Check AddInd SD, AC only when fitIerr = TRUE; #79

Blue-Matter · Jan 11, 2025 · 62d6f15 · 62d6f15
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commit 62d6f15
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Showing 2 changed files with 27 additions and 22 deletions.
diff --git a/NEWS.md b/NEWS.md
@@ -6,6 +6,7 @@ The current version of the `MSEtool` package is available for download from [CRA
 - `updateData` and `updateData_MS` use the Baranov catch equation to simulate `Data@CAA` in the projection. Previously, the catch at age was simulated with only the retention curve.
 - `multiMSE` solves for F from multi-fleet TAC simultaneously with function `CalcMPDynamics_MF`
 - fix check for simulated `Data@VInd` in `multiMSE`
+- turn off check for valid `Data@AddInd` statistics (AC, SD) when `cpars$AddIerr` is provided
 
 ## Updates
 - When indices are provided to the operating model, the default value of beta = 1 (hyperstability parameter) if not specified in `cpars`.

diff --git a/R/Data_make_update.R b/R/Data_make_update.R
@@ -1172,18 +1172,20 @@ AddRealData <- function(SimData, RealData, ObsPars, StockPars, FleetPars, nsim,
         # Calculate statistics
         Stats_List <- lapply(1:nsim, function(x) Calc_Stats(lResids_Hist[x,]))
         Stats <- do.call('rbind', Stats_List)
-        check_Index <- check_Index_Fit(Stats, i)
-        if (check_Index) {
-          # Generate residuals for projections
-          Resid_Hist <- exp(lResids_Hist) # historical residuals in normal space
-          Resid_Proj <- Gen_Residuals(Stats, nsim, proyears)
-
-          if (fitIerr) ObsPars$AddIerr[,i, ] <- cbind(Resid_Hist, Resid_Proj)
-          ObsPars$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
-        } else {
-          ObsPars$AddIerr[,i, ] <-  ObsPars$Ierr_y
-          ObsPars$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
+
+        if (fitIerr) {
+          check_Index <- check_Index_Fit(Stats, i)
+          if (check_Index) {
+            # Generate residuals for projections
+            Resid_Hist <- exp(lResids_Hist) # historical residuals in normal space
+            Resid_Proj <- Gen_Residuals(Stats, nsim, proyears)
+
+            ObsPars$AddIerr[,i, ] <- cbind(Resid_Hist, Resid_Proj)
+          } else {
+            ObsPars$AddIerr[,i, ] <-  ObsPars$Ierr_y
+          }
         }
+        ObsPars$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
       }
     }
   }
@@ -1687,18 +1689,20 @@ AddRealData_MS <- function(SimData,
         # Calculate statistics
         Stats_List <- lapply(1:nsim, function(x) Calc_Stats(lResids_Hist[x,]))
         Stats <- do.call('rbind', Stats_List)
-        check_Index <- check_Index_Fit(Stats, i)
-        if (check_Index) {
-          # Generate residuals for projections
-          Resid_Hist <- exp(lResids_Hist) # historical residuals in normal space
-          Resid_Proj <- Gen_Residuals(Stats, nsim, proyears)
-
-          if (fitIerr) ObsPars[[p]][[f]]$AddIerr[,i, ] <- cbind(Resid_Hist, Resid_Proj)
-          ObsPars[[p]][[f]]$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
-        } else {
-          ObsPars[[p]][[f]]$AddIerr[,i, ] <-  ObsPars[[p]][[f]]$Ierr_y
-          ObsPars[[p]][[f]]$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
+
+        if (fitIerr) {
+          check_Index <- check_Index_Fit(Stats, i)
+          if (check_Index) {
+            # Generate residuals for projections
+            Resid_Hist <- exp(lResids_Hist) # historical residuals in normal space
+            Resid_Proj <- Gen_Residuals(Stats, nsim, proyears)
+
+            ObsPars[[p]][[f]]$AddIerr[,i, ] <- cbind(Resid_Hist, Resid_Proj)
+          } else {
+            ObsPars[[p]][[f]]$AddIerr[,i, ] <-  ObsPars[[p]][[f]]$Ierr_y
+          }
         }
+        ObsPars[[p]][[f]]$AddInd_Stat[[i]] <- Stats[,1:2] # index fit statistics
       }
     }
   }