From 2a1c1180d139f6468985bba988ecda53a33d0421 Mon Sep 17 00:00:00 2001
From: Sean Anderson <sean@seananderson.ca>
Date: Tue, 20 Aug 2024 11:47:23 -0700
Subject: [PATCH] Add high/low discard scenario figs

---
 ss3/02-outside-ss3-r4ss.R    | 2 +-
 ss3/03-outside-ss3-figures.R | 7 ++++---
 ss3/99-model-names.R         | 6 ++++--
 3 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/ss3/02-outside-ss3-r4ss.R b/ss3/02-outside-ss3-r4ss.R
index 63e8c79..ddbd064 100644
--- a/ss3/02-outside-ss3-r4ss.R
+++ b/ss3/02-outside-ss3-r4ss.R
@@ -34,7 +34,7 @@ fit_ss3 <- function(model_dir = "model1",
 
 mods <- c("A1", "A0",
           "A2_USgrowth", "A3_highmat", "A4_USgrowth_highmat", "A5_highdiscard",
-          "A6_IPHC+CPUE", "A7_SYNonly", "A8_HBLLonly", "A9_lowM", "A10_highM", "A11_low_zfrac", "A12_high_zfrac", "A13_extraSD",
+          "A6_IPHC+CPUE", "A7_SYNonly", "A8_HBLLonly", "A9_lowM", "A10_highM", "A11_low_zfrac", "A12_high_zfrac", "A13_extraSD", "A14_lowdiscard",
           "B1_1990inc", "B2_2010step", "B3_2005step", "B4_1990inc_lowM", "B5_2010step_lowM")
 
 # # Make sure starter matches...
diff --git a/ss3/03-outside-ss3-figures.R b/ss3/03-outside-ss3-figures.R
index 8eef588..eee3d42 100644
--- a/ss3/03-outside-ss3-figures.R
+++ b/ss3/03-outside-ss3-figures.R
@@ -48,9 +48,9 @@ for (set_to_plot in c("growth", "index", "M", "zfrac")) {
   if (set_to_plot == "growth") {
 
     # Set A models with growth and maturity scenarios
-    mods <- c("A0", "A2_USgrowth", "A3_highmat", "A4_USgrowth_highmat", "A5_highdiscard")
+    mods <- c("A0", "A2_USgrowth", "A3_highmat", "A4_USgrowth_highmat", "A14_lowdiscard", "A5_highdiscard")
 
-    model_name <- c("(A0) BC growth\n(base)", "(A2) US growth", "(A3) BC growth,\nhigh maturity", "(A4) USgrowth,\nhigh maturity", "(A5) 100% discard\nmortality")
+    model_name <- c("(A0) BC growth\n(base)", "(A2) US growth", "(A3) BC growth,\nhigh maturity", "(A4) USgrowth,\nhigh maturity", "(A14) Low discard\nmortality", "(A5) High discard\nmortality")
 
     fig_dir <- "figs/ss3/set_a_mat"
 
@@ -221,7 +221,7 @@ for (set_to_plot in c("growth", "index", "M", "zfrac")) {
         select(Sex, Yr, `0`) %>%
         rename(M = `0`) %>%
         mutate(scen = model_name[x]) |>
-        mutate(scen = forcats::fct_inorder(scen))
+        mutate(scen = factor(scen, levels = model_name))
     })
 
     rr <- Minc |>
@@ -304,6 +304,7 @@ for (set_to_plot in c("growth", "index", "M", "zfrac")) {
   g <- Map(SS3_index, multi_rep, model_name, figure = FALSE) %>%
     bind_rows() %>%
     mutate(scen = forcats::fct_inorder(scen)) |>
+    mutate(scen = factor(scen, levels = model_name)) |>
     left_join(fleet_names, by = "Fleet_name") %>%
     ggplot(aes(Yr, Obs, ymin = exp(log(Obs) - 1.96 * SE), ymax = exp(log(Obs) + 1.96 * SE))) +
     geom_linerange() +
diff --git a/ss3/99-model-names.R b/ss3/99-model-names.R
index 38b6730..51b0bea 100644
--- a/ss3/99-model-names.R
+++ b/ss3/99-model-names.R
@@ -1,7 +1,8 @@
 mods <- c(
   "A1", "A0",
   "A2_USgrowth", "A3_highmat", "A4_USgrowth_highmat", "A5_highdiscard",
-  "A6_IPHC+CPUE", "A7_SYNonly", "A8_HBLLonly", "A9_lowM", "A10_highM", "A11_low_zfrac", "A12_high_zfrac", "A13_extraSD",
+  "A6_IPHC+CPUE", "A7_SYNonly", "A8_HBLLonly", "A9_lowM", "A10_highM", "A11_low_zfrac",
+  "A12_high_zfrac", "A13_extraSD", "A14_lowdiscard",
   "B1_1990inc", "B2_2010step", "B3_2005step", "B4_1990inc_lowM", "B5_2010step_lowM"
 )
 
@@ -11,7 +12,7 @@ model_name <- c(
   "(A2) US growth",
   "(A3) BC growth, high maturity",
   "(A4) US growth, high maturity",
-  "(A5) 100% discard m.",
+  "(A5) High discard mortality",
   "(A6) IPHC + CPUE",
   "(A7) SYN only",
   "(A8) HBLL only",
@@ -24,6 +25,7 @@ model_name <- c(
   # "(A12) zfrac = 0.6, Beta = 2",
   "(A12) High productivity",
   "(A13) Extra SD on IPHC",
+  "(A14) Low discard mortality",
   "(B1) M = 0.074, inc. 1990",
   "(B2) M = 0.074, step 2010",
   "(B3) M = 0.074, step 2005",