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Gulf-IEA · Oct 18, 2024 · 2bb2a35 · 2bb2a35
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diff --git a/.quarto/cites/index.json b/.quarto/cites/index.json
@@ -1 +1 @@
-{"Report_book_files\\Performance_indicators.qmd":[],"index.qmd":[],"Report_book_files\\Report4.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"OA.qmd":[],"Lab-report\\OA.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"Report_book_files\\FMP_objectives.qmd":[]}
+{"Report_book_files\\Performance_indicators.qmd":[],"Lab-report\\OA.qmd":[],"Report_book_files\\Report4.qmd":[],"index.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"OA.qmd":[],"Report_book_files\\FMP_objectives.qmd":[]}
diff --git a/Average maximum length of catch.png b/Average maximum length of catch.png
diff --git a/_book/Report_book_files/Performance_indicators.html b/_book/Report_book_files/Performance_indicators.html
diff --git a/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_Puerto Rico East.png b/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_Puerto Rico East.png
diff --git a/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_Puerto Rico West.png b/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_Puerto Rico West.png
diff --git a/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_St. Croix.png b/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_St. Croix.png
diff --git a/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_St. Thomas & St. John.png b/_book/indicator_plots/CSVI_plots/Faceted_Bar_Plot_St. Thomas & St. John.png
diff --git a/_book/indicator_plots/FRsection_plot_final.png b/_book/indicator_plots/FRsection_plot_final.png
diff --git a/_book/indicator_plots/GDP_plot_final.png b/_book/indicator_plots/GDP_plot_final.png
diff --git a/_book/indicator_plots/PD_ratio_plot_final.png b/_book/indicator_plots/PD_ratio_plot_final.png
diff --git a/_book/indicator_plots/PR_Lmax_classes_plot_final.png b/_book/indicator_plots/PR_Lmax_classes_plot_final.png
diff --git a/_book/indicator_plots/RVC_PR_plot_final.png b/_book/indicator_plots/RVC_PR_plot_final.png
diff --git a/_book/indicator_plots/RVC_STSJ_plot_final.png b/_book/indicator_plots/RVC_STSJ_plot_final.png
diff --git a/_book/indicator_plots/RVC_STX_plot_final.png b/_book/indicator_plots/RVC_STX_plot_final.png
diff --git a/_book/indicator_plots/STT_Lmax_classes_plot_final.png b/_book/indicator_plots/STT_Lmax_classes_plot_final.png
diff --git a/_book/indicator_plots/STX_Lmax_classes_plot_final.png b/_book/indicator_plots/STX_Lmax_classes_plot_final.png
diff --git a/_book/indicator_plots/coral_spprichness_cover_plot_final.png b/_book/indicator_plots/coral_spprichness_cover_plot_final.png
diff --git a/_book/indicator_plots/cruise_plot_final.png b/_book/indicator_plots/cruise_plot_final.png
diff --git a/_book/indicator_plots/enforcement_plot_final.png b/_book/indicator_plots/enforcement_plot_final.png
diff --git a/_book/indicator_plots/fish_density_plot_final.png b/_book/indicator_plots/fish_density_plot_final.png
diff --git a/_book/indicator_plots/gearTypes_PR.png b/_book/indicator_plots/gearTypes_PR.png
diff --git a/_book/indicator_plots/gearTypes_STT.png b/_book/indicator_plots/gearTypes_STT.png
diff --git a/_book/indicator_plots/gearTypes_STX.png b/_book/indicator_plots/gearTypes_STX.png
diff --git a/_book/indicator_plots/gini_plot_final.png b/_book/indicator_plots/gini_plot_final.png
diff --git a/_book/indicator_plots/marine_debris_plot_final.png b/_book/indicator_plots/marine_debris_plot_final.png
diff --git a/_book/indicator_plots/oceanNAICS_plot_final.png b/_book/indicator_plots/oceanNAICS_plot_final.png
diff --git a/_book/indicator_plots/outreach_plot_final.png b/_book/indicator_plots/outreach_plot_final.png
diff --git a/_book/indicator_plots/per_landings_PR.png b/_book/indicator_plots/per_landings_PR.png
diff --git a/_book/indicator_plots/per_landings_STT.png b/_book/indicator_plots/per_landings_STT.png
diff --git a/_book/indicator_plots/per_landings_STX.png b/_book/indicator_plots/per_landings_STX.png
diff --git a/_book/indicator_plots/pollution_plot_final.png b/_book/indicator_plots/pollution_plot_final.png
diff --git a/_book/indicator_plots/population_plot_final.png b/_book/indicator_plots/population_plot_final.png
diff --git a/_book/indicator_plots/prop_diving_trips_plot_final.png b/_book/indicator_plots/prop_diving_trips_plot_final.png
diff --git a/_book/indicator_plots/tier3_plot_final.png b/_book/indicator_plots/tier3_plot_final.png
diff --git a/_book/indicator_plots/total_landings_plot_final.png b/_book/indicator_plots/total_landings_plot_final.png
diff --git a/_book/indicator_plots/total_rec_catch_plot_final.png b/_book/indicator_plots/total_rec_catch_plot_final.png
diff --git a/_book/indicator_plots/unemployment_plot_final.png b/_book/indicator_plots/unemployment_plot_final.png
diff --git a/_book/search.json b/_book/search.json
@@ -8,5 +8,85 @@
     "crumbs": [
       "<span class='chapter-number'>4</span>  <span class='chapter-title'>4. Risks to meeting fishery management objectives</span>"
     ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html",
+    "href": "Report_book_files/Performance_indicators.html",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "",
+    "text": "5.1 Food production",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#food-production",
+    "href": "Report_book_files/Performance_indicators.html#food-production",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "",
+    "text": "Fishery independent surveys of economically important species\nIndicator 16 - abundance of economically important fish\n\n\n\nRVC PR\n\n\n\n\n\nRVC STSJ\n\n\n\n\n\nRVC STX\n\n\nIndicator 17 - abundance of commercial fish and slope of the size spectrum based on TCRMP and PRCRMP\n\n\n\nfish density\n\n\n\n\nPelagic:demersal ratio\nIndicator 18\n\n\n\nPD ratio\n\n\n\n\nMaximum length and size structure\nIndicator 19 - Lmax indicator\n\n\n\nPR Lmax\n\n\n\n\n\nSTT Lmax\n\n\n\n\n\nSTX Lmax\n\n\n\n\nCommercial landings\nIndicator 20 - total landings\n\n\n\nTotal landings",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#socioeconomic-health",
+    "href": "Report_book_files/Performance_indicators.html#socioeconomic-health",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.2 Socioeconomic health",
+    "text": "5.2 Socioeconomic health\n\nTotal, lobster and conch revenues\nIndicator 21 - percent revenues by species group\n  \n\n\nTotal, lobster and conch trips\nIndicator 22 - number of trips\n  \n\n\nOcean economy establishments, employment, and wages\nIndicator 23\n\n\n\nOcean economy\n\n\n\n\nGDP\nIndicator 24\n\n\n\nGDP\n\n\n\n\nUnemployment\nIndicator 25\n\n\n\nUnemployment",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#equity",
+    "href": "Report_book_files/Performance_indicators.html#equity",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.3 Equity",
+    "text": "5.3 Equity\n\nGini coefficient for distribution of landings and revenue\nIndicator 26\n\n\n\nGini coefficient\n\n\n\n\nEnvironmental justice, economic, and gentrification pressure\nIndicator 27",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#engagement-and-participation",
+    "href": "Report_book_files/Performance_indicators.html#engagement-and-participation",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.4 Engagement and participation",
+    "text": "5.4 Engagement and participation\n\nRecreational landings\nIndicator 28\n\n\n\nRec catch\n\n\n\n\nCommercial fishing engagement and reliance\nIndicator 29",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#bycatch-reduction",
+    "href": "Report_book_files/Performance_indicators.html#bycatch-reduction",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.5 Bycatch reduction",
+    "text": "5.5 Bycatch reduction\n\nChanges in gear type\nIndicator 30\n  \n\n\n\ndiving trips\n\n\n\n\n\nNon-selective gears",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#governance",
+    "href": "Report_book_files/Performance_indicators.html#governance",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.5 Governance",
+    "text": "5.5 Governance\n\nNumber of new regulations\nIndicator 31\n\n\n\nRegulations\n\n\n\n\nPercent of species with informative catch limits\nIndicator 32\n\n\n\nTier 3 plot\n\n\n\n\nNumber of education and outreach events\nIndicator 33\n\n\n\nOutreach\n\n\n\n\nNumber of enforcement actions\nIndicator 34\n\n\n\nEnforcement",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
+  },
+  {
+    "objectID": "Report_book_files/Performance_indicators.html#protection-of-ecosystems",
+    "href": "Report_book_files/Performance_indicators.html#protection-of-ecosystems",
+    "title": "5. Tracking performance toward fishery management objectives",
+    "section": "5.6 Protection of ecosystems",
+    "text": "5.6 Protection of ecosystems\n\nPercent coral cover and coral species diversity\nIndicator 35\n\n\n\nCoral",
+    "crumbs": [
+      "<span class='chapter-number'>5</span>  <span class='chapter-title'>5. Tracking performance toward fishery management objectives</span>"
+    ]
   }
 ]
diff --git a/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_PR.RData b/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_PR.RData
diff --git a/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_STT.RData b/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_STT.RData
diff --git a/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_STX.RData b/indicator_data/intermediateFiles/fish-dep-indicators/Lmax_STX.RData
diff --git a/indicator_objects/PD_ratio.RData b/indicator_objects/PD_ratio.RData
diff --git a/indicator_objects/PR_Lmax_classes.RData b/indicator_objects/PR_Lmax_classes.RData
diff --git a/indicator_objects/STT_Lmax_classes.RData b/indicator_objects/STT_Lmax_classes.RData
diff --git a/indicator_objects/STX_Lmax_classes.RData b/indicator_objects/STX_Lmax_classes.RData
diff --git a/indicator_objects/disturbance.RData b/indicator_objects/disturbance.RData
diff --git a/indicator_objects/gini_revenue.RData b/indicator_objects/gini_revenue.RData
diff --git a/indicator_objects/mean_Lmax.RData b/indicator_objects/mean_Lmax.RData
diff --git a/indicator_objects/prop_diving_trips.RData b/indicator_objects/prop_diving_trips.RData
diff --git a/indicator_objects/prop_trips_bycatch.RData b/indicator_objects/prop_trips_bycatch.RData
diff --git a/indicator_objects_old/ACEindex.RData b/indicator_objects_old/ACEindex.RData
diff --git a/indicator_objects_old/Carib_SST.RData b/indicator_objects_old/Carib_SST.RData
diff --git a/indicator_objects_old/DegreeHeatingWeeks.RData b/indicator_objects_old/DegreeHeatingWeeks.RData
diff --git a/indicator_objects_old/FRsection.RData b/indicator_objects_old/FRsection.RData
diff --git a/indicator_objects_old/GDP.RData b/indicator_objects_old/GDP.RData
diff --git a/indicator_objects_old/OA.RData b/indicator_objects_old/OA.RData
diff --git a/indicator_objects_old/PD_ratio.RData b/indicator_objects_old/PD_ratio.RData
diff --git a/indicator_objects_old/PR_Lmax_classes.RData b/indicator_objects_old/PR_Lmax_classes.RData
diff --git a/indicator_objects_old/PR_mean_Lmax.RData b/indicator_objects_old/PR_mean_Lmax.RData
diff --git a/indicator_objects_old/RVC_PR.RData b/indicator_objects_old/RVC_PR.RData
diff --git a/indicator_objects_old/RVC_STSJ.RData b/indicator_objects_old/RVC_STSJ.RData
diff --git a/indicator_objects_old/RVC_STX.RData b/indicator_objects_old/RVC_STX.RData
diff --git a/indicator_objects_old/STT_Lmax_classes.RData b/indicator_objects_old/STT_Lmax_classes.RData
diff --git a/indicator_objects_old/STX_Lmax_classes.RData b/indicator_objects_old/STX_Lmax_classes.RData
diff --git a/indicator_objects_old/Sargassum.RData b/indicator_objects_old/Sargassum.RData
diff --git a/indicator_objects_old/avgLmax.RData b/indicator_objects_old/avgLmax.RData
diff --git a/indicator_objects_old/carib_Chl.RData b/indicator_objects_old/carib_Chl.RData
diff --git a/indicator_objects_old/coral_spprichness_cover.RData b/indicator_objects_old/coral_spprichness_cover.RData
diff --git a/indicator_objects_old/cruise.RData b/indicator_objects_old/cruise.RData
diff --git a/indicator_objects_old/disturbance.RData b/indicator_objects_old/disturbance.RData
diff --git a/indicator_objects_old/earthquakes.RData b/indicator_objects_old/earthquakes.RData
diff --git a/indicator_objects_old/enforcement.RData b/indicator_objects_old/enforcement.RData
diff --git a/indicator_objects_old/fish_density.RData b/indicator_objects_old/fish_density.RData
diff --git a/indicator_objects_old/gini.RData b/indicator_objects_old/gini.RData
diff --git a/indicator_objects_old/gini_landings.RData b/indicator_objects_old/gini_landings.RData
diff --git a/indicator_objects_old/gini_revenue.RData b/indicator_objects_old/gini_revenue.RData
diff --git a/indicator_objects_old/marine_debris.RData b/indicator_objects_old/marine_debris.RData
diff --git a/indicator_objects_old/mean_Lmax.RData b/indicator_objects_old/mean_Lmax.RData
diff --git a/indicator_objects_old/oceanNAICS.RData b/indicator_objects_old/oceanNAICS.RData
diff --git a/indicator_objects_old/outreach.RData b/indicator_objects_old/outreach.RData
diff --git a/indicator_objects_old/pollution.RData b/indicator_objects_old/pollution.RData
diff --git a/indicator_objects_old/population.RData b/indicator_objects_old/population.RData
diff --git a/indicator_objects_old/prop_diving_trips.RData b/indicator_objects_old/prop_diving_trips.RData
diff --git a/indicator_objects_old/prop_trips_bycatch.RData b/indicator_objects_old/prop_trips_bycatch.RData
diff --git a/indicator_objects_old/regulations.RData b/indicator_objects_old/regulations.RData
diff --git a/indicator_objects_old/tier3.RData b/indicator_objects_old/tier3.RData
diff --git a/indicator_objects_old/total_landings.RData b/indicator_objects_old/total_landings.RData
diff --git a/indicator_objects_old/total_rec_catch.RData b/indicator_objects_old/total_rec_catch.RData
diff --git a/indicator_objects_old/turbidity.RData b/indicator_objects_old/turbidity.RData
diff --git a/indicator_objects_old/unemployment.RData b/indicator_objects_old/unemployment.RData
diff --git a/indicator_plots/ACEindex_plot_final.png b/indicator_plots/ACEindex_plot_final.png
diff --git a/indicator_plots/Carib_SST_plot_final.png b/indicator_plots/Carib_SST_plot_final.png
diff --git a/indicator_plots/DegreeHeatingWeeks_plot_final.png b/indicator_plots/DegreeHeatingWeeks_plot_final.png
diff --git a/indicator_plots/FRsection_plot_final.png b/indicator_plots/FRsection_plot_final.png
diff --git a/indicator_plots/GDP_plot_final.png b/indicator_plots/GDP_plot_final.png
diff --git a/indicator_plots/NMDSgear_PR.png b/indicator_plots/NMDSgear_PR.png
diff --git a/indicator_plots/OA_plot_final.png b/indicator_plots/OA_plot_final.png
diff --git a/indicator_plots/PD_ratio_plot_final.png b/indicator_plots/PD_ratio_plot_final.png
diff --git a/indicator_plots/PR_Lmax_classes_plot_final.png b/indicator_plots/PR_Lmax_classes_plot_final.png
diff --git a/indicator_plots/RVC_PR_plot_final.png b/indicator_plots/RVC_PR_plot_final.png
diff --git a/indicator_plots/RVC_STSJ_plot_final.png b/indicator_plots/RVC_STSJ_plot_final.png
diff --git a/indicator_plots/RVC_STX_plot_final.png b/indicator_plots/RVC_STX_plot_final.png
diff --git a/indicator_plots/STT_Lmax_classes_plot_final.png b/indicator_plots/STT_Lmax_classes_plot_final.png
diff --git a/indicator_plots/STX_Lmax_classes_plot_final.png b/indicator_plots/STX_Lmax_classes_plot_final.png
diff --git a/indicator_plots/Sargassum_plot_final.png b/indicator_plots/Sargassum_plot_final.png
diff --git a/indicator_plots/avgLmax_plot_final.png b/indicator_plots/avgLmax_plot_final.png
diff --git a/indicator_plots/carib_Chl_plot_final.png b/indicator_plots/carib_Chl_plot_final.png
diff --git a/indicator_plots/coral_spprichness_cover_plot_final.png b/indicator_plots/coral_spprichness_cover_plot_final.png
diff --git a/indicator_plots/cruise_plot_final.png b/indicator_plots/cruise_plot_final.png
diff --git a/indicator_plots/disturbance_plot_final.png b/indicator_plots/disturbance_plot_final.png
diff --git a/indicator_plots/earthquakes_plot_final.png b/indicator_plots/earthquakes_plot_final.png
diff --git a/indicator_plots/enforcement_plot_final.png b/indicator_plots/enforcement_plot_final.png
diff --git a/indicator_plots/fish_density_plot_final.png b/indicator_plots/fish_density_plot_final.png
diff --git a/indicator_plots/gearTypes_PR.png b/indicator_plots/gearTypes_PR.png
diff --git a/indicator_plots/gini_plot_final.png b/indicator_plots/gini_plot_final.png
diff --git a/indicator_plots/marine_debris_plot_final.png b/indicator_plots/marine_debris_plot_final.png
diff --git a/indicator_plots/oceanNAICS_plot_final.png b/indicator_plots/oceanNAICS_plot_final.png
diff --git a/indicator_plots/outreach_plot_final.png b/indicator_plots/outreach_plot_final.png
diff --git a/indicator_plots/per_landings_PR.png b/indicator_plots/per_landings_PR.png
diff --git a/indicator_plots/per_landings_STT.png b/indicator_plots/per_landings_STT.png
diff --git a/indicator_plots/per_landings_STX.png b/indicator_plots/per_landings_STX.png
diff --git a/indicator_plots/pollution_plot_final.png b/indicator_plots/pollution_plot_final.png
diff --git a/indicator_plots/population_plot_final.png b/indicator_plots/population_plot_final.png
diff --git a/indicator_plots/prop_diving_trips_plot_final.png b/indicator_plots/prop_diving_trips_plot_final.png
diff --git a/indicator_plots/prop_trips_bycatch_plot_final.png b/indicator_plots/prop_trips_bycatch_plot_final.png
diff --git a/indicator_plots/tier3_plot_final.png b/indicator_plots/tier3_plot_final.png
diff --git a/indicator_plots/total_landings_plot_final.png b/indicator_plots/total_landings_plot_final.png
diff --git a/indicator_plots/total_rec_catch_plot_final.png b/indicator_plots/total_rec_catch_plot_final.png
diff --git a/indicator_plots/turbidity_plot_final.png b/indicator_plots/turbidity_plot_final.png
diff --git a/indicator_plots/unemployment_plot_final.png b/indicator_plots/unemployment_plot_final.png
diff --git a/indicator_processing/CalculateAllIndicators.R b/indicator_processing/CalculateAllIndicators.R
@@ -5,8 +5,28 @@
 # load libraries ---------------------------------
 rm(list = ls())
 
+packages = c("data.table", "dplyr", "ggplot2", "ggrepel", "httr", "jsonlite", "lubridate", 
+             "maps", "pals", "pdftools", "plotTimeSeries", "readr", "readxl", "rerddap", "rvest", 
+              "stringr", "tidyr", "vegan", "xml2", "modi", "devtools")
+
+## Now load or install & load all
+package.check <- lapply(
+  packages,
+  FUN = function(x) {
+    if (!require(x, character.only = TRUE)) {
+      install.packages(x, dependencies = TRUE)
+      library(x, character.only = TRUE)
+    }
+  }
+)
+
+devtools::install_github('jeremiaheb/rvc')
+library(rvc)
+install_github("MandyKarnauskas-NOAA/plotTimeSeries")
 library(plotTimeSeries)
 
+search()
+
 #  find root directory for project ---------------
 
 directory <- rprojroot::find_rstudio_root_file()

diff --git a/indicator_processing/PlotAllIndicators.R b/indicator_processing/PlotAllIndicators.R
@@ -45,10 +45,10 @@ dev.off()
 
 ### 6 - marine debris
 
-png(filename = "indicator_plots/marine_debris_plot_final.png", width = 10, height = 4, units = "in", res = 300)
-load("indicator_objects/marine_debris.RData")
-plotIndicatorTimeSeries(ind, coltoplot = 1, plotrownum = 1, plotcolnum = 1, trendAnalysis = FALSE, dateformat = "%b%Y", sublabel = F, widadj = 1, hgtadj = 1, anom = "none", yposadj = 1, cex.axis = 1, cex.lab = 1, cex.main = 1)
-dev.off()
+#png(filename = "indicator_plots/marine_debris_plot_final.png", width = 10, height = 4, units = "in", res = 300)
+#load("indicator_objects/marine_debris.RData")
+#plotIndicatorTimeSeries(ind, coltoplot = 1, plotrownum = 1, plotcolnum = 1, trendAnalysis = FALSE, dateformat = "%b%Y", sublabel = F, widadj = 1, hgtadj = 1, anom = "none", yposadj = 1, cex.axis = 1, cex.lab = 1, cex.main = 1)
+#dev.off()
 
 ### 7 - identified point source pollution sites
 
@@ -141,7 +141,7 @@ dev.off()
 ### 19 - Lmax indicator
 
 png(filename = "indicator_plots/avgLmax_plot_final.png", width = 7, height = 6, units = "in", res = 300)
-load("indicator_objects/avgLmax.RData")
+load("indicator_objects/mean_Lmax.RData")
 plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, plotcolnum = 1, trendAnalysis = TRUE, dateformat = "%b%Y", sublabel = TRUE, widadj = 1, hgtadj = 0.5, anom = "none", yposadj = 1, sameYscale = TRUE, cex.axis = 1.2, cex.lab = 1.4, cex.main = 1.5)
 dev.off()
 
@@ -199,7 +199,7 @@ dev.off()
 ### 26 - Gini coefficient
 
 png(filename = "indicator_plots/gini_plot_final.png", width = 7, height = 8, units = "in", res = 300)
-load("indicator_objects/gini.RData")
+load("indicator_objects/gini_revenue.RData")
 plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, plotcolnum = 1, trendAnalysis = TRUE, dateformat = "%b%Y", sublabel = TRUE, widadj = 1, hgtadj = 0.5, anom = "none", yposadj = 1.2, cex.axis = 1.2, cex.lab = 1.5, cex.main = 1.6, sameYscale = TRUE)
 dev.off()
 

diff --git a/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_PR.R b/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_PR.R
@@ -296,10 +296,39 @@ plotIndicatorTimeSeries(s, coltoplot = 1:3,plotrownum = 3, sublabel = T, widadj
 
 dev.off()
 
+# figure out what is going on in 2018 with spike in pelagics -------------------
+
+# plot(styear:enyear, pdrat, type = "b", las = 2, pch = 19)
+# matplot(styear:enyear, pd, axes = F, type = "b", pch = 19)
+# axis(1, at = styear:enyear, las = 2)
+# 
+# tabp <- tab[grep("pelagic", splisref$PD), ]
+# tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
+# 
+# matplot(styear:enyear, t(tabp[1:10, ]), type = "l", col = glasbey(10), lwd = 2, lty = 1)
+# legend("topright", rownames(tabp)[1:10], col = glasbey(10), lwd = 2, lty = 1)
+# abline(v = c(2008, 2019))  # driven ~50% by dolphinfish catch
+# 
+# tabd <- tab[-grep("pelagic", splisref$PD), ]
+# tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
+# 
+# matplot(styear:enyear, t(tabd[1:10, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
+# legend("topright", rownames(tabd)[1:10], col = glasbey(10), lwd = 2, lty = 1)
+# abline(v = c(2008, 2019))
+# 
+
 #######################  END P:D ratio  ################################
 
 # Lmax calculations -----------------------------------------
 
+# based on feedback from seminar -- calculate Lmax based on demersals only
+
+table(dbf$PD, useNA = "always")
+table(dbf$PD2, useNA = "always")
+dbf <- dbf[which(dbf$PD2 == "demersal"), ]
+dim(dbf)
+head(dbf)
+
 tab <- tapply(dbf$ADJUSTED_POUNDS, list(dbf$ITIS_SCIENTIFIC_NAME, dbf$YEAR_LANDED), sum, na.rm = T)
 tab[is.na(tab)] <- 0
 tab
@@ -364,6 +393,9 @@ sort(table(splisref$famcode[which(splisref$Lmax_cat == "(100,200]")]))
 
 splisref$recLand <- rowSums(tab)
 
+sm <- splisref[which(splisref$Lmax_cat == "(40,60]"), ]
+head(sm[order(sm$recLand, decreasing = T), ], 15)
+
 plate <- splisref[which(splisref$Lmax_cat == "(60,100]"), ]
 head(plate[order(plate$recLand, decreasing = T), ], 15)
 # the 60-100cm category is mostly driven by deepwater snapper species, also yellowtail, hogfish and red hind
@@ -422,26 +454,6 @@ findat <- data.frame(cbind(styear:enyear, lmax))
 
 save(findat, file = "indicator_data/intermediateFiles/fish-dep-indicators/Lmax_PR.RData")
 
-
-
-# figure out what is going on in 2018 with spike in pelagics -------------------
-
-plot(styear:enyear, pdrat, type = "b", las = 2, pch = 19)
-matplot(styear:enyear, pd, axes = F, type = "b", pch = 19)
-axis(1, at = styear:enyear, las = 2)
-
-tabp <- tab[grep("pelagic", splisref$PD), ]
-tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
-
-matplot(styear:enyear, t(tabp[1:10, ]), type = "l", col = glasbey(10), lwd = 2, lty = 1)
-legend("topright", rownames(tabp)[1:10], col = glasbey(10), lwd = 2, lty = 1)
-abline(v = c(2008, 2019))  # driven ~50% by dolphinfish catch
-
-tabd <- tab[-grep("pelagic", splisref$PD), ]
-tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
-
-matplot(styear:enyear, t(tabd[1:10, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
-legend("topright", rownames(tabd)[1:10], col = glasbey(10), lwd = 2, lty = 1)
-abline(v = c(2008, 2019))
+#############  END  ######################
 
 print("PR indicators -- SUCCESSFULLY RUN")
diff --git a/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STT.R b/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STT.R
@@ -247,6 +247,14 @@ dev.off()
 
 # Lmax calculations -----------------------------------------
 
+# based on feedback from seminar -- calculate Lmax based on demersals only
+
+table(dbf$PD, useNA = "always")
+table(dbf$PD2, useNA = "always")
+dbf <- dbf[which(dbf$PD2 == "demersal"), ]
+dim(dbf)
+head(dbf)
+
 tab <- tapply(dbf$POUNDS_LANDED, list(dbf$SPECIES_NM, dbf$TRIP_YEAR), sum, na.rm = T)
 tab[is.na(tab)] <- 0
 
@@ -324,6 +332,11 @@ big <- splisref[which(splisref$Lmax_cat == "(100,200]"), ]
 head(big[order(big$recLand, decreasing = T), ], 15)
 # mainly tunas and mackerels, also red grouper
 
+xl <- splisref[which(splisref$Lmax_cat == "(200,2e+03]"), ]
+head(xl[order(xl$recLand, decreasing = T), ], 15)
+# mainly tunas and mackerels, also red grouper
+
+
 # calculate average Lmax indicator -----------------------------------------------
 
 # formula from https://www.sciencedirect.com/science/article/pii/135223109400210C
@@ -360,7 +373,7 @@ indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
 s <- list(labels = indnames, indicators = inddata, datelist = datdata, ulim = inddata + lmax_sem, llim = inddata - lmax_sem)
 class(s) <- "indicatordata"
 
-plotIndicatorTimeSeries(s, coltoplot = 1, sublabel = T, outtype = "png", widadj = 1.65, hgtadj = 0.6)
+plotIndicatorTimeSeries(s, coltoplot = 1, sublabel = T, widadj = 1.65, hgtadj = 0.6)
 
 dev.off()
 
@@ -369,23 +382,23 @@ findat <- data.frame(cbind(yrs, lmax))
 save(findat, file = "indicator_data/intermediateFiles/fish-dep-indicators/Lmax_STT.RData")
 
 # figure out what is going on in 2018 with spike in pelagics -------------------
-
-plot(yrs, pdrat, type = "b", las = 2)
-matplot(yrs, pd, axes = F, type = "b")
-axis(1, at = yrs, las = 2)
-
-tabp <- tab[grep("pelagic", splisref$PD), ]
-tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
-
-matplot(yrs, t(tabp[1:10, ]), type = "l", col = glasbey(10), lwd = 2, lty = 1)
-legend("topleft", rownames(tabp)[1:20], col = glasbey(10), lwd = 2, lty = 1, cex = 0.7)
-# pelagic catch influenced by dolphinfish and tunas
-
-tabd <- tab[-grep("pelagic", splisref$PD), ]
-tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
-
-matplot(yrs, t(tabd[1:20, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
-legend("topright", rownames(tabd)[1:20], col = glasbey(10), lwd = 2, lty = 1)
+# 
+# plot(yrs, pdrat, type = "b", las = 2)
+# matplot(yrs, pd, axes = F, type = "b")
+# axis(1, at = yrs, las = 2)
+# 
+# tabp <- tab[grep("pelagic", splisref$PD), ]
+# tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
+# 
+# matplot(yrs, t(tabp[1:10, ]), type = "l", col = glasbey(10), lwd = 2, lty = 1)
+# legend("topleft", rownames(tabp)[1:20], col = glasbey(10), lwd = 2, lty = 1, cex = 0.7)
+# # pelagic catch influenced by dolphinfish and tunas
+# 
+# tabd <- tab[-grep("pelagic", splisref$PD), ]
+# tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
+# 
+# matplot(yrs, t(tabd[1:20, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
+# legend("topright", rownames(tabd)[1:20], col = glasbey(10), lwd = 2, lty = 1)
 
 ##############  END  ########################
 

diff --git a/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STX.R b/indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STX.R
@@ -248,6 +248,14 @@ dev.off()
 
 # Lmax calculations -----------------------------------------
 
+# based on feedback from seminar -- calculate Lmax based on demersals only
+
+table(dbf$PD, useNA = "always")
+table(dbf$PD2, useNA = "always")
+dbf <- dbf[which(dbf$PD2 == "demersal"), ]
+dim(dbf)
+head(dbf)
+
 tab <- tapply(dbf$POUNDS_LANDED, list(dbf$SPECIES_NM, dbf$TRIP_YEAR), sum, na.rm = T)
 tab[is.na(tab)] <- 0
 
@@ -316,7 +324,7 @@ small <- splisref[which(splisref$Lmax_cat == "(0,40]"), ]
 head(small[order(small$recLand, decreasing = T), ], 15)
 #driven by redband parrotfish and princess parrotfish.  also herrings and surgeonfishes
 
-plate <- splisref[which(splisref$Lmax_cat == "(60,100]"), ]
+plate <- splisref[which(splisref$Lmax_cat == "(40,60]"), ]
 head(plate[order(plate$recLand, decreasing = T), ], 15)
 # mainly stoplight and queen parrotfishes.  Also blackfin and silk snapper and red hind
 
@@ -374,20 +382,20 @@ save(findat, file = "indicator_data/intermediateFiles/fish-dep-indicators/Lmax_S
 
 # look at what is driving PD ratio  -------------------
 
-plot(yrs, pdrat, type = "b", las = 2)
-matplot(yrs, pd, axes = F, type = "b")
-axis(1, at = yrs, las = 2)
-
-tabp <- tab[grep("pelagic", splisref$PD), ]
-tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
-
-matplot(yrs, t(tabp), type = "l", col = glasbey(10), lwd = 2, lty = 1)
-legend("topleft", rownames(tabp), col = glasbey(10), lwd = 2, lty = 1, cex = 0.7)
-
-tabd <- tab[-grep("pelagic", splisref$PD), ]
-tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
-
-matplot(yrs, t(tabd[1:20, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
-legend("topright", rownames(tabd)[1:20], col = glasbey(10), lwd = 2, lty = 1)
+# plot(yrs, pdrat, type = "b", las = 2)
+# matplot(yrs, pd, axes = F, type = "b")
+# axis(1, at = yrs, las = 2)
+# 
+# tabp <- tab[grep("pelagic", splisref$PD), ]
+# tabp <- tabp[order(rowSums(tabp), decreasing = T), ]
+# 
+# matplot(yrs, t(tabp), type = "l", col = glasbey(10), lwd = 2, lty = 1)
+# legend("topleft", rownames(tabp), col = glasbey(10), lwd = 2, lty = 1, cex = 0.7)
+# 
+# tabd <- tab[-grep("pelagic", splisref$PD), ]
+# tabd <- tabd[order(rowSums(tabd), decreasing = T), ]
+# 
+# matplot(yrs, t(tabd[1:20, ]), type = "b", col = glasbey(10), lwd = 2, lty = 1, pch = 19, las = 2)
+# legend("topright", rownames(tabd)[1:20], col = glasbey(10), lwd = 2, lty = 1)
 
 print("STX indicators -- SUCCESSFULLY RUN")
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		{"Report_book_files\\Performance_indicators.qmd":[],"index.qmd":[],"Report_book_files\\Report4.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"OA.qmd":[],"Lab-report\\OA.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"Report_book_files\\FMP_objectives.qmd":[]}
		{"Report_book_files\\Performance_indicators.qmd":[],"Lab-report\\OA.qmd":[],"Report_book_files\\Report4.qmd":[],"index.qmd":[],"Report_book_files\\Discussion_material.qmd":[],"Report_book_files\\Intro_text.qmd":[],"Report_book_files\\Risk_indicators.qmd":[],"OA.qmd":[],"Report_book_files\\FMP_objectives.qmd":[]}