moving plot all indicators file

.Rhistory

@@ -1,38 +1,4 @@
 datdata <- 2001:2021
-inddata <- data.frame(cbind(RUVdensity_PRICO_BAL_VETU$species_data.density, RUVdensity_PRICO_EPI_GUTT$species_data.density, RUVdensity_PRICO_LUT_ANAL$species_data.density, RUVdensity_PRICO_OCY_CHRY$species_data.density, RUVdensity_PRICO_SPA_AURO$species_data.density, RUVdensity_PRICO_SPA_VIRI$species_data.density))
-labs <- c("PR" , "Density", "queen triggerfish",
-"PR" , "Density", "red hind",
-"PR" , "Density", "mutton snapper",
-"PR" , "Density", "yellowtail snapper",
-"PR" , "Density", "redband parrotfish",
-"PR" , "Density", "stoplight parrotfish")
-indnames <- data.frame(matrix(labs, nrow = 6, byrow = F))
-inddata <- list(labels = indnames, indicators = inddata, datelist = datdata)
-class(inddata) <- "indicatordata"
-save(inddata, file = "indicator_objects/RVC_PR.RData")
-View(RUVdensity_PRICO_SPA_VIRI)
-View(RUVdensity_PRICO_SPA_VIRI)
-load("../indicator_objects/RVC_PR.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
-load("../indicator_objects/landings.RData")
-load("../indicator_objects/RVC_PR.RData")
-load("../indicator_objects/landings.RData")
-load("../indicator_objects/fish_density.RData")
-# Puerto Rico
-datdata <- 2001:2021
-inddata <- data.frame(cbind(RUVdensity_PRICO_BAL_VETU$species_data.density, RUVdensity_PRICO_EPI_GUTT$species_data.density, RUVdensity_PRICO_LUT_ANAL$species_data.density, RUVdensity_PRICO_OCY_CHRY$species_data.density, RUVdensity_PRICO_SPA_AURO$species_data.density, RUVdensity_PRICO_SPA_VIRI$species_data.density))
-labs <- c("PR" , "Density", "queen triggerfish",
-"PR" , "Density", "red hind",
-"PR" , "Density", "mutton snapper",
-"PR" , "Density", "yellowtail snapper",
-"PR" , "Density", "redband parrotfish",
-"PR" , "Density", "stoplight parrotfish")
-indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
-inddata <- list(labels = indnames, indicators = inddata, datelist = datdata)
-class(inddata) <- "indicatordata"
-save(inddata, file = "indicator_objects/RVC_PR.RData")
-# St. Thomas & St. John
-datdata <- 2001:2021
 inddata <- data.frame(cbind(RUVdensity_STTSTJ_BAL_VETU$species_data.density, RUVdensity_STTSTJ_EPI_GUTT$species_data.density, RUVdensity_STTSTJ_LUT_ANAL$species_data.density, RUVdensity_STTSTJ_OCY_CHRY$species_data.density, RUVdensity_STTSTJ_SPA_AURO$species_data.density, RUVdensity_STTSTJ_SPA_VIRI$species_data.density))
 labs <- c("STTSTJ" , "Density", "queen triggerfish",
 "STTSTJ" , "Density", "red hind",
@@ -510,3 +476,37 @@ rm(list = ls())
 library(plotTimeSeries)
 directory <- rprojroot::find_rstudio_root_file()
 plot(1)
+rm(list = ls())
+directory <- rprojroot::find_rstudio_root_file()
+setwd(directory)
+dir("indicator_objects")
+library(plotTimeSeries)
+library(spam)
+load("DegreeHeatingWeeks.RData")
+# load libraries ---------------------------------
+rm(list = ls())
+library(plotTimeSeries)
+directory <- rprojroot::find_rstudio_root_file()
+setwd(directory)
+dir("indicator_objects")
+load("DegreeHeatingWeeks.RData")
+setwd(directory)
+dir("indicator_objects")
+load("indicator_objects/DegreeHeatingWeeks.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%m", plotrownum = 2, plotcolnum = 1)
+rm(list = ls())
+directory <- rprojroot::find_rstudio_root_file()
+setwd(directory)
+library(plotTimeSeries)
+library(spam)
+load("indicator_objects/DegreeHeatingWeeks.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%m", plotrownum = 2, plotcolnum = 1)
+load("../indicator_objects/OA.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+load("../indicator_objects/ACEindex.RData")
+load("indicator_objects/OA.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+load("indicator_objects/ACEindex.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+load("indicator_objects/Sargassum.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)

indicator_objects/PlotAllIndicators.R

@@ -0,0 +1,189 @@
+# 
+# script to plot ALL indicators for report - DRAFT, STILL WORKING ON 
+# C. Gervasi Jun 6 2024
+
+rm(list = ls())
+
+#  find root directory for project ---------------
+
+directory <- rprojroot::find_rstudio_root_file()
+setwd(directory)
+
+
+library(plotTimeSeries)
+library(spam)
+
+### 1. Degree heating weeks
+
+load("indicator_objects/DegreeHeatingWeeks.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%m", plotrownum = 2, plotcolnum = 1)
+
+### 2. Ocean acidification via aragonite saturation state
+
+load("indicator_objects/OA.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+
+### 3. Hurricane activity
+
+load("indicator_objects/ACEindex.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+
+### 4. Turbidity
+
+load("indicator_objects/turbidity.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, dateformat = "%m-%Y", sublabel = T)
+
+### 5. Sea surface temperature
+
+load("indicator_objects/Carib_SST.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, trendAnalysis = T, sublabel = T, dateformat = "%m-%Y")
+
+### 6. Marine debris
+
+load("indicator_objects/marine_debris.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = F)
+
+### 7. Identified point source pollution sites
+
+load("indicator_objects/pollution.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = F, sublabel = T)
+
+### 8. Primary productivity via ocean color
+
+load("indicator_objects/carib_Chl.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T, dateformat = "%m-%Y")
+
+### 9. Coastal development via land cover
+
+# Just a figure
+
+### 10. Number of major earthquakes
+
+load("indicator_objects/earthquakes.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+
+### 11. Fishery/market disturbance indicator 
+
+load("indicator_objects/disturbance.RData")
+plotIndicatorTimeSeries(inddata, coltoplot = 1:3, trendAnalysis = T, sublabel = T)
+
+### 12. Sargassum inundation
+
+load("indicator_objects/Sargassum.RData")
+plotIndicatorTimeSeries(ind, trendAnalysis = T)
+
+### 13. Tourism via hotel occupancy
+
+load("indicator_objects/hotel_occupancy_rates_USVI_and_PR.RData")
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T, dateformat = "%Y%b")
+
+load("indicator_objects/hotel_occupancy.RData")                      
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = T, trendAnalysis = T,dateformat = "%Y%b")
+                                                                                          ### 14. Population change
+
+#14 - MAPS but also should be census data
+
+### 15. Fishery independent surveys of economically important species
+
+load("../indicator_objects/RVC_PR.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+
+load("../indicator_objects/RVC_STSJ.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+
+load("../indicator_objects/RVC_STX.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+
+#Indicator 16.1 - abundance of commercial fish based on TCRMP and PRCRMP 
+
+#Indicator 16.2 - slope of the size spectrum based on TCRMP and PRCRMP
+
+### 17. Commercial landings
+
+load("../indicator_objects/landings.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
+
+load("../indicator_objects/fish_density.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T)
+
+### 18. Pelagic:demersal ratio
+
+#Indicator 18
+
+### 19 Maximum length and size structure
+
+#Indicator 19 - Lmax indicator
+
+### 20. Changes in target species / landing composition
+
+load("../indicator_objects/total_landings.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:9, plotrownum = 3, plotcolnum = 3, trendAnalysis = T, sublabel = T)
+
+### 21. Total, lobster and conch revenues
+
+# Just figures
+
+### 22. Total, lobster and conch trips
+
+# Indicator 22 - number of trips
+
+### 23. Ocean economy employment and wages
+
+load("../indicator_objects/OceanNAICS.RData")
+plotIndicatorTimeSeries(inddata, coltoplot = 1:8, plotrownum = 2, trendAnalysis = T, sublabel = T)
+
+### 24. GDP
+
+load("../indicator_objects/GDP.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T)
+
+### 25. Unemployment
+
+load("../indicator_objects/unemployment.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%b")
+
+### 26. Gini coefficient for distribution of landings and revenue
+
+load("../indicator_objects/gini.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:3, plotrownum = 2, trendAnalysis = T, sublabel = T) 
+
+### 27. Commercial fishing community engagement and reliance
+
+# Indicator 27 - working with Tarsila on
+
+### 28. Recreational fishing engagement and participation
+
+load("../indicator_objects/total_rec_catch.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, trendAnalysis = T, sublabel = T) 
+
+### 29. Commercial fishing engagement and participation
+
+# Indicator 29
+
+### 30. Changes in gear type
+
+# Just plots
+
+### 31. Number of seasonal closures implemented
+
+#Indicator 31
+
+### 32. Number of education and outreach events
+
+#Indicator 32
+
+### 33. Number of enforcement actions
+
+#Indicator 33
+
+### 34 Percent coral cover
+
+load("../indicator_objects/NCRMP_coral_cover_richness.RData") 
+plotIndicatorTimeSeries(inddata, coltoplot = 1:6, sublabel = T, trendAnalysis = F) 
+
+### 35. Coral species diversity
+
+load("../indicator_objects/coral_spprichness_cover.RData")
+plotIndicatorTimeSeries(ind, coltoplot = 1:4, sublabel = T, trendAnalysis = T)
+
+

indicator_processing/CalculateAllIndicators.R

@@ -84,3 +84,7 @@ enyear <- terminal_year
 save(ind, file = "indicator_objects/INDICATOR_NAME.RData")
 
 ##
+
+
+
+