add script for exploring rec selectivity

Rscripts/explore_selectivity_for_rec_fleets.R

@@ -0,0 +1,57 @@
+# compare rec selectivity separate or mirrored
+yt1 <- SS_output("Model_Runs/base_2017_3.30.23")
+yt2 <- SS_output("Model_Runs/2017_plus_mirror_rec_selex")
+
+png("figures/explore_selectivity_for_rec_fleets.png",
+  width = 6.5, height = 6.5, res = 300, units = "in"
+)
+par(mfrow = c(2, 1))
+SSplotSelex(yt1c,
+  subplots = 1, fleets = 3:4, years = 1900:2025,
+  mar = c(2, 2, 1, 1), legendloc = "topleft"
+)
+SSplotSelex(yt2,
+  subplots = 1, fleets = 3:4, years = 1900:2025,
+  mar = c(2, 2, 1, 1), legendloc = NA
+)
+dev.off()
+
+# calculate fraction of catch from rec fleets
+catch_by_fleet <- yt1$timeseries |>
+  dplyr::filter(Yr < 2017) |>
+  dplyr::select(dplyr::starts_with("dead(B)"))
+catch_by_fleet$total <- rowSums(catch_by_fleet)
+catch_total_across_years <- colSums(catch_by_fleet)
+catch_by_fleet_proportions <- catch_by_fleet
+catch_proportion_across_years <- catch_total_across_years
+for (i in 1:5) {
+  catch_by_fleet_proportions[, i] <- round(catch_by_fleet[, i] /
+    catch_by_fleet$total, 3)
+  catch_proportion_across_years[i] <- round(catch_total_across_years[i] /
+    catch_total_across_years[5], 3)
+}
+
+# proportion of total
+catch_proportion_across_years
+# dead(B):_1 dead(B):_2 dead(B):_3 dead(B):_4      total
+#      0.935      0.053      0.009      0.004      1.000
+
+# max proportion among all years
+apply(catch_by_fleet_proportions, 2, max, na.rm = TRUE)
+# dead(B):_1 dead(B):_2 dead(B):_3 dead(B):_4      total
+#      1.000      0.336      0.051      0.044      1.000
+
+SStableComparisons(SSsummarize(list(yt1, yt2)), names = "Bratio_2017")
+#              Label      model1      model2
+# 1       TOTAL_like 1058.150000 1080.350000
+# 2      Survey_like   -3.141660   -3.207830
+# 3 Length_comp_like  344.774000  365.853000
+# 4    Age_comp_like  808.718000  809.827000
+# 5 Parm_priors_like    0.354722    0.342573
+# 6      Bratio_2017    0.761776    0.763372
+
+SSplotComps(yt2, plot = FALSE, print = TRUE, subplots = 21, fleets = 3:4, maxrows = 1, pheight = 3, plotdir = "figures")
+file.rename("figures/comp_lenfit__aggregated_across_time.png", "figures/comp_lenfit__aggregated_across_time_mirror.png")
+SSplotComps(yt1, plot = FALSE, print = TRUE, subplots = 21, fleets = 3:4, maxrows = 1, pheight = 3, plotdir = "figures")
+
+SSplotComps(yt1, plot = FALSE, print = TRUE, subplots = 24, fleets = 3:4, plotdir = "figures")