5 models running

2023_runs/README.md

@@ -7,7 +7,21 @@ sep23 is the base selected change model from september which has:
   - spawning biomass weight-at-age set to the RE model estimates from fishery data for the A-season
   - the new AVO time series
   - modest process error in ATS selectivity variability
-  - Pete Hulson's publication on effective sample size for bottom-trawl survey data
+  - Pete Hulson's publication on effective sample size for bottom-trawl survey data @hulson2023
+  - 
+### Directory layout
+
+Directory structure sequence is:
+    m0	last year’s model    
+    m1	Sept version through 2022    
+    m2	As m1 but with 2023 AVO data point included    
+    m3	As m2 but with 2022 age composition data updated (very minor change)    
+    m4	As m3 but addition of fishery catch-age to 2022    
+    m5	As m4 but addition of BTS index through 2023    
+    m6	As m5 but with BTS age compositions included through 2023    
+    m7	As m6 but with Hulsons BTS input sample sizes    
+
+
 
 
 

2023_runs/addatsage/Makefile

@@ -0,0 +1,59 @@
+EXEC = pm
+PROJ = spm
+	PROJDIST = ~/_mymods/afsc-assessments/spmR/src/
+ifeq ($(SAFE),TRUE)
+	DIST = ../../src/
+else
+	DIST = ../../src/
+endif
+ARGS = -nox -iprint 150 
+ARGS2 = -nox -iprint 150 -binp pm.bar -phase 22 -sdonly
+
+ifdef ComSpec
+    RM=del /F /Q
+else
+    RM=rm -rf
+endif
+
+all: mpd $(DIST)$(EXEC).tpl
+$(EXEC): $(DIST)$(EXEC).tpl
+	ln -sf $(DIST)$(EXEC) $@
+	ln -sf $(DIST)$(EXEC).tpl $@.tpl
+	ln -sf $(PROJDIST)$(PROJ) $(PROJ)
+
+$(DIST)$(EXEC).tpl:
+	$(MAKE) --directory=../../src
+
+
+mpd: $(EXEC)
+	./$(EXEC) $(ARGS)
+	@$(RM) $(EXEC).*[0123456789] *.rpt *.log variance gradient.* *tmp admodel.* *.eva
+
+mcmc: $(EXEC)
+	./$(EXEC) $(ARGS) -mcmc 3000000 -mcsave 600
+	./$(EXEC) -mceval 
+
+proj: $(EXEC)
+	./$(EXEC) $(ARGS2)
+	$(MAKE) --directory=proj
+
+debug: $(EXEC)
+	./$(EXEC) $(ARGS)
+
+plot:
+	R CMD BATCH plot.R
+
+clean:
+	@$(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

2023_runs/addatsage/README.md

@@ -0,0 +1,8 @@
+# Model config
+
+  - Ignores 1978 YC in SRR fit
+	- Uses USV DB estimates with std 20% CVs
+	- includes cold pool extent
+	- includes 2021 prelim length and catch dat
+	- 8 scenarios, 22scen has the 22 version
+  - RUN TO SEE THE EFFECT OF THE ATS SURVEY

2023_runs/addatsage/compweights.ctl

@@ -0,0 +1 @@
+1.0 1.0 1.0 1.0

2023_runs/addatsage/control.dat

@@ -0,0 +1,175 @@
+#DoCovBTS
+1
+#SrType
+1
+#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
+0.12
+#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_group_fsh
+4
+#last_age_sel_group_bts
+8
+#last_age_sel_group_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
+1
+1
+2
+1
+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