diff --git a/R/MS_functions.R b/R/MS_functions.R index f96635a5..7a08e28f 100644 --- 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 index 660c109f..970b376b 100644 --- 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 index 472854a4..d29dd2bd 100644 --- 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)