Step one to start organizgin working examples

examples/BSAI NRS/ForProjections.dat

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+fm_projection_model_output  
+0 # SSL Species???         
+0 # Constant  buffer  of  Dorn? 
+1 # Number  of  fsheries    
+2 # Number  of  sexes??     
+0.0698939 # averagei 5yr f
+1.0 # author  f            
+0.4     # SPR ABC          
+0.35    # SPR MSY          
+2 # Spawnmo                
+20  # Number  of  ages     
+1 # Fratio                 
+#females first             
+0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 0.15 
+#male
+0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 0.172865 
+# Maturity Females
+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 
+# Maturity Males same as females!!    
+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 
+# Wt  spawn females                                 
+0 0.0143 0.0426333 0.0880667 0.135333 0.249269 0.36119 0.4164 0.459727 0.488625 0.525333 0.61875 0.6755 0.7158 0.72725 0.629667 0.725308 0.7105 0.79275 0.927545 
+# WtAge Females,  by  fishery                               
+0 0.01 0.070674 0.119675 0.163832 0.243534 0.309472 0.388137 0.450988 0.527343 0.546709 0.566713 0.575558 0.548343 0.568974 0.600366 0.606937 0.644775 0.604785 0.65195 
+# WtAge Males,  by  fishery                               
+0 0.01 0.0706607 0.115078 0.181837 0.239772 0.280924 0.318739 0.399935 0.37515 0.421513 0.401573 0.314375 0.382681 0.415436 0.401458 0.411747 0.406325 0.449322 0.519749 
+# Selectivity Females,  by  fishery                               
+0.000311118 0.000842886 0.00228149 0.00616031 0.0165244 0.0435607 0.10989 0.250739 0.475649 0.71089 0.869541 0.947554 0.97999 0.992523 0.997229 0.998976 0.999622 0.999622 0.999622 0.999622 
+# Selectivity males,  by  fishery
+0.00020912 0.000738778 0.00260599 0.00914349 0.031494 0.10209 0.279024 0.547414 0.752056 0.840996 0.870105 0.878709 0.881174 0.881874 0.882073 0.882129 0.882144 0.882144 0.882144 0.882144 
+# N at  age in  endyr  Females,  Males                         
+440.236 361.536 1568.42 685.803 390.204 399.757 283.75 145.383 22.4396 36.8494 23.2145 15.9373 6.9824 8.43125 9.7935 20.1012 51.2928 33.37 31.563 87.4915 
+440.236 353.362 1498.29 640.245 355.799 355.337 245.094 121.789 18.1604 28.7295 17.4556 11.5895 4.92134 5.79107 6.56302 13.109 32.6172 20.979 19.8522 53.4976 
+# No  Recruitments 
+40
+# Recruitment  1978-2004
+280.595 274.373 360.874 653.349 666.766 615.804 1010.65 874.832 835.076 1414.25 2165.87 751.508 643.514 1442.41 711.898 366.867 542.332 286.298 278.206 383.692 219.987 336.756 314.047 666.997 1037.49 1229.31 923.733 746.552 892.496 278.217 110.018 77.902 53.3355 100.487 120.679 158.777 80.5199 435.205 713.113 852.928 
+# SSB       
+# used only for S/R analysis 
+54.1439 67.006 82.3962 94.4856 100.706 100.453 105.69 119.585 116.998 123.639 148.617 155.766 163.769 177.721 199.031 215.356 272.954 317.17 366.632 450.015 493.62 485.398 509.759 533.741 549.379 557.758 568.449 551.987 470.123 431.805 407.609 388.716 354.036 375.854 429.022 461.09 469.144 473.966 485.95 433.155 

examples/BSAI NRS/spm.dat

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+#rn
+NRS_test 
+#Tier
+3
+#nalts
+7    
+#alts
+1
+2
+3
+4
+5
+6
+7
+#tac_flag
+1    
+#srr_type
+1    
+#srr_form
+1    
+#srr_conditioning
+0    
+#srr_reserved
+0  
+#spm_detail_flag
+1    
+#nprj_yrs
+14  
+#nsims
+1000 
+#beg_yr
+2022 
+#nyrs_fixed_catch
+2
+#nspp
+1 
+#OY_min
+10  
+#OY_max                      
+1943.248  
+#data_files for each species                 
+../fm.prj
+#ABC_mults                                           
+1
+#scalars                   
+1
+#alt4_spr                   
+0.6
+#nTAC_cat
+1 
+#TACind
+1
+#fixed_catch           
+2022 16.0143 #Beginning of October catch
+2023 40.760 #10 yr average up to 2021.

examples/Misc/Makefile

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+run   = ../src/spm -nox -nohess >/dev/null
+data  =  data/$(stock)_spcat.dat
+outdir = $(stock)_out
+RM = rm
+.PHONY: all run
+
+all: 
+ifneq "$(wildcard $(data) )" ""
+	cp $(data) spp_catch.dat
+	@echo $(outdir)
+	$(run)
+ifneq "$(wildcard $(outdir) )" ""
+else
+	mkdir $(outdir)
+endif
+	mv *.out $(outdir)/
+	mv spm.rep $(outdir)/report.out
+	$(RM) rm eigv.rpt variance admodel.* *.r0? *.p0? fmin.log *.b0? 
+else
+  # if it doesn't:
+	@echo   "Oops...error, file " $(data) " appears to be missing...  "
+endif
+
+
+clean:
+	$(RM) $(outdir)/*
+
+
+EXEC = spm
+DIST = ../src/
+ARGS = -nox -iprint 150 
+
+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
+	$(MAKE) --directory=../../src
+
+$(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: $(PROJ)
+	./$(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

examples/Misc/README.md

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+# Example projection model run
+
+## To do list...
+
+ -  [ ]  get datafiles updated in examples directory
+ -  [ ]  make sure script runs
+ -  [ ]  write R script for settings and inputs and running
+ -  [ ]  include post-processing R script
+
+
+## Options
+
+ make mydat
+
+ run.bat mydat
+
+