line(size=2) + theme_few() # Pool up retro results------------------ df_retro <- data.frame(matrix(ncol=9,nrow=0, dimnames=list(NULL, c("Year","Peel","SSB","SSB_sd","Totbio","Totbio_sd","Rec","Rec_sd","run")))) -j=1; i=2 +j=1; i=4 for(j in 1:length(retros_sub)) { - for(i in 1:length(endyrvec)){ + for(i in 0:length(endyrvec)){ retro_dir <- paste0(main_dir,"/",retros_sub[j],i ) + print(c(retros_sub[j],i )) rep <- read_rep(paste0(retro_dir,"/fm.rep")) df_tmp <- data.frame( Year = rep$SSB[,1], @@ -132,6 +140,7 @@ for(j in 1:length(retros_sub)) { df_retro <- rbind(df_retro,df_tmp) } } +setwd(master) write.csv(df_retro,"yfs_retros.csv") ###--jim stopped here...------------------------------------- diff --git a/src/fm.tpl b/src/fm.tpl index c62e802..0ba540a 100644 --- a/src/fm.tpl +++ b/src/fm.tpl @@ -1010,8 +1010,6 @@ PROCEDURE_SECTION get_numbers_at_age(); //if(active(R_logalpha)) compute_sr_fit(); - - if (sd_phase() || mceval_phase()) { get_msy(); @@ -1598,6 +1596,9 @@ FUNCTION compute_sr_fit // sigmaR = 0.6; R_alpha=mfexp(R_logalpha); R_beta=mfexp(R_logbeta); + //R_alpha= 0.0160063; + // = 0.00302922; + for (int i=styr_sr; i <= endyr_sr; i++) { SAM_recruits(i)= 2.*natage_f(i,1); @@ -1892,6 +1893,8 @@ FUNCTION write_srec phizero=get_spr(0.0); // cout<