add fleetnames_all where get_F() function is called to account for fl…

…eets type==3
nmfs-fish-tools · Jan 26, 2024 · 7d4748b · 7d4748b
1 parent 70410ff
commit 7d4748b
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Showing 3 changed files with 7 additions and 4 deletions.
diff --git a/R/MS_functions.R b/R/MS_functions.R
@@ -499,7 +499,8 @@ get_no_EM_catch_df <- function(OM_dir, yrs, MS = "last_yr_catch") {
     )
     # get F.
     F_vals <- get_F(outlist[["timeseries"]],
-      fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"]
+      fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"],
+      fleetnames_all = dat[["fleetinfo"]][["fleetname"]]
     )
     catch_F <- F_vals[["F_rate_fcast"]][
       ,

diff --git a/R/extendOM.R b/R/extendOM.R
@@ -379,7 +379,8 @@ update_OM <- function(OM_dir,
       # Extract the achieved F and Catch
       F_list <- get_F(
         timeseries = outlist[["timeseries"]],
-        fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"]
+        fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"],
+        fleetnames_all = dat[["fleetinfo"]][["fleetname"]] # added to account for fleets of type==3
       )
 
       units_of_catch <- dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "units"]

diff --git a/R/initOM.R b/R/initOM.R
@@ -199,8 +199,9 @@ create_OM <- function(OM_out_dir,
   # use report.sso time series table to find the F's to put into the parlist.
   F_list <- get_F(
     timeseries = outlist[["timeseries"]],
-    fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"]
-  )
+    fleetnames = dat[["fleetinfo"]][dat[["fleetinfo"]][["type"]] %in% c(1, 2), "fleetname"],
+    fleetnames_all = dat[["fleetinfo"]][["fleetname"]] # add to account for fleets type=3
+  ) 
 
   # SINGLE_RUN_MODS:
   update_F_years <- (dat[["endyr"]] + 1):(dat[["endyr"]] + nyrs)