create a new plot all indicators script

.Rhistory

@@ -1,8 +1,3 @@
-class(inddata) <- "indicatordata"
-save(inddata, file = "indicator_objects/RVC_STX.RData")
-load("../indicator_objects/RVC_PR.RData")
-plotIndicatorTimeSeries(inddata, coltoplot = 1:6, trendAnalysis = T, sublabel = T)
-# 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",
@@ -510,3 +505,8 @@ load("../indicator_objects/unemployment.RData")
 plotIndicatorTimeSeries(ind, coltoplot = 1:2, trendAnalysis = T, sublabel = T, dateformat = "%Y%b")
 load("../indicator_objects/coral_spprichness_cover.RData")
 plotIndicatorTimeSeries(ind, coltoplot = 1:4, sublabel = T, trendAnalysis = T)
+# load libraries ---------------------------------
+rm(list = ls())
+library(plotTimeSeries)
+directory <- rprojroot::find_rstudio_root_file()
+plot(1)

indicator_processing/PlotAllIndicators.R

@@ -0,0 +1,87 @@
+# 
+# script to plot ALL indicators for report 
+# C. Gervasi Jun 6 2024
+
+# load libraries ---------------------------------
+rm(list = ls())
+
+library(plotTimeSeries)
+
+#  find root directory for project ---------------
+
+directory <- rprojroot::find_rstudio_root_file()
+
+# source all .RData files in indicator_objects folder --------------
+
+# run all scripts in folder ---------------------
+
+setwd(directory)
+dir("indicator_objects")
+
+# fully automated - pull from internet ----------
+
+#source("sst.RData")                   # sea surface temperature
+source("ACEindex.RData")       # hurricane energy index
+source("carib_Chl.RData")         # primary productivity
+source("DegreeHeatingWeeks.RData")                   # degree heating weeks
+source("earthquakes.RData")           # earthquakes
+#source("kd490.R")                 # turbidity from Kd490   # THIS DOWNLOAD CAN BE FINICKY
+source("unemployment.RData")          # unemployment rate
+source("GDP.RData")                   # Gross Domestic Product
+
+# partially automated - pull from data in folder ----------------------
+
+source("marine_debris.RData")         # marine debris
+source("OA.RData")                    # ocean acidification
+source("indicator_processing/non_automated/CRMP_compile.R")          # fishery-indepenedent fish density, slope of size spectrum, coral cover indicators
+source("indicator_processing/non_automated/Sargassum_inundation.R")  # sargassum indicator
+source("indicator_processing/non_automated/SAU_recreational_catch.R") # recreational catch based on Sea Around Us database
+source("indicator_processing/non_automated/pollution.R")              # reported superfund sites etc. 
+
+# fishery indicators - includes confidential data ----------------------
+
+confpath <- "C:/Users/mandy.karnauskas/Desktop/CONFIDENTIAL/CaribbeanData/"
+
+dir("indicator_processing/fishery_dependent/")
+
+source("indicator_processing/fishery_dependent/INDICATOR_total_landings.R")   #  calc total landings by group
+source("indicator_processing/fishery_dependent/INDICATOR_gearchanges.R")      #  produces plots but no indicator objects
+source("indicator_processing/fishery_dependent/INDICATOR_gini.R")             #  calculate gini index based on revenues
+# not done below
+
+# 
+source("indicator_processing/fishery_dependent/INDICATOR_disturbance.R")                # 
+source("indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_PR.R")      # 
+source("indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STT.R")     #  
+source("indicator_processing/fishery_dependent/INDICATOR_fishery_indicators_STX.R")     #  
+
+
+
+
+
+###############################################################
+
+# Notes for standardizing scripts:  
+
+#  Top: 
+
+# specification file and libraries -----------------------------
+rm(list = ls())
+dev.off()
+
+library(maps)
+library(plotTimeSeries)
+
+load("../spec_file.RData")
+
+# define years  --------------------------------
+styear <- 1961
+enyear <- terminal_year
+
+
+#  Bottom: 
+#  save all indicators as "ind" object
+
+save(ind, file = "../../indicator_objects/INDICATOR_NAME.RData")
+
+##