m2018 and m2019 are the new filenames for those accepted models.

assessments/yfs/runs/m2018/Makefile

@@ -0,0 +1,44 @@
+EXEC = fm
+DIST = ../../../../src/
+ARGS = -nox -iprint 50 -hbf 1
+
+ts := $(shell /bin/date "+%Y-%m-%d---%H-%M-%S")
+pn = fmpl_$(ts)
+
+R_OPTS=--no-save --no-restore --no-init-file --no-site-file -e 'library(knitr); knit("plot.Rmd")'
+plotscript = plot.md
+all: run
+
+$(EXEC): $(DIST)$(EXEC).tpl
+	ln -sf $(DIST)$(EXEC) $@
+
+$(DIST)$(EXEC).tpl:
+	$(MAKE) --directory=../../../../src
+
+run: $(EXEC)
+	 ./$(EXEC) $(ARGS)
+
+mcmc: $(EXEC)
+	 ./$(EXEC) $(ARGS) -mcmc 1000000 -rwm -hbf 1 -mcsave 20
+png: 
+	R CMD BATCH plot.R
+
+# Need to add test for existence of plot.md...
+html:
+	R ${R_OPTS} # -e 'library(knitr); knit("plot.Rmd")'
+	pandoc -V geometry:margin=1in plot.md -o ${pn}.html 
+	open ${pn}.html
+pdf:
+	R ${R_OPTS} # -e 'library(knitr); knit("plot.Rmd")'
+	pandoc -V geometry:margin=1in plot.md -o ${pn}.pdf 
+	open ${pn}.html
+
+clean:
+	rm -f $(EXEC)
+	rm -f admodel.*
+	rm -f plot.md
+	rm -f plot.html
+	rm -f $(EXEC)  $(EXEC).[brces]* $(EXEC).*[0123456789] *.rpt *.log variance
+
+clobber: clean
+	rm -f *.par *_in.* *.rep

assessments/yfs/runs/m2018/fm.dat

@@ -0,0 +1,4 @@
+#model_name 
+base
+#datafile 
+../data/yfs_2018_new_base.dat

assessments/yfs/runs/m2018/fut_temp.dat

@@ -0,0 +1,87 @@
+#N future years
+#83
+10
+#2018-2100
+-0.358391631
+-0.347389771
+-0.23299361
+-0.363436188
+-0.374168873
+-0.466159574
+-0.397734359
+-0.473374033
+-0.35259982
+-0.427406789
+-0.536620301
+-0.288011103
+-0.427231357
+-0.377261477
+-0.413241613
+-0.4692572
+-0.443232264
+-0.477669517
+-0.495102228
+-0.406864429
+-0.416883432
+-0.441118599
+-0.453100594
+-0.465847135
+-0.412503807
+-0.483580835
+-0.38016306
+-0.437023253
+-0.52201819
+-0.494401352
+-0.412069233
+-0.448720967
+-0.435581036
+-0.497845796
+-0.463215974
+-0.463015821
+-0.486233223
+-0.412786672
+-0.525440631
+-0.408374652
+-0.48095149
+-0.452790003
+-0.495745754
+-0.479617244
+-0.443970574
+-0.586021279
+-0.604914604
+-0.567569778
+-0.553606784
+-0.480537665
+-0.502569986
+-0.526704327
+-0.627752566
+-0.572927277
+-0.547301022
+-0.53006411
+-0.600494695
+-0.526809771
+-0.532722628
+-0.593818989
+-0.495105039
+-0.519518144
+-0.590966658
+-0.700360433
+-0.568325618
+-0.584653425
+-0.59185876
+-0.717599857
+-0.649290639
+-0.588195375
+-0.561241518
+-0.584396551
+-0.585143841
+-0.598280276
+-0.667336744
+-0.693354561
+-0.627986347
+-0.571240584
+-0.633938514
+-0.674148226
+-0.66426305
+-0.681221066
+-0.65154423

assessments/yfs/runs/m2018/future_catch.dat

@@ -0,0 +1,10 @@
+265.65 
+245.416 
+225.365 
+216.31 
+211.123 
+220.789 
+226.696 
+235.658 
+249.825 
+267.304 

assessments/yfs/runs/m2018/mod.ctl

@@ -0,0 +1,84 @@
+#Growth_Option
+	1
+#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
+#phase_F40           
+	-6
+#phase_fmort        
+	3
+#phase_proj        
+	7
+#phase_logist_sel    
+	5
+#phase_logist_sel_devs    
+	4
+#phase_male_sel      
+	4
+#phase_q
+	-5
+#q_alpha_prior
+	-0.071768
+#phase_q_alpha
+	4
+#q_beta_prior
+	0.09287
+#phase_q_beta_in
+	5
+#phase_m_f
+	-6
+#phase_m_m
+	-7
+#phase_sr
+	6
+#phase_env_cov  
+	4
+#phase_sigmaR  
+	-5
+#phase_wtfmsy 
+	-4
+#pf_sigma    
+	0.05
+#a50_sigma   
+	0.2
+#slp_sigma   
+	0.4
+#q_exp   
+	1
+#q_sigma
+	0.9
+#m_exp
+	0.12
+#m_sigma
+	0.8
+#sigmaR_exp
+	0.6
+#sigmaR_sigma
+	0.1
+#nselages            
+	17
+#lambda
+1 1 300 -1 1 1 1 1 1 1 	
+#styr_sr         
+	1978
+#endyr_sr       
+	2012
+#styr_wt       
+	1982
+#endyr_wt     
+	2012
+#yr1_futcat       
+	150
+#yr2_futcat      
+	150
+#n_retro
+0

assessments/yfs/runs/m2018/mod0.ctl

@@ -0,0 +1,88 @@
+#model_name 
+base
+#datafile 
+../data/yfs_2018.dat
+#Growth_Option
+	1
+#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
+#phase_F40           
+	-6
+#phase_fmort        
+	3
+#phase_proj        
+	7
+#phase_logist_sel    
+	5
+#phase_logist_sel_devs    
+	4
+#phase_male_sel      
+	4
+#phase_q
+	-5
+#q_alpha_prior
+	-0.071768
+#phase_q_alpha
+	4
+#q_beta_prior
+	0.09287
+#phase_q_beta_in
+	5
+#phase_m_f
+	-6
+#phase_m_m
+	-7
+#phase_sr
+	6
+#phase_env_cov  
+	4
+#phase_sigmaR  
+	-5
+#phase_wtfmsy 
+	-4
+#pf_sigma    
+	0.05
+#a50_sigma   
+	0.2
+#slp_sigma   
+	0.4
+#q_exp   
+	1
+#q_sigma
+	0.9
+#m_exp
+	0.12
+#m_sigma
+	0.8
+#sigmaR_exp
+	0.6
+#sigmaR_sigma
+	0.1
+#nselages            
+	17
+#lambda
+1 1 300 -1 1 1 1 1 1 1 	
+#styr_sr         
+	1978
+#endyr_sr       
+	2012
+#styr_wt       
+	1982
+#endyr_wt     
+	2012
+#yr1_futcat       
+	150
+#yr2_futcat      
+	150
+	# n_retro;
+	0

assessments/yfs/runs/m2019/BSAIyfs_sara2019.txt

@@ -0,0 +1,67 @@
+Yellowfin sole       # stock  
+BSAI       # region     (AI AK BOG BSAI EBS GOA SEO WCWYK)
+2019       # ASSESS_YEAR - year assessment is presented to the SSC
+1a         # TIER  (1a 1b 2a 2b 3a 3b 4 5 6) 
+none       # TIER2  if mixed (none 1a 1b 2a 2b 3a 3b 4 5 6)
+full       # UPDATE (new benchmark full partial)
+2          # LIFE_HIST - SAIP ratings (0 1 2 3 4 5)
+3          # ASSES_FREQ - SAIP ratings (0 1 2 3 4 5) 
+5          # ASSES_LEV - SAIP ratings (0 1 2 3 4 5)
+5          # CATCH_DAT - SAIP ratings (0 1 2 3 4 5) 
+3          # ABUND_DAT - SAIP ratings (0 1 2 3 4 5)
+771590     # Minimum B  Lower 95% confidence interval for spawning biomass in assessment year
+974705     # Maximum B  Upper 95% confidence interval for spawning biomass in assessment year
+466029     # BMSY  is equilibrium spawning biomass at MSY (Tiers 1-2) or 7/8 x B40% (Tier 3)
+ADMB       # MODEL - Required only if NMFS toolbox software used; optional otherwise 
+NA         # VERSION - Required only if NMFS toolbox software used; optional otherwise
+2          # number of sexes  if 1 sex=ALL elseif 2 sex=(FEMALE, MALE) 
+1          # number of fisheries
+1000000000    # multiplier for recruitment, N at age, and survey number (1,1000,1000000)
+1          # recruitment age used by model or size
+1          # age+ or mmCW+ used for biomass estimate
+"Exploitation rate"        # Fishing mortality type such as "Single age" or "exploitation rate"
+"Model"         # Fishing mortality source such as "Model" or "(total catch (t))/(survey biomass (t))"
+"Age of maximum F"  # Fishing mortality range such as "Age of maximum F"   Note this is age 20 averaged between males and females
+#FISHERYDESC -list of fisheries (ALL TWL LGL POT FIX FOR DOM TWLJAN LGLMAY POTAUG ...)
+ALL
+#FISHERYYEAR - list years used in the model 
+1954	1955	1956	1957	1958	1959	1960	1961	1962	1963	1964	1965	1966	1967	1968	1969	1970	1971	1972	1973	1974	1975	1976	1977	1978	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	2018	2019	
+#AGE - list of ages used in the model
+1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20	
+#RECRUITMENT - Number of recruits by year    x10^9
+1.94993	1.38866	0.951048	3.22487	2.35051	1.81088	1.71342	0.991699	1.88664	0.993851	0.920333	1.19106	1.21421	2.54748	3.89245	3.98456	5.25379	5.8402	4.59227	3.1814	4.27908	5.02676	3.30642	4.16333	2.72694	1.74233	3.37191	2.51542	7.2899	1.34937	6.03681	2.08803	1.6038	2.19146	3.00491	3.00665	1.50318	1.69057	3.75504	2.24147	1.89179	1.90407	4.69665	2.02933	1.68411	2.06347	2.89069	1.87124	2.53639	2.44556	3.81271	1.68788	1.92906	2.3986	2.2239	2.59427	3.69835	1.26049	0.671084	1.75547	2.64331	3.92014	3.02667	2.13396	2.33455	2.35635	
+#SPAWNBIOMASS - Spawning biomass by year in metric tons 
+965158  974459  965754  941927  906162  832051  652714  361924   45710   11860   24620   48392   86021  118571  139155 143969  113134   97696   80098   81620   90687  143051  203863  296593  413333  531772  663688  785482  853817  956448 1037190 1085280 1072290 1066030 1008210  981091  992275 1073950 1157280 1193070 1196390 1195780 1129020 1092730 1028330 1020410 1007340 1003530 1002120 1011580 1043250 1059980 1081370 1087170 1062840 1027080 1002260  978890  959962  947229 901370  888472  884057  859657  855966  867221
+#TOTALBIOMASS - Total biomass by year in metric tons    age 1+
+2484650 2451510 2408740 2356300 2315220 2268910 2090600 1649190 1140420  801564  843483  838642  887269  876554  803736 838578  811896  876630  948363 1203680 1455070 1816730 2129020 2445170 2746130 2911620 3099080 3270070 3387390 3366060 3597530 3610280 3322840 3286430 3191390 3253770 3118970 3241290 3454780 3492620 3538370 3308440 3225530 3244380 2966150 2777970 2828020 2751650 2793390 3010240 3222040 3326660 3299880 3295220 3144840 2961960 2991290 2997540 2946940 2862240 2637930 2630700 2754150 2672270 2748760 2786330
+#TOTFSHRYMORT - Fishing mortality rate by year 
+0.00646841	0.00769074	0.0133253	0.0135686	0.0261411	0.122356	0.403915	0.940816	4.95084	0.325401	0.281184	0.240864	0.444727	0.602492	0.480008	0.680365	0.739359	0.624338	0.329621	0.448382	0.148071	0.128721	0.123797	0.0572027	0.112652	0.065543	0.0729825	0.0578596	0.0433072	0.0445586	0.0692929	0.102934	0.0946669	0.0929473	0.117804	0.087892	0.0381922	0.0429417	0.0700095	0.0524246	0.0626013	0.0542695	0.0586417	0.0873172	0.0498563	0.0384036	0.0468891	0.0348606	0.0387266	0.0370562	0.0342783	0.045673	0.0433914	0.0587483	0.066766	0.0506756	0.0539156	0.069976	0.0681468	0.0848905	0.084017	0.0780943	0.0806627	0.0764166	0.0754418	0.0681623	
+#TOTALCATCH - Total catch by year in metric tons 
+12.562	14.69	24.697	24.145	44.153	185.321	456.103	553.742	420.703	85.81	111.177	53.81	102.353	162.228	84.189	167.134	133.079	160.399	47.856	78.24	42.235	64.69	56.221	58.373	138.433	99.017	87.391	97.301	95.712	108.385	159.526	227.107	208.597	181.428	223.156	153.17	80.584	95	159.038	106.101	144.544	124.74	129.659	181.389	101.201	67.32	83.85	63.395	72.999	74.418	69.046	94.683	99.068	121.029	148.894	107.528	118.624	151.164	147.183	164.944	156.778	126.933	135.353	132.297	131.544	118.642	
+#MATURITY - Maturity ratio by age (females only)
+ 0.0001 0.0003 0.0008 0.0018 0.0042 0.011 0.0382 0.097 0.2134 0.4134 0.6459 0.825 0.9195 0.9675 0.9855 0.996 0.9985 1 1 1
+#SPAWNWT - Average spawning weight (in kg) for ages 8-20
+0.165 0.212 0.259 0.292 327.8 0.361 0.39 0.412 0.429 0.46 0.47 0.49 0.56
+
+#NATMORT - Natural mortality rate for females then males
+0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	
+0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	0.12	
+#N_AT_AGE - Estimated numbers of female (first) then male (second) fish at age     x10^9
+1.1781800 1.0352600 0.8392600 1.0555900 1.2120400 0.7238530 0.4246280 0.1423480 0.2308870 0.5739320 0.3382960 0.2431960 0.2171340 0.1411840 0.0988367 0.1812720 0.0959620 0.0824048 0.0502457 0.3762710
+1.1781800 1.0352700 0.8392590 1.0556100 1.2121800 0.7241640 0.4252100 0.1428850 0.2329150 0.5836370 0.3458480 0.2469170 0.2166640 0.1384890 0.0960737 0.1759800 0.0935983 0.0814397 0.0500336 0.3733290
+#FSHRY_WT_KG - Fishery weight at age (in kg) females (first) males (second), only one fishery
+ 0.006 0.008 0.02 0.031 0.055 0.133 0.204 0.244 0.288 0.327 0.368 0.382 0.404 0.412 0.449 0.459 0.486 0.469 0.51 0.53	
+ 0 0.004 0.015 0.034 0.06 0.134 0.191 0.241 0.257 0.293 0.312 0.328 0.341 0.358 0.36 0.368 0.376 0.41 0.383 0.413	
+#SELECTIVITY - Estimated fishery selectivity for females (first) males (second) at age 
+  0.000105493 0.000349541 0.00115751 0.00382598 0.0125688 0.0404781 0.122662 0.316643 0.605629 0.835784 0.944033 0.982426 0.994632 0.998374 0.999509 0.999852 0.999955 0.999955 0.999955 0.999955
+  4.80905e-05 0.000193345 0.000776988 0.00311696 0.0124164 0.0481216 0.168938 0.44976 0.766722 0.929657 0.98153 0.995342 0.998838 0.999711 0.999928 0.999982 0.999996 0.999996 0.999996 0.999996
+#SURVEYDESC
+EBS_trawl_survey 
+SURVEYMULT
+1
+#EBS_trawl_survey - Bering Sea shelf survey biomass (Year, Obs_biomass, Pred_biomass) 
+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 2019	
+3509130 3672420 3341320 2398080 2031600 2511840 2180750 2313620 2179610 2391860 2201520 2468430 2597190 2012400 2216500 2161400 2210180 1257180 1589780 1679520 1910070 2158130 2542070 2820840 2132480 2153090 2099670 1739430 2368260 2403220 1951410 2279020 2512260 1932350 2859810 2787520 1892920 2006510
+2127280 2630130 2710580 2674470 2217380 2416890 2312810 2513960 2375750 2571140 2528790 2689000 2344080 2343330 2525100 2434520 2340530 1265370 1688740 1955760 2205550 2440870 2532190 2562170 2198300 2665440 2141900 1982740 2224830 2231470 1991240 2266830 2131280 2110470 2447660 1959450 2224950 2313750
+#STOCKNOTES
+"SAFE report indicates that this stock was not subjected to overfishing in 2019 and is neither overfished nor approaching a condition of being overfished in 2020."