Fix plot_biomass and update naming convention for catch in SS3 converter

R/convert_output.R

@@ -372,6 +372,8 @@ convert_output <- function(
                       grepl(":_[0-9][0-9]$", label) ~ stringr::str_extract(label, "(?<=_)[0-9][0-9]+"),
                       TRUE ~ NA
                     )
+                  } else if ("fleet_name" %in% colnames(df3)) {
+                    fleet_name
                   } else {
                     fleet
                   },
@@ -1222,8 +1224,13 @@ convert_output <- function(
         paste0("Some parameters were not found or included in the output file. The following parameters were not added into the new output file: \n", paste(miss_parms, collapse = "\n"))
       )
     }
-    out_new <- Reduce(rbind, out_list) |>
-      dplyr::mutate(fleet = fleet_names[fleet])
+    out_new <- Reduce(rbind, out_list)
+    out_new <- out_new |>
+      dplyr::mutate(fleet = dplyr::case_when(
+        any(unique(out_new$fleet) %in% fleet_names) ~ fleet,
+        TRUE ~ fleet_names[fleet]
+      )
+    )
   } else if (model %in% c("bam", "BAM")) {
     #### BAM ####
     # Extract values from BAM output - model file after following ADMB2R

R/plot_biomass.R

@@ -78,7 +78,7 @@ plot_biomass <- function(
   # Filter data for spawning biomass
   prepared_data <- filter_data(
     dat = dat,
-    label_name = "^biomass$|^biomass_retained$|^biomass_dead$",
+    label_name = "^biomass$",
     geom = geom,
     group = group,
     facet = facet,

R/table_landings.R

@@ -23,7 +23,7 @@
 #' table_landings(
 #'   stockplotr::example_data,
 #'   unit_label = "landings label",
-#'   group =
+#'   group = "fleet"
 #'   )
 table_landings <- function(
   dat,

inst/resources/ss3_var_names.csv

@@ -91,13 +91,13 @@ SPAWN_RECRUIT,mature_num,mature_abundance
 TIME_SERIES,mature_num,mature_abundance
 SPAWN_RECRUIT,raw_dev,
 TIME_SERIES,bio_all,biomass
-TIME_SERIES,bio_smry,biomass_midyear
+TIME_SERIES,bio_smry,biomass_reference_age
 TIME_SERIES,recruit,recruitment
 TIME_SERIES,smrybio,biomass_midyear
 TIME_SERIES,smrynum,abundance_midyear
-TIME_SERIES,sel(b),biomass
-TIME_SERIES,dead(b),biomass_dead
-TIME_SERIES,retain(b),biomass_retained
+TIME_SERIES,sel(b),catch_selected
+TIME_SERIES,dead(b),catch_dead
+TIME_SERIES,retain(b),catch_retained
 TIME_SERIES,sel(n),numbers
 TIME_SERIES,dead(n),numbers_dead
 TIME_SERIES,retain(n),numbers_retained