Merge branch 'main' of https://github.com/pfmc-assessments/yellowtail…

…_2025

Rscripts/explore_indices.R

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+# load new triennial index run with indexwc/sdmTMB
+tri_new <- read.csv("\\\\nwcfile/fram/Assessments/CurrentAssessments/yellowtail_rockfish_north/data/surveys/triennial/delta_gamma/index/est_by_area.csv")
+# repurpose area column to indicate which model run
+tri_new <- tri_new |> 
+  dplyr::filter(area == "North of Cape Mendocino") |> 
+  dplyr::mutate(area = "new indexwc")
+
+# load old model (3.30.23 version separates input and adjusted SE in output)
+yt1 <- SS_output("Model_Runs/base_2017_3.30.23")
+# format old model index to match indexwc output
+tri_old <- yt1$cpue |> 
+  dplyr::filter(Fleet_name == "Triennial" & Use == 1) |> 
+  dplyr::select(Yr, Obs, SE_input) |> 
+  dplyr::mutate(area = "old VAST from 2017", .before = "Yr") |> 
+  dplyr::rename(year = "Yr", est = Obs, se = SE_input) |> 
+  dplyr::mutate(
+    lwr = qlnorm(p = 0.025, meanlog = log(est), sdlog = se),
+    upr = qlnorm(p = 0.975, meanlog = log(est), sdlog = se),
+    log_est = log(est),
+    .before = "se"
+  ) |> 
+  dplyr::mutate(type = "index")
+
+# use indexwc function
+index_compare <- indexwc::plot_indices(rbind(tri_new, tri_old)) + 
+  ggplot2::scale_color_discrete()  # viridis default yellow was too pale
+# replace file saved by indexwc::plot_indices() with viridis colors
+ggsave("figures/index_comparisons_triennial_sdmTMB_vs_VAST.png")