projections and ref points with mulitple fleets now fixed

timjmiller · Nov 10, 2022 · 65c0130 · 65c0130
1 parent c7194c6
commit 65c0130
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Showing 4 changed files with 8 additions and 6 deletions.
diff --git a/R/fit_wham.R b/R/fit_wham.R
@@ -108,7 +108,8 @@ fit_wham = function(input, n.newton = 3, do.sdrep = TRUE, do.retro = TRUE, n.pee
     mod <- check_which_F_age(mod)
     mod <- check_FXSPR(mod)
     print(mod$env$data$n_fleets)
-    if(mod$env$data$n_fleets == 1 & mod$env$data$do_proj==1) mod <- check_projF(mod) #projections added.
+    #if(mod$env$data$n_fleets == 1 & mod$env$data$do_proj==1) mod <- check_projF(mod) #projections added.
+    if(mod$env$data$do_proj==1) mod <- check_projF(mod) #projections added.
     if(do.sdrep) mod <- do_sdrep(mod, save.sdrep = save.sdrep)
 
     # retrospective analysis

diff --git a/R/project_wham.R b/R/project_wham.R
@@ -122,7 +122,8 @@ project_wham = function(model, proj.opts=list(n.yrs=3, use.last.F=TRUE, use.avg.
     mod$rep = mod$report()
     mod$parList <- mod$env$parList(x=mle)
     mod <- check_FXSPR(mod)
-    if(mod$env$data$n_fleets == 1) mod <- check_projF(mod) #projections added.
+    #if(mod$env$data$n_fleets == 1) mod <- check_projF(mod) #projections added.
+    mod <- check_projF(mod) #projections added.
     if(is.fit & do.sdrep) # only do sdrep if no error and the model has been previously fitted.
     {
       mod$sdrep <- try(TMB::sdreport(mod))

diff --git a/src/helper_functions.hpp b/src/helper_functions.hpp
@@ -90,7 +90,7 @@ vector<Type> get_waa_y(array<Type> waa, int y, int na, int pointer){
 }
 
 template <class Type>
-vector<Type> get_waacatch_y(array<Type> waa, int y, int na, vector<int> pointer){
+matrix<Type> get_waacatch_y(array<Type> waa, int y, int na, vector<int> pointer){
   matrix<Type> waay(pointer.size(), na);
   for(int f = 0; f< pointer.size(); f++) for(int a = 0; a < na; a++) waay(f,a) = waa(pointer(f)-1, y, a);
   return(waay);
@@ -937,7 +937,7 @@ matrix<Type> get_F_proj(int y, int n_fleets, vector<int> proj_F_opt, array<Type>
     percentFMSY:  percentage (0-100) of FMSY to use in catch.
     */
   int n_toavg = avg_years_ind.size();
-  int n_ages = waacatch.size();
+  int n_ages = waacatch.cols();
   int proj_F_opt_y = proj_F_opt(y-n_years_model);
 
   //proj_F_opt == 1, last year F (default)

diff --git a/src/wham_v0.cpp b/src/wham_v0.cpp
@@ -1180,9 +1180,9 @@ Type objective_function<Type>::operator() ()
         waacatch = get_waacatch_y(waa, yi, n_ages, waa_pointer_fleets);
         for(int f = 0; f < n_fleets; f++) {
           CAA_proj(f,i,a) =  NAA(yi,a) * FAA(yi,f,a) * (1 - exp(-ZAA(yi,a)))/ZAA(yi,a);
-          catch_proj(i,f) += waacatch(f,a) * CAA_proj(i,a);
-          log_catch_proj(i,f) = log(catch_proj(i,f) + Type(1.0e-15));
+          catch_proj(i,f) += waacatch(f,a) * CAA_proj(f,i,a);
         }
+        for(int f = 0; f < n_fleets; f++) log_catch_proj(i,f) = log(catch_proj(i,f) + Type(1.0e-15));
         //CAA_proj(i,a) =  NAA(yi,a) * FAA_tot(yi,a) * (1 - exp(-ZAA(yi,a)))/ZAA(yi,a);
         //waacatch(a) = waa(waa_pointer_totcatch-1, yi, a);
       }