Updating F-related key quantities' calculations

nmfs-ost · Jan 17, 2025 · 59be9e1 · 59be9e1
1 parent 5ab2a8f
commit 59be9e1
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Showing 2 changed files with 49 additions and 15 deletions.
diff --git a/R/utils.R b/R/utils.R
@@ -90,6 +90,45 @@ add_more_key_quants <- function(
     dplyr::filter(label == topic,
                   type == fig_or_table)
 
+
+  # calculate key quantities that rely on end_year for calculation
+  ## terminal fishing mortality
+  if (topic_cap_alt$label == "fishing.mortality") {
+
+    F.end.year <- dat |>
+      dplyr::filter(
+        c(label == 'fishing_mortality' &
+            year == end_year) |
+          c(label == 'terminal_fishing_mortality' & is.na(year))
+      ) |>
+      dplyr::pull(estimate) |>
+      as.numeric() |>
+      round(digits = 2)
+
+    # COMMENTING OUT THESE LINES because the current alt text/captions csv
+    # doesn't include Ftarg or F.Ftarg. If we alter them to include them,
+    # then uncomment these lines and add code that would substitute the key
+    # quantities into the df, like at the bottom of write_captions.
+    #
+    # # recalculate Ftarg for F.Ftarg, below
+    # Ftarg <- dat |>
+    #   dplyr::filter(grepl('f_target', label) |
+    #                   grepl('f_msy', label) |
+    #                   c(grepl('fishing_mortality_msy', label) &
+    #                       is.na(year))) |>
+    #   dplyr::pull(estimate) |>
+    #   as.numeric() |>
+    #   round(digits = 2)
+    #
+    # # Terminal year F respective to F target
+    # F.Ftarg <- F.end.year / Ftarg
+
+    if (!is.null(F.end.year)){
+      end_year <- as.character(F.end.year)
+    }
+  }
+
+
   # replace placeholders (e.g., if "end.year" is found in topic_alt, replace it with end_year)
   ## end_year-----
   if(!is.null(end_year)){

diff --git a/R/write_captions.R b/R/write_captions.R
@@ -135,8 +135,15 @@ write_captions <- function(dat, # converted model output object
     dplyr::filter(
       label == stringr::str_to_lower("F_targ") |
         label == stringr::str_to_lower("F_proxy") |
-        label == stringr::str_to_lower("F_msy")
+        label == stringr::str_to_lower("F_msy") |
+        label == "F_target"
+        # label == "F40"
+        # label == "F30"
+        # label == "F50"
+        # label == "F_initial"
+        # label == "Fmsy"
     ) |>
+    dplyr::filter(module_name == "DERIVED_QUANTITIES" | module_name == "parms") |>
     dplyr::pull(estimate) |>
     as.numeric() |>
     round(digits = 2)
@@ -149,16 +156,7 @@ write_captions <- function(dat, # converted model output object
     as.numeric()
 
   # terminal fishing mortality
-  # TODO: Put this in utils function, since F.end.year needs end_year
-  # F.end.year <- dat |>
-  #   dplyr::filter(
-  #     c(label == 'fishing_mortality' &
-  #         year == end_year) |
-  #       c(label == 'terminal_fishing_mortality' & is.na(year))
-  #   ) |>
-  #   dplyr::pull(estimate) |>
-  #   as.numeric() |>
-  # round(digits = 2)
+  # F.end.year : added with add_more_key_quants
 
   # minimum F
   F.min <- dat |>
@@ -216,8 +214,7 @@ write_captions <- function(dat, # converted model output object
     round(digits = 2)
 
   # Terminal year F respective to F target
-  # TODO: Put this in utils function, since F.end.year needs end_year
-  # F.Ftarg <- F.end.year / Ftarg
+  # F.Ftarg : added with add_more_key_quants
 
 
   ## landings plot
@@ -809,11 +806,9 @@ write_captions <- function(dat, # converted model output object
     ## mortality (F) plot
    'F.ref.pt' = as.character(F.ref.pt),
    'F.start.year' = as.character(F.start.year),
-   # 'F.end.year' = as.character(F.end.year),
    'F.min' = as.character(F.min),
    'F.max' = as.character(F.max),
    'Ftarg' = as.character(Ftarg),
-   # 'F.Ftarg' = as.character(F.Ftarg),
 
     ## landings plot
    'landings.start.year' = as.character(landings.start.year),