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| Original file line number | Diff line number | Diff line change |
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| EXEC = pm | ||
| PROJ = spm | ||
| PROJDIST = ~/_mymods/afsc-assessments/spmR/src/ | ||
| ifeq ($(SAFE),TRUE) | ||
| DIST = ../../../source/ | ||
| else | ||
| DIST = ../../../source/ | ||
| endif | ||
| ARGS = -nox -iprint 150 | ||
| ARGS2 = -nox -iprint 150 -binp pm.bar -phase 22 -sdonly | ||
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| ifdef ComSpec | ||
| RM=del /F /Q | ||
| else | ||
| RM=rm -rf | ||
| endif | ||
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| all: mpd $(DIST)$(EXEC).tpl | ||
| $(EXEC): $(DIST)$(EXEC).tpl | ||
| ln -sf $(DIST)$(EXEC) $@ | ||
| ln -sf $(DIST)$(EXEC).tpl $@.tpl | ||
| ln -sf $(PROJDIST)$(PROJ) $(PROJ) | ||
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| $(DIST)$(EXEC).tpl: | ||
| $(MAKE) --directory=../../src | ||
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| mpd: $(EXEC) | ||
| ./$(EXEC) $(ARGS) | ||
| @$(RM) $(EXEC).*[0123456789] *.rpt *.log variance gradient.* *tmp admodel.* *.eva | ||
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| mcmc: $(EXEC) | ||
| ./$(EXEC) $(ARGS) -mcmc 3000000 -mcsave 600 | ||
| ./$(EXEC) -mceval | ||
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| proj: $(EXEC) | ||
| ./$(EXEC) $(ARGS2) | ||
| $(MAKE) --directory=proj | ||
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| debug: $(EXEC) | ||
| ./$(EXEC) $(ARGS) | ||
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| plot: | ||
| R CMD BATCH plot.R | ||
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| clean: | ||
| @$(RM) $(EXEC) | ||
| @$(RM) $(EXEC) $(EXEC).[brces]* $(EXEC).*[0123456789] *.rpt *.log variance gradient.* *tmp | ||
| @$(RM) admodel.* | ||
| @$(RM) checkfile.rep | ||
| @$(RM) mcout.rep | ||
| @$(RM) plot.Rout | ||
| @$(RM) Rplots.pdf | ||
| @$(RM) *.rep | ||
| @$(RM) Fprof.yld | ||
| @$(RM) *.prj | ||
| @$(RM) pm.par | ||
| @$(RM) SIS_out.rep | ||
| @$(RM) mceval.dat |
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,2 @@ | ||
| #Simple directory containing the bare minimum files to start a run using pm(.tpl) | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1 @@ | ||
| 1.0 1.0 1.0 1.0 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,175 @@ | ||
| #DoCovBTS | ||
| 1 | ||
| #SrType | ||
| 2 | ||
| #Do_Combined | ||
| 0 | ||
| #use_age_err | ||
| 0 | ||
| #use_age1_ats | ||
| 1 | ||
| #age1_sigma_ats | ||
| 1 | ||
| #use_endyr_len | ||
| 0 | ||
| #use_popwts_ssb | ||
| 1 | ||
| #natmortprior | ||
| 0.3 | ||
| #cvnatmortprior | ||
| 0.1 | ||
| #natmort_in | ||
| 0.9 | ||
| 0.45 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| 0.3 | ||
| #q_all_prior | ||
| 0 | ||
| #q_all_sigma | ||
| 2 | ||
| #q_bts_prior | ||
| 0 | ||
| #q_bts_sigma | ||
| 2 | ||
| #sigrprior | ||
| 1 | ||
| #cvsigrprior | ||
| 0.2 | ||
| #phase_sigr | ||
| 6 | ||
| #steepnessprior | ||
| 0.6 | ||
| #cvsteepnessprior | ||
| 10.12 | ||
| #phase_steepness | ||
| 5 | ||
| #use_spr_msy_pen | ||
| 0 | ||
| #sigma_spr_msy | ||
| 0.20 | ||
| #use_last_ats_ac | ||
| 1 | ||
| #nyrs_sel_avg | ||
| 2 | ||
| #do_bts_bio | ||
| 1 | ||
| #do_ats_bio | ||
| 1 | ||
| #srprior_a | ||
| 14.93209877 | ||
| #srprior_b | ||
| 14.93209877 | ||
| #nyrs_future | ||
| 5 | ||
| #next_yrs_catch | ||
| 1350 | ||
| #nscen | ||
| 8 | ||
| #fixed_catch_fut2 | ||
| 1400 | ||
| #fixed_catch_fut3 | ||
| 1200 | ||
| #phase_F40 | ||
| 6 | ||
| #robust_phase | ||
| 1350 | ||
| #ats_robust_phase | ||
| 1350 | ||
| #ats_like_type | ||
| 0 | ||
| #phase_logist_fsh | ||
| -1 | ||
| #phase_logist_bts | ||
| 2 | ||
| #phase_seldevs_fsh | ||
| 4 | ||
| #phase_seldevs_bts | ||
| 5 | ||
| #phase_age1devs_bts | ||
| 3 | ||
| #phase_selcoffs_ats | ||
| 3 | ||
| #phase_sel_ats_dev | ||
| 5 | ||
| #phase_natmort | ||
| -6 | ||
| #phase_q_bts | ||
| 3 | ||
| #phase_q_std_area | ||
| -4 | ||
| #phase_q_ats | ||
| 4 | ||
| #phase_bt | ||
| -6 | ||
| #phase_rec_devs | ||
| 3 | ||
| #phase_larv | ||
| -3 | ||
| #phase_sr | ||
| 5 | ||
| #wt_fut_phase | ||
| 6 | ||
| #last_age_sel_fsh | ||
| 4 | ||
| #last_age_sel_bts | ||
| 8 | ||
| #last_age_sel_ats | ||
| 8 | ||
| #ctrl_flag | ||
| 200 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 12.5 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 1 | ||
| 3.125 | ||
| 5 | ||
| 1 | ||
| 5 | ||
| 0 | ||
| 1 | ||
| 2 | ||
| 0 | ||
| 0 | ||
| 2 | ||
| 1 | ||
| #sel_dev_shift | ||
| 0 | ||
| #phase_coheff | ||
| 1 | ||
| #phase_yreff | ||
| 1 | ||
| #switch_temp_rec | ||
| 0 | ||
| #phase_temp_rec | ||
| 6 | ||
| #switch_pred_mort | ||
| 0 | ||
| #phase_pred_mort | ||
| 1 | ||
| #switch_mspp_func_resp | ||
| 1 |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,10 @@ | ||
| UseVAST_AGE_Hulson_ISS | ||
| ../data/pm_23.8.dat | ||
| ../data/selvar23.dat | ||
| control.dat | ||
| ../data/pm_fmsy_alt.dat | ||
| ../data/cov_2023.dat | ||
| ../data/wtage2023.dat | ||
| ../data/surveycpue.dat | ||
| ../data/temp_paul23.dat | ||
| ../data/q_bts.dat |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,29 @@ | ||
| EBS_Pollock_2023 | ||
| 1 # SSLn species... | ||
| 0 # Buffer of Dorn | ||
| 1 # Number of fsheries | ||
| 1 # Number of sexes | ||
| 0.237303 # averagei 5yr f | ||
| 1 # author f | ||
| 0.4 # ABC SPR | ||
| 0.35 # MSY/OFL SPR | ||
| 4 # Spawnmo | ||
| 15 # Number of ages | ||
| 1 # Fratio | ||
| 0.9 0.45 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 0.3 # Natural Mortality | ||
| # Maturity | ||
| 0 0.008 0.289 0.641 0.842 0.901 0.947 0.963 0.97 1 1 1 1 1 1 | ||
| # Wt spawn | ||
| 0.0848817 0.195868 0.319566 0.490613 0.604994 0.738365 0.851658 0.960207 1.03066 1.10148 1.21865 1.26473 1.30452 1.35788 1.43261 | ||
| # Wt fsh | ||
| 0.0251823 0.186222 0.382396 0.514465 0.713513 0.783949 0.851316 0.960344 1.05614 1.10786 1.17923 1.29141 1.29349 1.30849 1.37907 | ||
| # selectivity | ||
| 0.00014647 0.0580014 0.218331 0.347531 0.536233 0.911763 1.46748 1.59033 1.51136 1.44769 1.46686 1.36107 1.36107 1.36107 1.36107 | ||
| # natage | ||
| 21987.8 8595.85 4649.01 2424.6 2255.9 5443.38 819.65 266.836 136.547 150.712 136.752 46.7647 9.40197 6.77993 15.4783 | ||
| # Nrec | ||
| 45 | ||
| # rec | ||
| 23700.7 58115.3 24087 30138.7 17160.8 49088.9 13271.3 32996.9 12751.9 7222.43 5601.13 11570.3 48798.9 25503.9 21297.9 44508.6 14994.8 10339.9 22091.1 30273.5 14768.8 15803.7 24544 34287.3 22923.4 14043.7 6389.81 4573.53 11457.2 24376.9 13319.7 49160.7 21882.7 13123.1 11616.5 42740.5 48465.7 20761.2 7945.67 8541.89 15110.8 72487.4 18811.1 13452.5 18211.2 21143.1 | ||
| # SpawningBiomass | ||
| 1097.29 998.239 943.564 1129.34 1715.4 2343.46 3084.42 3154.02 3617.9 3541.34 3608.11 3448.78 3001.89 2542.29 2036.84 1952.23 2609.23 3028.19 3230.54 3169.52 3076.87 2608.47 2746.03 2670.05 2726.61 2545.58 2595.15 2902.27 2559.21 2338.85 1905.44 1444.55 1526.5 1567.17 1934.24 2366.94 2686.14 2615.13 2437.07 2696.77 3132.21 2983.67 2898.03 2222.34 2330.63 3121.06 |
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