exclude 2000

also need to update this code to re-run

2024/R/2024_analysis.R

@@ -132,12 +132,15 @@ flc0 %>% filter(sex == 'F') %>%
   arrange(year) %>%
   ## drop the years before 2000 since Lcomps are available
   mutate(Seas = 7, 
-         FltSvy = ifelse(year %in% unique(fac0$year[which(fac0$year > 2000)]), -1, 1),  
+         FltSvy = ifelse(year %in% unique(fac0$year[which(fac0$year >= 2000)]), -1, 1),  
          Gender = 3, 
-         Part = 0, Ageerr = 1, LbinLo = -1, LbinHi = -1, Nsamp = n_h) %>%
+         Part = 0, 
+         Nsamp = n_h) %>%
   select(Yr = year, Seas, FltSvy, Gender, Part, Ageerr, LbinLo, LbinHi, Nsamp, everything(), -sex, -n_s, -n_h) %>% 
   write.csv(., file = here::here(year,'data','output','fsh_len_comp_ss3.csv'), row.names = FALSE)
 
+afscassess::fish_length_comp(year, lenbins = len_bins,rec_age = 0)
+
 ## survey comps to CAALs ----
 
 

2024/model_runs/18.2c_2020_ss3v33022w-new_fsh_len_comps/ss.p01

@@ -1,14 +1,14 @@
-# Number of parameters = 10 Objective function value = 2161.12186865965  Maximum gradient component = 8.32587790239827
+# Number of parameters = 10 Objective function value = 2151.32830066648  Maximum gradient component = 1.89485129388500
 # dummy_parm:
 1.00000000000
 # MGparm[1]:
 0.200000000000
 # MGparm[2]:
-14.3704995338
+14.3505993371
 # MGparm[3]:
-44.4547967382
+44.3672006502
 # MGparm[4]:
-0.140524487583
+0.141788668298
 # MGparm[5]:
 0.124606000000
 # MGparm[6]:
@@ -28,11 +28,11 @@
 # MGparm[13]:
 0.200000000000
 # MGparm[14]:
-14.1656487540
+14.1467803085
 # MGparm[15]:
-37.1576456297
+37.1002795137
 # MGparm[16]:
-0.219642168377
+0.221568941844
 # MGparm[17]:
 0.142118000000
 # MGparm[18]:
@@ -46,7 +46,7 @@
 # MGparm[22]:
 0.500000000000
 # SR_parm[1]:
-13.8233320698
+13.8235036741
 # SR_parm[2]:
 1.00000000000
 # SR_parm[3]:
@@ -62,13 +62,13 @@
 # Fcast_recruitments:
  0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000
 # init_F[1]:
-0.0229258078456
+0.0229454424637
 # Q_parm[1]:
 0.00000000000
 # selparm[1]:
-38.7339422598
+39.0299412903
 # selparm[2]:
-7.95407107934
+8.00059840421
 # selparm[3]:
 -2.95869000000
 # selparm[4]:

2024/model_runs/18.2c_2020_ss3v33022w-new_fsh_len_comps/ss.p02

@@ -1,18 +1,18 @@
-# Number of parameters = 76 Objective function value = 1807.00919847066  Maximum gradient component = 186.225120262395
+# Number of parameters = 76 Objective function value = 1793.82611685550  Maximum gradient component = 55.2581529055675
 # dummy_parm:
 1.00000000000
 # MGparm[1]:
 0.200000000000
 # MGparm[2]:
-14.2900833127
+14.2783054168
 # MGparm[3]:
-45.0195180169
+44.9015475399
 # MGparm[4]:
-0.139424807776
+0.141165644935
 # MGparm[5]:
-0.111165559876
+0.111863212550
 # MGparm[6]:
-0.0855457646278
+0.0848348778913
 # MGparm[7]:
 2.98000000000e-06
 # MGparm[8]:
@@ -28,15 +28,15 @@
 # MGparm[13]:
 0.200000000000
 # MGparm[14]:
-14.1220412220
+14.1108866304
 # MGparm[15]:
-37.7088412719
+37.6737509524
 # MGparm[16]:
-0.215418911086
+0.216459462518
 # MGparm[17]:
-0.123657846053
+0.125365748518
 # MGparm[18]:
-0.0678594833424
+0.0665701134670
 # MGparm[19]:
 2.98000000000e-06
 # MGparm[20]:
@@ -46,7 +46,7 @@
 # MGparm[22]:
 0.500000000000
 # SR_parm[1]:
-13.7732842608
+13.7679069571
 # SR_parm[2]:
 1.00000000000
 # SR_parm[3]:
@@ -56,31 +56,31 @@
 # SR_parm[5]:
 0.00000000000
 # recdev_early:
- -0.724720049970 -0.790908065597 -0.840642892161 -0.889346736234 -0.896004610959 -0.830278838490 -0.777906461135 -0.726786252021 -0.726142023777 -0.767293146651
+ -0.732003343127 -0.788668540432 -0.832011644741 -0.871200295661 -0.859881945572 -0.848214972507 -0.750367829668 -0.697174871694 -0.727626232820 -0.774561834771
 # recdev1:
- -0.898346744189 -0.624991613465 -0.420933268960 -0.409305234814 -0.443641367681 -0.0803014722144 0.0418362894490 0.168000874584 0.944852174410 0.0805084528954 -0.0636041797985 0.277911040671 0.831188435408 -0.0279925404321 0.918821208333 -0.420361583740 0.0954185952736 0.240992171652 0.0836101122320 0.210971260963 -0.137918802947 -0.233984858103 -0.181914258229 0.157847063658 0.160203854917 0.163514783067 -0.0965736450104 -0.182441782003 0.131726779171 0.291949792146 0.610190678785 -0.968710505093 0.0529200019446 -0.180164443687 -0.527563480799 -0.292928950028 -0.291538231268 -0.658511988218 0.645880376329 -0.483029863140 0.336272753584 0.130595960779 1.01095945503 0.0385866985355
+ -0.896519741462 -0.658015153778 -0.410123598837 -0.390000268480 -0.437283926724 -0.0841531887991 0.0609282334291 0.148544593347 0.948864381612 0.0956897103479 -0.0838410998527 0.260055543019 0.874799851612 -0.114047064992 0.971452528806 -0.487107390619 0.132473075806 0.233573656898 0.0654877960718 0.175778925958 -0.163911272930 -0.243039477636 -0.170566314923 0.159790722638 0.172622000559 0.162369319425 -0.0898388780237 -0.176925324384 0.140447802716 0.302525553851 0.611974612695 -0.938694265537 0.0496611120242 -0.158812484861 -0.518380700900 -0.279937397542 -0.279884293067 -0.655273434171 0.658315052791 -0.496780000872 0.342158189549 0.129171268095 1.01464589631 0.0218054508262
 # Fcast_recruitments:
  0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000
 # init_F[1]:
-0.0237270051777
+0.0238029345069
 # Q_parm[1]:
 0.00000000000
 # selparm[1]:
-37.4509278839
+37.8022303645
 # selparm[2]:
-7.61544982061
+7.65635628584
 # selparm[3]:
--2.54619517995
+-2.66528784888
 # selparm[4]:
--0.447687050623
+-0.333803116834
 # selparm[5]:
 1.00000000000
 # selparm[6]:
-6.82775506255
+6.83122285859
 # selparm[7]:
 12.0000000000
 # selparm[8]:
-2.06822503382
+2.07087511999
 # selparm[9]:
 3.00000000000
 # selparm[10]:
@@ -98,12 +98,12 @@
 # selparm[16]:
 1.00000000000
 # selparm[17]:
-23.3641279218
+23.4119902406
 # selparm[18]:
-6.80793709685
+6.77632414015
 # selparm[19]:
-1.11459437267
+0.923776805666
 # selparm[20]:
-1.07814237230
+0.843401962690
 # checksum999:
 999.000000000

2024/model_runs/18.2c_2020_ss3v33022w-new_fsh_len_comps/ss.par

@@ -1,18 +1,18 @@
-# Number of parameters = 78 Objective function value = 1806.14468929356  Maximum gradient component = 0.000377495364858599
+# Number of parameters = 78 Objective function value = 1793.05907818675  Maximum gradient component = 0.684443378183779
 # dummy_parm:
 1.00000000000
 # MGparm[1]:
 0.200000000000
 # MGparm[2]:
-14.2994272740
+14.2785205660
 # MGparm[3]:
-45.0102231844
+44.8914639592
 # MGparm[4]:
-0.139626110103
+0.141498996960
 # MGparm[5]:
-0.111066009247
+0.111955879795
 # MGparm[6]:
-0.0857343508296
+0.0849041354901
 # MGparm[7]:
 2.98000000000e-06
 # MGparm[8]:
@@ -28,15 +28,15 @@
 # MGparm[13]:
 0.200000000000
 # MGparm[14]:
-14.1085142590
+14.0990908382
 # MGparm[15]:
-37.7226130751
+37.6785735236
 # MGparm[16]:
-0.215220356897
+0.216455272771
 # MGparm[17]:
-0.123819628664
+0.125296494933
 # MGparm[18]:
-0.0678511751129
+0.0665063504372
 # MGparm[19]:
 2.98000000000e-06
 # MGparm[20]:
@@ -46,7 +46,7 @@
 # MGparm[22]:
 0.500000000000
 # SR_parm[1]:
-13.7698091978
+13.7694874630
 # SR_parm[2]:
 1.00000000000
 # SR_parm[3]:
@@ -56,54 +56,54 @@
 # SR_parm[5]:
 0.00000000000
 # recdev_early:
- -0.739070628512 -0.796771425201 -0.845667273144 -0.879455945453 -0.886573964046 -0.852598927882 -0.777072047583 -0.707687404904 -0.723363145063 -0.772043661105
+ -0.735917848165 -0.793505414952 -0.842209581270 -0.875912561571 -0.883114764565 -0.849213265206 -0.773768531895 -0.704196702315 -0.719993335911 -0.769017852536
 # recdev1:
- -0.898961402801 -0.657971202672 -0.414847469742 -0.382124090425 -0.450446753178 -0.0824012475326 0.0540749103849 0.156388537160 0.943930844707 0.0892719575095 -0.0756428444261 0.298041493930 0.828203925147 -0.0202814394718 0.928189790213 -0.448979165117 0.112727179796 0.231375322363 0.0964380550476 0.217057420917 -0.135938594094 -0.232920503920 -0.181161939407 0.154787612864 0.166647170554 0.162588143510 -0.0956744855869 -0.182374966011 0.132485866130 0.296437776763 0.606326858913 -0.938858787532 0.0419777657550 -0.170340616718 -0.532198956905 -0.291442567928 -0.293708525706 -0.666654243173 0.642804562876 -0.502456532788 0.331787687005 0.120437334992 1.00806574431 0.0353403742861
+ -0.896086212874 -0.657270420486 -0.414888421972 -0.383248901137 -0.452691348230 -0.0849803592100 0.0466118706735 0.155098773459 0.939311055530 0.0876088347971 -0.0726181247810 0.295795388335 0.834115196653 -0.0148740939573 0.943161963861 -0.437764214685 0.126651965153 0.226064272030 0.0753392786458 0.173574118286 -0.168920958557 -0.245692993899 -0.176120168880 0.157324554294 0.163886228761 0.162684296731 -0.0915309393337 -0.180850192100 0.139762219803 0.298612647434 0.609319178315 -0.936998035496 0.0418831993377 -0.164817496506 -0.526755892442 -0.287862628836 -0.286046576245 -0.662114557545 0.649375932249 -0.496574510252 0.335087347226 0.124656278905 1.01215894770 0.0406234992433
 # Fcast_recruitments:
  0.00000000000 0.00000000000 0.00000000000 0.00000000000 0.00000000000
 # init_F[1]:
-0.0236682398882
+0.0236846179983
 # Q_parm[1]:
 0.00000000000
 # selparm[1]:
-37.3029172513
+37.8056621399
 # selparm[2]:
-7.55499696134
+7.64950914439
 # selparm[3]:
--2.47915271277
+-2.67193516821
 # selparm[4]:
--0.292752603720
+-0.331054916677
 # selparm[5]:
 1.00000000000
 # selparm[6]:
-6.70934361954
+6.69528665494
 # selparm[7]:
 12.0000000000
 # selparm[8]:
-2.03595928964
+2.03029053351
 # selparm[9]:
 3.00000000000
 # selparm[10]:
 -1000.00000000
 # selparm[11]:
 20.0000000000
 # selparm[12]:
--0.784814551110
+-0.779241393591
 # selparm[13]:
--0.311714232668
+-0.309977927192
 # selparm[14]:
 0.00000000000
 # selparm[15]:
 0.00000000000
 # selparm[16]:
 1.00000000000
 # selparm[17]:
-23.3303522115
+23.2849545383
 # selparm[18]:
-6.69888519673
+6.67941047855
 # selparm[19]:
-0.967819795303
+0.993986103907
 # selparm[20]:
-0.884513249174
+0.906305756908
 # checksum999:
 999.000000000