Merge branch 'master' of https://github.com/jimianelli/flatfish

# Conflicts:
#	assessments/yfs/runs/surveyloss/yfs_red.R

assessments/nrs/2018/fm.htp

@@ -52,6 +52,11 @@ class model_data : public ad_comm{
   data_number yr1_futcat;
   data_number yr2_futcat;
   data_number n_retro;
+  data_number surv_dwnwt;
+  data_number cv_inc;
+  data_number n_comp;
+  data_number eof_check;
+  int phase_male_sel_offset;
   data_int nyrs_fut;
   data_vector fut_temp;
   data_int styr;
@@ -130,13 +135,15 @@ class model_data : public ad_comm{
   dvector srv_mo_frac;
   data_matrix n_wts;
   data_vector growth_cov;
+  data_int Check;
   int styr_fut;
   int endyr_fut;
   int num_proj_Fs;
   int npfs;
   dvector offset_srv;
   dvector offset_fsh;
   double R_guess;
+  data_matrix future_ABC;
   ~model_data();
   model_data(int argc,char * argv[]);
   friend class model_parameters;
@@ -149,7 +156,6 @@ public:
   ~model_parameters();
   void preliminary_calculations(void);
   void set_runtime(void);
-  virtual void * mycast(void) {return (void*)this;}
   static int mc_phase(void)
   {
     return initial_params::mc_phase;
@@ -176,6 +182,12 @@ public:
     return *objective_function_value::pobjfun;
   }
 private:
+  dvariable adromb(dvariable(model_parameters::*f)(const dvariable&), double a, double b, int ns)
+  {
+    using namespace std::placeholders;
+    _func func = std::bind(f, this, _1);
+    return function_minimizer::adromb(func, a, b, ns);
+  }
   ivector integer_control_flags;
   dvector double_control_flags;
   param_init_vector ln_q_srv;
@@ -217,6 +229,7 @@ private:
   param_number slope_tmp;
   param_number sel50_tmp;
   param_init_vector sel_slope_fsh_m;
+  param_init_bounded_number male_sel_offset;
   param_init_bounded_matrix sel_slope_fsh_devs_m;
   param_init_vector sel50_fsh_m;
   param_init_bounded_matrix sel50_fsh_devs_m;
@@ -343,6 +356,7 @@ private:
   param_stddev_number endbiom;
   param_stddev_number depletion;
   param_stddev_matrix future_catch;
+  param_stddev_vector future_Fs;
   param_stddev_matrix future_SSB;
   param_stddev_matrix future_TotBiom;
 public:

assessments/nrs/2018/mod.ctl

@@ -1,91 +1,92 @@
 #Growth_Option
-1
+0
 #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
-#
--6
-#
+#phase_F40           
+8
+#phase_fmort        
 3
-#
-7
-#
+#phase_proj        
+6
+#phase_logist_sel    
 4
-#
+#phase_logist_sel_devs    
 4
-#
+#phase_male_sel      
 5
-#
+#phase_q
 5
-#
--0.136
-#
+#q_alpha_prior
+-0.336
+#phase_q_alpha
 -4
-#
-0.05
-#
--5
-#
+#q_beta_prior
+0.01
+#phase_q_beta_in
+-4
+#phase_m_f
 -6
-#
+#phase_m_m
 -7
-#
-6
-#
+#phase_sr
+-33
+#phase_env_cov  
 -4
-#
+#phase_sigmaR  
 -5
-#
+#phase_wtfmsy 
 -4
-#
+#pf_sigma    
 0.05
-#
+#a50_sigma   
 0.35
-#
+#slp_sigma   
 0.2
-#
-1.5
-#
-0.05
-#
+#q_exp   
+1.0
+#q_sigma
+0.056
+#m_exp
 0.15
-#
+#m_sigma
 0.2
-#
+#sigmaR_exp
 0.6
-#
+#sigmaR_sigma
 0.6
-#
+#nselages
 17
-1
-#
-1
-#
-300
--1
-1
-1
-1
-1
-1
-1
+#lambda
+1 1 200 1 1 1 1 1 1 1
+#styr_sr         
 1978
+#endyr_sr       
 2012
+#styr_wt       
 1982
+#endyr_wt     
 2012
+#yr1_futcat       
 65
+#yr2_futcat      
 65
+#n_retro
 0
-1
+#surv_dwnwt
+0
+#cv_inc
 10
+#n_comp
 1
+#eof_check
 123456

assessments/yfs/runs/surveyloss/orig/Makefile

@@ -1,7 +1,6 @@
 EXEC = fm
 DIST = ../../../../../../src/
 ARGS = -nox -iprint 50 
-ARGS = -nox -iprint 50 -hbf 1
 
 ts := $(shell /bin/date "+%Y-%m-%d---%H-%M-%S")
 pn = fmpl_$(ts)

assessments/yfs/runs/surveyloss/orig/mod.ctl

@@ -13,11 +13,11 @@
 #phase_mn_f
 	2
 #phase_F40           
-	6
+	4
 #phase_fmort        
 	3
 #phase_proj        
-	7
+	8
 #phase_logist_sel    
 	5
 #phase_logist_sel_devs    
@@ -49,9 +49,9 @@
 #pf_sigma    
 	0.05
 #a50_sigma   
-	0.2
+	0.1
 #slp_sigma   
-	0.4
+	0.2
 #q_exp   
 	1
 #q_sigma
@@ -67,7 +67,7 @@
 #nselages            
 	17
 #lambda
-1 1 300 -1 1 1 1 1 1 1 	
+1 1 200 -1 1 1 1 1 1 1 	
 #styr_sr         
 	1978
 #endyr_sr       

assessments/yfs/runs/surveyloss/yfs_red.R

@@ -64,25 +64,33 @@ spp="yfs"
 #6.3. Get projection results
 ############################################################################################################################################################
 #files to copy to retrospective subfolders
-j=1
+j=2
+i=10
 #retro_sub = "retro" or "survRed_retro"
 	#6.1. Run for full time series
 	#Create main retrospective subfolder
+do_run <- FALSE
 df_res <- NULL
 for(j in 1:length(retros_sub)) {
+	setwd(master)
 	cpto <- 	paste0(main_dir,"/",retros_sub[j],"0" )
 	fc <- paste0("mkdir -p ",cpto," ; cp orig/* ",cpto)
 	system("fc")  #IS added "fc"
 	#Command line to run assessment model *.exe
 	setwd(file.path(main_dir,paste0(retros_sub[j],"0")))
-	system("make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED 
+	if (do_run) system("rm fm.std; make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED 
 	#6.2 Get tier one projections
 	dftmp        <- data.frame(read.table("ABC_OFL.rep",header=TRUE))
 	dftmp$peel   <- 0
 	dftmp$retros <- retros_sub[j] 
 	df_res       <- rbind(df_res,dftmp)
+<<<<<<< HEAD
 	setwd(master)
 	for(i in 0:length(endyrvec)){
+=======
+	for(i in 1:length(endyrvec)){
+	  setwd(master)
+>>>>>>> 85e590bda024c8467c4a2fe9a16e3e9e3af480cc
 	  cpto <- 	paste0(main_dir,"/",retros_sub[j],i )
 	  fc <- paste0("mkdir -p ",cpto," ; cp orig/* ",cpto)
 	  system(fc)
@@ -91,18 +99,17 @@ for(j in 1:length(retros_sub)) {
 	  ctl$n_retro     <- i
 	  ctl$surv_dwnwt  <- j-1
 	  write_dat(ctl,"mod.ctl")
-	  system("make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED 
+	  if (do_run) system("rm fm.std; make") #### CHANGE TO WHATEVER YOUR EXE IS CALLED 
 	  dftmp        <- data.frame(read.table("ABC_OFL.rep",header=TRUE))
 	  dftmp$peel   <- -i
 	  dftmp$retros <- retros_sub[j] 
 	  df_res       <- rbind(df_res,dftmp)
-	  setwd(master)
 	}	
 }
 setwd(master)
 
 
-6. Summarize results
+#6. Summarize results
 write.csv(df_res,"yfs_results.csv")
 names(df_res)
 # Some dumb figure----------
@@ -111,10 +118,11 @@ ggplot(aes(x=Endyr,y=SSB,color=retros)) + geom_line(size=2) + theme_few()
 
 # Pool up retro results------------------
 df_retro <- data.frame(matrix(ncol=9,nrow=0, dimnames=list(NULL, c("Year","Peel","SSB","SSB_sd","Totbio","Totbio_sd","Rec","Rec_sd","run"))))
-j=1; i=2
+j=1; i=4
 for(j in 1:length(retros_sub)) {
-	for(i in 1:length(endyrvec)){
+	for(i in 0:length(endyrvec)){
 	  retro_dir <- 	paste0(main_dir,"/",retros_sub[j],i )
+	  print(c(retros_sub[j],i ))
 	  rep <- read_rep(paste0(retro_dir,"/fm.rep"))
 	  df_tmp <- data.frame(
 	  	Year      = rep$SSB[,1],
@@ -132,6 +140,7 @@ for(j in 1:length(retros_sub)) {
 	  df_retro <- rbind(df_retro,df_tmp)
   }
 }
+setwd(master)
 write.csv(df_retro,"yfs_retros.csv")
 
 ###--jim stopped here...-------------------------------------