Plots for individual groups

afsc-gap-products · Nov 8, 2024 · 8b4c183 · 8b4c183
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: esrindex
 Type: Package
 Title: Abundance index products for Alaska ESRs
 Version: 1.0.0
-Date: 2024-11-01
+Date: 2024-11-08
 Authors@R: c(person("Sean", "Rohan", email = "sean.rohan@noaa.gov", role = c("aut", "cre")),
           person("Thaddaeus", "Buser", email = "thaddaeus.buser@noaa.gov", role = "ctb"),
           person("Christina", "Conrath", email = "christina.conrath@noaa.gov", role = "ctb"),

diff --git a/NEWS b/NEWS
@@ -1,3 +1,12 @@
+esrindex 1.0.0 (November 8, 2024) - First production release
+----------------------------------------------------------------
+
+NEW FEATURES
+
+- plot_region_rema() makes individual timeseries plots for each
+  group.
+
+
 esrindex 0.1.4 (October 1, 2024)
 ----------------------------------------------------------------
 

diff --git a/R/plot_region_rema.R b/R/plot_region_rema.R
@@ -334,6 +334,239 @@ plot_region_rema <- function(x,
 
     plot_list[[ii]] <- p1
 
+    # Plots for individual groups
+    for(kk in 1:length(group_name)) {
+
+      sel_group_fit <- fit_dat[fit_dat$group_name == group_name[kk], ]
+
+      sel_group_obs <- obs_dat[obs_dat$group_name == group_name[kk], ]
+
+      sel_group_ts_summary <- ts_summary[ts_summary$group_name == group_name[kk], ]
+
+      if(error_bar & benchmarks == "none") {
+
+        p1 <- ggplot() +
+          geom_ribbon(data = sel_group_fit,
+                      mapping = aes(x = year,
+                                    ymin = pred_lci,
+                                    ymax = pred_uci),
+                      alpha = 0.3,
+                      fill = ribbon_fill) +
+          geom_errorbar(data = sel_group_obs,
+                        mapping = aes(x = YEAR,
+                                      ymin = BIOMASS_PLUS2_SD,
+                                      ymax = BIOMASS_MINUS2_SD), 
+                        width = 0.5,
+                        color = errorbar_color) +
+          geom_point(data = sel_group_obs,
+                     mapping = aes(x = YEAR, y = BIOMASS_MT),
+                     color = point_color) +
+          geom_path(data = sel_group_fit,
+                    mapping = aes(x = year, y = pred),
+                    color = timeseries_color,
+                    size = rel(1.1)) +
+          scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), 
+                             expand = expansion(mult = c(0, 0.05)), 
+                             labels = lab_fun(trim = lab_trim)) +
+          scale_x_continuous(name = "Year",
+                             breaks = year_breaks,
+                             labels = year_labels) +
+          expand_limits(y = y_axis_min) +
+          facet_wrap(~group_name[kk]) +
+          theme_blue_strip()
+
+      }
+
+      if(error_bar & benchmarks == "zscore") {
+
+        p1 <- ggplot() +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = z_mean),
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = plus1), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = minus1), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_ribbon(data = sel_group_fit,
+                      mapping = aes(x = year,
+                                    ymin = pred_lci,
+                                    ymax = pred_uci),
+                      alpha = 0.3,
+                      fill = ribbon_fill) +
+          geom_errorbar(data = sel_group_obs,
+                        mapping = aes(x = YEAR,
+                                      ymin = BIOMASS_PLUS2_SD,
+                                      ymax = BIOMASS_MINUS2_SD), 
+                        width = 0.5,
+                        color = errorbar_color) +
+          geom_path(data = sel_group_fit,
+                    mapping = aes(x = year, 
+                                  y = pred),
+                    color = timeseries_color,
+                    size = rel(1.1)) +
+          geom_point(data = sel_group_obs,
+                     mapping = aes(x = YEAR, y = BIOMASS_MT),
+                     color = point_color) +
+          scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), 
+                             expand = expansion(mult = c(0, 0.05)), 
+                             labels = lab_fun(trim = lab_trim)) +
+          scale_x_continuous(name = "Year",
+                             breaks = year_breaks,
+                             labels = year_labels) +
+          expand_limits(y = y_axis_min) +
+          facet_wrap(~group_name) +
+          theme_blue_strip()
+
+      }
+
+      if(!error_bar & benchmarks == "zscore") {
+        p1 <- ggplot() +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = z_mean)) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = plus1), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = minus1), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_ribbon(data = sel_group_fit,
+                      mapping = aes(x = year,
+                                    ymin = pred_lci,
+                                    ymax = pred_uci),
+                      alpha = 0.3,
+                      fill = ribbon_fill) +
+          geom_path(data = sel_group_fit,
+                    mapping = aes(x = year, y = pred),
+                    color = timeseries_color,
+                    size = rel(1.1)) +
+          geom_point(data = sel_group_obs,
+                     mapping = aes(x = YEAR, y = BIOMASS_MT),
+                     color = point_color) +
+          scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), 
+                             expand = expansion(mult = c(0, 0.05)), 
+                             labels = lab_fun(trim = lab_trim)) +
+          scale_x_continuous(name = "Year",
+                             breaks = year_breaks,
+                             labels = year_labels) +
+          expand_limits(y = y_axis_min) +
+          facet_wrap(~group_name) +
+          theme_blue_strip()
+      }
+
+
+      if(error_bar & benchmarks == "quantile") {
+
+        p1 <- ggplot() +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q50)) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q75), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q100), 
+                     linetype = 3,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q25), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q0), 
+                     linetype = 3,
+                     color = hline_color) +
+          geom_ribbon(data = sel_group_fit,
+                      mapping = aes(x = year,
+                                    ymin = pred_lci,
+                                    ymax = pred_uci),
+                      alpha = 0.3,
+                      fill = ribbon_fill) +
+          geom_path(data = sel_group_fit,
+                    mapping = aes(x = year, y = pred),
+                    color = timeseries_color,
+                    size = rel(1.1)) +
+          geom_point(data = sel_group_obs,
+                     mapping = aes(x = YEAR, y = BIOMASS_MT),
+                     color = point_color) +
+          scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), 
+                             expand = expansion(mult = c(0, 0.05)), 
+                             labels = lab_fun(trim = lab_trim)) +
+          scale_x_continuous(name = "Year",
+                             breaks = year_breaks,
+                             labels = year_labels) +
+          expand_limits(y = y_axis_min) +
+          facet_wrap(~group_name) +
+          theme_blue_strip()
+
+      }
+
+      if(!error_bar & benchmarks == "quantile") {
+        p1 <- ggplot() +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q50)) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q75), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q100), 
+                     linetype = 3,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q25), 
+                     linetype = 2,
+                     color = hline_color) +
+          geom_hline(data = sel_group_ts_summary,
+                     mapping = aes(yintercept = q0), 
+                     linetype = 3,
+                     color = hline_color) +
+          geom_ribbon(data = sel_group_fit,
+                      mapping = aes(x = year,
+                                    ymin = pred_lci,
+                                    ymax = pred_uci),
+                      alpha = 0.3,
+                      fill = ribbon_fill) +
+          geom_path(data = sel_group_fit,
+                    mapping = aes(x = year, y = pred),
+                    color = timeseries_color,
+                    size = rel(1.1)) +
+          geom_point(data = sel_group_obs,
+                     mapping = aes(x = YEAR, y = BIOMASS_MT),
+                     color = point_color) +
+          scale_y_continuous(name = paste0("Biomass Index (", set_unit, ")"), 
+                             expand = expansion(mult = c(0, 0.05)), 
+                             labels = lab_fun(trim = lab_trim)) +
+          scale_x_continuous(name = "Year",
+                             breaks = year_breaks,
+                             labels = year_labels) +
+          expand_limits(y = y_axis_min) +
+          facet_wrap(~group_name) +
+          theme_blue_strip()
+      }
+
+      suppressWarnings(dir.create(paste0("./plots/", region, "/plots_by_group"), recursive = TRUE))
+
+      grDevices::png(filename = paste0("./plots/", region, "/", "/plots_by_group/", region, "_rema_", 
+                                       gsub(x = indicator_name[ii], pattern = " ", replacement = "_"),
+                                       "_",
+                                       gsub(x = group_name[kk], pattern = " ", replacement = "_"),
+                                       "_full_region", append_filename, ".png"),
+                     width = 169,
+                     height = 60,
+                     units = "mm",
+                     res = 300)
+      print(p1)
+      grDevices::dev.off()
+
+
+    }
+
   }
 
   return(plot_list)

diff --git a/man/esrindex-package.Rd b/man/esrindex-package.Rd
diff --git a/plots/AI/AI_rema_forage_fish_full_region_ze.png b/plots/AI/AI_rema_forage_fish_full_region_ze.png
diff --git a/plots/AI/AI_rema_misc_species_full_region_ze.png b/plots/AI/AI_rema_misc_species_full_region_ze.png
diff --git a/plots/AI/AI_rema_structural_epifauna_full_region_ze.png b/plots/AI/AI_rema_structural_epifauna_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_forage_fish_Myctophids_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_forage_fish_Myctophids_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_jellyfish_Jellyfish_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_jellyfish_Jellyfish_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_misc_species_Eelpouts_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_misc_species_Eelpouts_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_misc_species_Poachers_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_misc_species_Poachers_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_misc_species_Sea_stars_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_misc_species_Sea_stars_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_misc_species_Shrimps_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_misc_species_Shrimps_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_structural_epifauna_Corals_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_structural_epifauna_Corals_full_region_ze.png
diff --git a/...s/AI/plots_by_group/AI_rema_structural_epifauna_Sea_anemones_full_region_ze.png b/...s/AI/plots_by_group/AI_rema_structural_epifauna_Sea_anemones_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_structural_epifauna_Sea_pens_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_structural_epifauna_Sea_pens_full_region_ze.png
diff --git a/plots/AI/plots_by_group/AI_rema_structural_epifauna_Sponges_full_region_ze.png b/plots/AI/plots_by_group/AI_rema_structural_epifauna_Sponges_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_jellyfish_Jellyfish_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_jellyfish_Jellyfish_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_misc_species_Eelpouts_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_misc_species_Eelpouts_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_misc_species_Poachers_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_misc_species_Poachers_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_misc_species_Sea_stars_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_misc_species_Sea_stars_full_region_ze.png
diff --git a/...EBS/plots_by_group/EBS_rema_structural_epifauna_Sea_anemones_full_region_ze.png b/...EBS/plots_by_group/EBS_rema_structural_epifauna_Sea_anemones_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_structural_epifauna_Sea_pens_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_structural_epifauna_Sea_pens_full_region_ze.png
diff --git a/plots/EBS/plots_by_group/EBS_rema_structural_epifauna_Sponges_full_region_ze.png b/plots/EBS/plots_by_group/EBS_rema_structural_epifauna_Sponges_full_region_ze.png
diff --git a/plots/GOA/GOA_rema_forage_fish_full_region_ze.png b/plots/GOA/GOA_rema_forage_fish_full_region_ze.png
diff --git a/plots/GOA/GOA_rema_misc_species_full_region_ze.png b/plots/GOA/GOA_rema_misc_species_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Capelin_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Capelin_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Eulachon_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Eulachon_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Myctophids_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Myctophids_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pacific_herring_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pacific_herring_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pacific_sandfish_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pacific_sandfish_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pricklebacks_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Pricklebacks_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_forage_fish_Sandlances_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_forage_fish_Sandlances_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_jellyfish_Jellyfish_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_jellyfish_Jellyfish_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_misc_species_Eelpouts_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_misc_species_Eelpouts_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_misc_species_Poachers_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_misc_species_Poachers_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_misc_species_Sea_stars_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_misc_species_Sea_stars_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_misc_species_Shrimps_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_misc_species_Shrimps_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Corals_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Corals_full_region_ze.png
diff --git a/...GOA/plots_by_group/GOA_rema_structural_epifauna_Sea_anemones_full_region_ze.png b/...GOA/plots_by_group/GOA_rema_structural_epifauna_Sea_anemones_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Sea_pens_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Sea_pens_full_region_ze.png
diff --git a/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Sponges_full_region_ze.png b/plots/GOA/plots_by_group/GOA_rema_structural_epifauna_Sponges_full_region_ze.png
diff --git a/plots/NBS/plots_by_group/NBS_rema_jellyfish_Jellyfish_full_region_ze.png b/plots/NBS/plots_by_group/NBS_rema_jellyfish_Jellyfish_full_region_ze.png
diff --git a/plots/NBS/plots_by_group/NBS_rema_misc_species_Eelpouts_full_region_ze.png b/plots/NBS/plots_by_group/NBS_rema_misc_species_Eelpouts_full_region_ze.png
diff --git a/plots/NBS/plots_by_group/NBS_rema_misc_species_Poachers_full_region_ze.png b/plots/NBS/plots_by_group/NBS_rema_misc_species_Poachers_full_region_ze.png
diff --git a/plots/NBS/plots_by_group/NBS_rema_misc_species_Sea_stars_full_region_ze.png b/plots/NBS/plots_by_group/NBS_rema_misc_species_Sea_stars_full_region_ze.png
diff --git a/...NBS/plots_by_group/NBS_rema_structural_epifauna_Sea_anemones_full_region_ze.png b/...NBS/plots_by_group/NBS_rema_structural_epifauna_Sea_anemones_full_region_ze.png
diff --git a/plots/NBS/plots_by_group/NBS_rema_structural_epifauna_Sponges_full_region_ze.png b/plots/NBS/plots_by_group/NBS_rema_structural_epifauna_Sponges_full_region_ze.png