revising plots for TAP presentation

Gulf-IEA · Jul 15, 2024 · f3bfb0f · f3bfb0f
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diff --git a/PPT.pptx b/PPT.pptx
diff --git a/indicator_data/RVC/RUVdensity_PRICO_BAL VETU.RData b/indicator_data/RVC/RUVdensity_PRICO_BAL VETU.RData
diff --git a/indicator_data/RVC/RUVdensity_PRICO_EPI GUTT.RData b/indicator_data/RVC/RUVdensity_PRICO_EPI GUTT.RData
diff --git a/indicator_data/RVC/RUVdensity_PRICO_LUT ANAL.RData b/indicator_data/RVC/RUVdensity_PRICO_LUT ANAL.RData
diff --git a/indicator_data/RVC/RUVdensity_PRICO_OCY CHRY.RData b/indicator_data/RVC/RUVdensity_PRICO_OCY CHRY.RData
diff --git a/indicator_data/RVC/RUVdensity_PRICO_SPA AURO.RData b/indicator_data/RVC/RUVdensity_PRICO_SPA AURO.RData
diff --git a/indicator_data/RVC/RUVdensity_PRICO_SPA VIRI.RData b/indicator_data/RVC/RUVdensity_PRICO_SPA VIRI.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_BAL VETU.RData b/indicator_data/RVC/RUVdensity_STTSTJ_BAL VETU.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_EPI GUTT.RData b/indicator_data/RVC/RUVdensity_STTSTJ_EPI GUTT.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_LUT ANAL.RData b/indicator_data/RVC/RUVdensity_STTSTJ_LUT ANAL.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_OCY CHRY.RData b/indicator_data/RVC/RUVdensity_STTSTJ_OCY CHRY.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_SPA AURO.RData b/indicator_data/RVC/RUVdensity_STTSTJ_SPA AURO.RData
diff --git a/indicator_data/RVC/RUVdensity_STTSTJ_SPA VIRI.RData b/indicator_data/RVC/RUVdensity_STTSTJ_SPA VIRI.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_BAL VETU.RData b/indicator_data/RVC/RUVdensity_STX_BAL VETU.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_EPI GUTT.RData b/indicator_data/RVC/RUVdensity_STX_EPI GUTT.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_LUT ANAL.RData b/indicator_data/RVC/RUVdensity_STX_LUT ANAL.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_OCY CHRY.RData b/indicator_data/RVC/RUVdensity_STX_OCY CHRY.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_SPA AURO.RData b/indicator_data/RVC/RUVdensity_STX_SPA AURO.RData
diff --git a/indicator_data/RVC/RUVdensity_STX_SPA VIRI.RData b/indicator_data/RVC/RUVdensity_STX_SPA VIRI.RData
diff --git a/indicator_objects/avgLmax.RData b/indicator_objects/avgLmax.RData
diff --git a/indicator_objects/tier3.RData b/indicator_objects/tier3.RData
diff --git a/indicator_objects/turbidity.RData b/indicator_objects/turbidity.RData
diff --git a/indicator_plots/ACEindex_plot.png b/indicator_plots/ACEindex_plot.png
diff --git a/indicator_plots/ACEindex_plot_wide.png b/indicator_plots/ACEindex_plot_wide.png
diff --git a/indicator_plots/Carib_SST_plot.png b/indicator_plots/Carib_SST_plot.png
diff --git a/indicator_plots/Carib_SST_plot_TAP.png b/indicator_plots/Carib_SST_plot_TAP.png
diff --git a/indicator_plots/DegreeHeatingWeeks_plot.png b/indicator_plots/DegreeHeatingWeeks_plot.png
diff --git a/indicator_plots/GDP_plot.png b/indicator_plots/GDP_plot.png
diff --git a/indicator_plots/OA_plot.png b/indicator_plots/OA_plot.png
diff --git a/indicator_plots/OA_plot_wide.png b/indicator_plots/OA_plot_wide.png
diff --git a/indicator_plots/PD_ratio_plot.png b/indicator_plots/PD_ratio_plot.png
diff --git a/indicator_plots/PR_Lmax_classes_plot.png b/indicator_plots/PR_Lmax_classes_plot.png
diff --git a/indicator_plots/PR_Lmax_classes_plot_wide.png b/indicator_plots/PR_Lmax_classes_plot_wide.png
diff --git a/indicator_plots/RVC_PR_plot.png b/indicator_plots/RVC_PR_plot.png
diff --git a/indicator_plots/RVC_STSJ_plot.png b/indicator_plots/RVC_STSJ_plot.png
diff --git a/indicator_plots/RVC_STX_plot.png b/indicator_plots/RVC_STX_plot.png
diff --git a/indicator_plots/STT_Lmax_classes_plot.png b/indicator_plots/STT_Lmax_classes_plot.png
diff --git a/indicator_plots/STT_Lmax_classes_plot_wide.png b/indicator_plots/STT_Lmax_classes_plot_wide.png
diff --git a/indicator_plots/Sargassum_plot.png b/indicator_plots/Sargassum_plot.png
diff --git a/indicator_plots/Sargassum_plot_wide.png b/indicator_plots/Sargassum_plot_wide.png
diff --git a/indicator_plots/avgLmax_plot_TAP.png b/indicator_plots/avgLmax_plot_TAP.png
diff --git a/indicator_plots/carib_Chl_plot.png b/indicator_plots/carib_Chl_plot.png
diff --git a/indicator_plots/carib_Chl_plot_wide.png b/indicator_plots/carib_Chl_plot_wide.png
diff --git a/indicator_plots/coral_spprichness_cover_plot.png b/indicator_plots/coral_spprichness_cover_plot.png
diff --git a/indicator_plots/cruise_plot.png b/indicator_plots/cruise_plot.png
diff --git a/indicator_plots/cruise_plot_TAP.png b/indicator_plots/cruise_plot_TAP.png
diff --git a/indicator_plots/disturbance_plot.png b/indicator_plots/disturbance_plot.png
diff --git a/indicator_plots/disturbance_plot_TAP.png b/indicator_plots/disturbance_plot_TAP.png
diff --git a/indicator_plots/earthquakes_plot.png b/indicator_plots/earthquakes_plot.png
diff --git a/indicator_plots/earthquakes_plot_wide.png b/indicator_plots/earthquakes_plot_wide.png
diff --git a/indicator_plots/fish_density_plot.png b/indicator_plots/fish_density_plot.png
diff --git a/indicator_plots/fish_density_plot_TAP.png b/indicator_plots/fish_density_plot_TAP.png
diff --git a/indicator_plots/gini_plot.png b/indicator_plots/gini_plot.png
diff --git a/indicator_plots/gini_plot_TAP.png b/indicator_plots/gini_plot_TAP.png
diff --git a/indicator_plots/marine_debris_plot.png b/indicator_plots/marine_debris_plot.png
diff --git a/indicator_plots/marine_debris_plot_wide.png b/indicator_plots/marine_debris_plot_wide.png
diff --git a/indicator_plots/oceanNAICS_plot.png b/indicator_plots/oceanNAICS_plot.png
diff --git a/...lots/Accumulated cyclone energy index.png → ...lots/Accumulated cyclone energy index.png b/...lots/Accumulated cyclone energy index.png → ...lots/Accumulated cyclone energy index.png
diff --git a/...ots/Annual mean sargassum innundation.png → ...ots/Annual mean sargassum innundation.png b/...ots/Annual mean sargassum innundation.png → ...ots/Annual mean sargassum innundation.png
diff --git a/.../Average monthly degree heating weeks.png → .../Average monthly degree heating weeks.png b/.../Average monthly degree heating weeks.png → .../Average monthly degree heating weeks.png
diff --git a/indicator_plots/Commercial fish density.png → ...ots/old plots/Commercial fish density.png b/indicator_plots/Commercial fish density.png → ...ots/old plots/Commercial fish density.png
diff --git a/indicator_plots/Coral species richness.png → ...lots/old plots/Coral species richness.png b/indicator_plots/Coral species richness.png → ...lots/old plots/Coral species richness.png
diff --git a/indicator_plots/Gross domestic product.png → ...lots/old plots/Gross domestic product.png b/indicator_plots/Gross domestic product.png → ...lots/old plots/Gross domestic product.png
diff --git a/indicator_plots/Hotel occupancy rates.png → ...plots/old plots/Hotel occupancy rates.png b/indicator_plots/Hotel occupancy rates.png → ...plots/old plots/Hotel occupancy rates.png
diff --git a/indicator_plots/Total pelagic landings.png → ...lots/old plots/Total pelagic landings.png b/indicator_plots/Total pelagic landings.png → ...lots/old plots/Total pelagic landings.png
diff --git a/indicator_plots/Total recreational catch.png → ...ts/old plots/Total recreational catch.png b/indicator_plots/Total recreational catch.png → ...ts/old plots/Total recreational catch.png
diff --git a/...s/U.S. Caribbean primary productivity.png → ...s/U.S. Caribbean primary productivity.png b/...s/U.S. Caribbean primary productivity.png → ...s/U.S. Caribbean primary productivity.png
diff --git a/....S. Caribbean sea surface temperature.png → ....S. Caribbean sea surface temperature.png b/....S. Caribbean sea surface temperature.png → ....S. Caribbean sea surface temperature.png
diff --git a/indicator_plots/outreach_plot.png b/indicator_plots/outreach_plot.png
diff --git a/indicator_plots/pollution_plot.png b/indicator_plots/pollution_plot.png
diff --git a/indicator_plots/population_plot.png b/indicator_plots/population_plot.png
diff --git a/indicator_plots/tier3_plot.png b/indicator_plots/tier3_plot.png
diff --git a/indicator_plots/tier3_plot_TAP.png b/indicator_plots/tier3_plot_TAP.png
diff --git a/indicator_plots/total_landings_plot.png b/indicator_plots/total_landings_plot.png
diff --git a/indicator_plots/total_rec_catch_plot.png b/indicator_plots/total_rec_catch_plot.png
diff --git a/indicator_plots/turbidity_plot.png b/indicator_plots/turbidity_plot.png
diff --git a/indicator_plots/unemployment_plot.png b/indicator_plots/unemployment_plot.png
diff --git a/indicator_processing/PlotAllIndicators.R b/indicator_processing/PlotAllIndicators.R
diff --git a/indicator_processing/automated_download/cruise_visitors.R b/indicator_processing/automated_download/cruise_visitors.R
@@ -112,7 +112,7 @@ class(inddata) <- "indicatordata"
 # plot and save ----------------------------------
 
 ind <- inddata
-plotIndicatorTimeSeries(ind, coltoplot = 1:2, plotrownum = 2, sublabel = TRUE)
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, plotrownum = 2, plotcolnum = 1, trendAnalysis = TRUE, dateformat = "%b%Y", sublabel = TRUE, widadj = 1, hgtadj = 0.7, anom = "none", yposadj = 1)
 
 save(ind, file = "indicator_objects/cruise.RData")
 

diff --git a/indicator_processing/automated_download/kd490.R b/indicator_processing/automated_download/kd490.R
@@ -80,7 +80,7 @@ for (yr in styear:enyear) {
 
 datdata <- paste(sprintf('%02d',pr_dat$mon),pr_dat$year,sep='-')
 inddata <- data.frame(cbind(pr_dat$mean, st_dat$mean, sc_dat$mean), row.names = datdata)
-labs <- c(rep("Turbidity from ocean color data", 3), rep("Diffuse attenuation coefficient at 490 nm (m^-1)", 3), 
+labs <- c(rep("Turbidity from ocean color data", 3), rep("Diffuse attenuation coefficient\n at 490 nm (m^-1)", 3), 
           "Puerto Rico", "St. Thomas", "St. Croix")
 indnames <- data.frame(matrix(labs, nrow = 3, byrow = T))
 
@@ -91,6 +91,6 @@ class(ind) <- "indicatordata"
 
 save(ind, file = "indicator_objects/turbidity.RData")
 
-plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, dateformat = "%m-%Y", sublabel = T, trendAnalysis = F, widadj = 1.5)
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, dateformat = "%m-%Y", sublabel = T, trendAnalysis = F, widadj = 1.5, yposadj = 1.3)
 plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, dateformat = "%m-%Y", sublabel = T, trendAnalysis = F, widadj = 1.5, anom = "mon")
 
diff --git a/indicator_processing/non_automated/RVC.R b/indicator_processing/non_automated/RVC.R
@@ -101,7 +101,7 @@ stx = readRDS("indicator_data/RVC/combined_stx_2001_2023.rds")
 spcs = c("OCY CHRY", "LUT ANAL", "BAL VETU", "EPI GUTT", "SPA AURO", "SPA VIRI")
 
 
-
+#test = getDomainDensity(prico, species = "OCY CHRY")
 
 
 # Extract the time series for each species and each area
@@ -134,11 +134,13 @@ for(j in regions) {
 
     datdata <- species_data$YEAR
     inddata <- data.frame(species_data$density)
-    s <- cbind(datdata, inddata) 
+    vardata <- data.frame(species_data$var)
+    s1 <- cbind(datdata, inddata)
+    s2 <- cbind(s1, vardata)
 
     # save -----------------------------------------
 
-    save(s, file = paste("indicator_data/RVC/RUVdensity_", j, "_", i, ".RData", sep = ""))
+    save(s2, file = paste("indicator_data/RVC/RUVdensity_", j, "_", i, ".RData", sep = ""))
   }
 }
 

diff --git a/indicator_processing/non_automated/avgLmax.R b/indicator_processing/non_automated/avgLmax.R
@@ -0,0 +1,59 @@
+## Average Lmax per year by island
+
+rm(list = ls())
+dev.off()
+
+library(plotTimeSeries)
+library(dplyr)
+
+load("indicator_data/fish-dep-indicators/Lmax_PR.RData")
+PR_dat = as.data.frame(findat)
+
+load("indicator_data/fish-dep-indicators/Lmax_STT.RData")
+STT_dat = as.data.frame(findat)
+
+load("indicator_data/fish-dep-indicators/Lmax_STX.RData")
+STX_dat = as.data.frame(findat)
+
+
+styear = min(PR_dat$V1, STT_dat$yrs, STX_dat$yrs)
+enyear = max(PR_dat$V1, STT_dat$yrs, STX_dat$yrs)
+
+
+yrs = styear:enyear
+PR = PR_dat$lmax
+
+STT_dat2 = data.frame(yrs = yrs)
+STT_dat2 = STT_dat2 %>% 
+  left_join(STT_dat, by = "yrs")
+
+STT = STT_dat2$lmax
+
+
+STX_dat2 = data.frame(yrs = yrs)
+STX_dat2 = STX_dat2 %>% 
+  left_join(STX_dat, by = "yrs")
+
+STX = STX_dat2$lmax
+
+
+
+
+# save as indicator object ----------------------
+datdata <- yrs
+inddata <- data.frame(cbind(PR, STT, STX))
+labs <- c("Average Lmax" , "length (cm)", "Puerto Rico",
+          "Average Lmax" , "length (cm)", "St. Thomas and St. John",
+          "Average Lmax" , "length (cm)", "St. Croix")
+indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
+inddata <- list(labels = indnames, indicators = inddata, datelist = datdata)
+class(inddata) <- "indicatordata"
+
+# plot and save ----------------------------------
+
+ind <- inddata
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, plotcolnum = 1, trendAnalysis = TRUE, dateformat = "%b%Y", sublabel = TRUE, widadj = 1, hgtadj = 0.7, anom = "none", yposadj = 1, sameYscale = TRUE)
+
+save(ind, file = "indicator_objects/avgLmax.RData")
+
+###############################  END  #############################
diff --git a/indicator_processing/non_automated/tier_designation.R b/indicator_processing/non_automated/tier_designation.R
@@ -23,8 +23,8 @@ USVI = c(0,0,0,0,0,0,0,0,0,0,0,0,USVI_perc)
 # save as indicator object ----------------------
 datdata <- 2011:2023
 inddata <- data.frame(cbind(PR, USVI))
-labs <- c("Stocks/complexes with Tier 3 designation" , "Percent", "Puerto Rico",
-          "Stocks/complexes with Tier 3 designation" , "Percent", "USVI")
+labs <- c("Stocks/complexes with ACLs derived from stock assessments" , "Percent", "Puerto Rico",
+          "Stocks/complexes with ACLs derived from stock assessments" , "Percent", "USVI")
 indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
 inddata <- list(labels = indnames, indicators = inddata, datelist = datdata)
 class(inddata) <- "indicatordata"

diff --git a/test.pptx b/test.pptx
diff --git a/test.qmd b/test.qmd
@@ -0,0 +1,10 @@
+---
+title: "Presentation"
+format:
+  pptx:
+    reference-doc: PPT.pptx
+---
+
+# test
+
+## hi