fix file paths to work with main dir

Gulf-IEA · May 16, 2024 · 3fb83e7 · 3fb83e7
1 parent c5c45d5
commit 3fb83e7
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Showing 23 changed files with 71 additions and 414,341 deletions.
diff --git a/.Rhistory b/.Rhistory
@@ -0,0 +1,10 @@
+# load libraries ---------------------------------
+rm(list = ls())
+library(plotTimeSeries)
+directory <- rprojroot::find_rstudio_root_file()
+setwd(directory)
+plot(1)
+setwd(directory)
+setwd("indicator_processing/non_automated")
+dir()
+source("RVC.R")
diff --git a/chl.csv b/chl.csv
diff --git a/indicator_objects/GDP.RData b/indicator_objects/GDP.RData
diff --git a/indicator_objects/pollution.RData b/indicator_objects/pollution.RData
diff --git a/indicator_objects/total_rec_catch.RData b/indicator_objects/total_rec_catch.RData
diff --git a/indicator_objects/turbidity.RData b/indicator_objects/turbidity.RData
diff --git a/indicator_objects/unemployment.RData b/indicator_objects/unemployment.RData
diff --git a/indicator_processing/CalculateAllIndicators.R b/indicator_processing/CalculateAllIndicators.R
@@ -13,46 +13,35 @@ directory <- rprojroot::find_rstudio_root_file()
 
 # first process automated downloads --------------
 
-setwd(directory)
-
-
 # run all scripts in folder ---------------------
 
 plot(1)
 
 # fully automated - pull from internet ----------
 
 setwd(directory)
-setwd("indicator_processing/automated_download/")
-dir()
-
-source("ACE_index_Carib.R")       # hurricane energy index
-source("chl_caribbean.R")         # primary productivity
-source("DHW.R")                   # degree heating weeks
-source("earthquakes.R")           # earthquakes
-source("kd490.R")                 # turbidity from Kd490   
-source("sst.R")                   # sea surface temperature
-source("Unemployment.R")          # unemployment rate
-source("GDP.R")                   # Gross Domestic Product
-
-# pull from data in folder ----------------------
-
-setwd(directory)
-setwd("indicator_processing/non_automated")
-dir()
-
-source("marine_debris.R")         # marine debris
-source("OA.R")                    # ocean acidification
-source("CRMP_compile.R")          # fishery-indepenedent fish density, slope of size spectrum, coral cover indicators
+dir("indicator_processing/automated_download/")
 
-source("Sargassum_inundation.R")  # sargassum indicator
+source("indicator_processing/automated_download/sst.R")                   # sea surface temperature
+source("indicator_processing/automated_download/ACE_index_Carib.R")       # hurricane energy index
+source("indicator_processing/automated_download/chl_caribbean.R")         # primary productivity
+source("indicator_processing/automated_download/DHW.R")                   # degree heating weeks
+source("indicator_processing/automated_download/earthquakes.R")           # earthquakes
+source("indicator_processing/automated_download/kd490.R")                 # turbidity from Kd490   # THIS DOWNLOAD CAN BE FINICKY
+source("indicator_processing/automated_download/Unemployment.R")          # unemployment rate
+source("indicator_processing/automated_download/GDP.R")                   # Gross Domestic Product
 
+# partially automated - pull from data in folder ----------------------
 
+dir("indicator_processing/non_automated")
 
+source("indicator_processing/non_automated/marine_debris.R")         # marine debris
+source("indicator_processing/non_automated/OA.R")                    # 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. 
 
-source("SAU_recreational_catch.R")
-source("pollution.R")
-source("RVC.R")
 
 
 ###############################################################

diff --git a/indicator_processing/automated_download/ACE_index_Carib.R b/indicator_processing/automated_download/ACE_index_Carib.R
@@ -18,7 +18,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # define years  --------------------------------
 styear <- 1961
@@ -158,7 +158,7 @@ class(s) <- "indicatordata"
 plotIndicatorTimeSeries(s, widadj = 0.5)
 
 ind <- s
-save(ind, file = "../../indicator_objects/ACEindex.RData")
+save(ind, file = "indicator_objects/ACEindex.RData")
 
 #################################################################################
 

diff --git a/indicator_processing/automated_download/DHW.R b/indicator_processing/automated_download/DHW.R
@@ -7,7 +7,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 options(download.file.method="libcurl")
 
@@ -65,7 +65,7 @@ class(ind) <- "indicatordata"
 
 # save and plot -----------------------------------
 
-save(ind, file = "../../indicator_objects/DegreeHeatingWeeks.RData")
+save(ind, file = "indicator_objects/DegreeHeatingWeeks.RData")
 
 plotIndicatorTimeSeries(ind, coltoplot = 1:2, plotrownum = 2, sublabel = T, dateformat = "%Y%m", yposadj = 0.7,
                         sameYscale = T, type = "allLines")

diff --git a/indicator_processing/automated_download/GDP.R b/indicator_processing/automated_download/GDP.R
@@ -15,7 +15,7 @@ library(maps)
 library(plotTimeSeries)
 library(rvest)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # data download --------------------------------------------------------
 

diff --git a/indicator_processing/automated_download/Unemployment.R b/indicator_processing/automated_download/Unemployment.R
@@ -13,7 +13,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 
 # load data -------------------------------------
@@ -65,7 +65,7 @@ class(inddata) <- "indicatordata"
 ind <- inddata
 plotIndicatorTimeSeries(ind, plotrownum = 2, coltoplot = 1:2, sublabel = TRUE, dateformat = "%Y%b", trendAnalysis = T)
 
-save(ind, file = "../../indicator_objects/unemployment.RData")
+save(ind, file = "indicator_objects/unemployment.RData")
 
 #############################  END  ####################################
 
diff --git a/indicator_processing/automated_download/chl_caribbean.R b/indicator_processing/automated_download/chl_caribbean.R
@@ -17,7 +17,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # download data ------------------------------------------------
 
@@ -63,7 +63,7 @@ class(s) <- "indicatordata"
 # save and plot ------------------------------------------------------
 
 ind <- s
-save(ind, file = "../../indicator_objects/carib_Chl.RData")
+save(ind, file = "indicator_objects/carib_Chl.RData")
 
 plotIndicatorTimeSeries(ind, dateformat = "%m-%Y", sublabel = T, trendAnalysis = T, anom = "mon", 
                         widadj = 0.7, hgtadj = 0.8, type = "allLines")

diff --git a/indicator_processing/automated_download/earthquakes.R b/indicator_processing/automated_download/earthquakes.R
@@ -11,7 +11,7 @@ library(plotTimeSeries)
 library(xml2)
 library(rvest)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 
 # download data directly from site -----------------------------
@@ -71,7 +71,7 @@ class(ind) <- "indicatordata"
 
 plotIndicatorTimeSeries(ind)
 
-save(ind, file = "../../indicator_objects/earthquakes.RData")
+save(ind, file = "indicator_objects/earthquakes.RData")
 
 #################################################################################
 

diff --git a/indicator_processing/automated_download/kd490.R b/indicator_processing/automated_download/kd490.R
@@ -12,7 +12,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # define urls  --------------------------------
 
@@ -83,7 +83,7 @@ class(ind) <- "indicatordata"
 
 # save and plot ---------------------------------------
 
-save(ind, file = "../../indicator_objects/turbidity.RData")
+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, anom = "mon")

diff --git a/indicator_processing/automated_download/sst.R b/indicator_processing/automated_download/sst.R
@@ -8,7 +8,7 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # devtools::install_github("mdsumner/ncdf4")
 # library(ncdf4)
@@ -81,7 +81,7 @@ ind <- s
 
 # save and plot ---------------------------------------
 
-save(ind, file = "../../indicator_objects/Carib_SST.RData")
+save(ind, file = "indicator_objects/Carib_SST.RData")
 
 plotIndicatorTimeSeries(ind, coltoplot = 1:3, plotrownum = 3, dateformat = "%m-%Y", sublabel = T, 
                         trendAnalysis = T, widadj = 0.5, anom = "mon", type = "allLines") #  outtype = "png", hgtadj = 0.8)

diff --git a/indicator_processing/automated_download/st.csv b/indicator_processing/automated_download/st.csv
diff --git a/indicator_processing/non_automated/CRMP_compile.R b/indicator_processing/non_automated/CRMP_compile.R
@@ -10,10 +10,9 @@
 rm(list = ls())
 dev.off()
 
-directory <- rprojroot::find_rstudio_root_file()
-
-setwd(directory)
-dir()
+#directory <- rprojroot::find_rstudio_root_file()
+#setwd(directory)
+#dir()
 
 library(plotTimeSeries)
 

diff --git a/indicator_processing/non_automated/OA.R b/indicator_processing/non_automated/OA.R
@@ -20,9 +20,9 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
-dat <- read.table("../../indicator_data/surface_omega_series.txt", skip = 0, header = F)
+dat <- read.table("indicator_data/surface_omega_series.txt", skip = 0, header = F)
 
 head(dat)
 tail(dat)
@@ -43,6 +43,6 @@ plotIndicatorTimeSeries(s)
 
 ind <- s
 
-save(ind, file = "../../indicator_objects/OA.RData")
+save(ind, file = "indicator_objects/OA.RData")
 
 
diff --git a/indicator_processing/non_automated/SAU_recreational_catch.R b/indicator_processing/non_automated/SAU_recreational_catch.R
@@ -9,12 +9,19 @@
 # 
 ####################################################################
 
+# specification file and libraries -----------------------------
 rm(list = ls())
+dev.off()
+
+library(maps)
+library(plotTimeSeries)
+
+load("indicator_processing/spec_file.RData")
 
 styear <- 1995
 
 # load data -------------------------------------
-d <- read.csv("../indicator_data/SAU/SAU EEZ 630,850 v50-1.csv")
+d <- read.csv("indicator_data/SAU/SAU EEZ 630,850 v50-1.csv")
 head(d)
 
 # look at fields ------------------------------
@@ -55,10 +62,10 @@ indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
 inddata <- list(labels = indnames, indicators = inddats, datelist = datdata) #, ulim = ulidata, llim = llidata)
 class(inddata) <- "indicatordata"
 
-setwd("C:/Users/mandy.karnauskas/Desktop/Caribbean-ESR/indicator_plots/") 
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, plotrownum = 2, sublabel = T, sameYscale = F, outtype = "png")
+plotIndicatorTimeSeries(inddata, coltoplot = 1:2, plotrownum = 2, sublabel = T, sameYscale = F)
 
 # plot and save ----------------------------------
-save(inddata, file = "C:/Users/mandy.karnauskas/Desktop/Caribbean-ESR/indicator_objects/total_rec_catch.RData")
+ind <- inddata
+save(ind, file = "indicator_objects/total_rec_catch.RData")
 
 
diff --git a/indicator_processing/non_automated/Sargassum_inundation.R b/indicator_processing/non_automated/Sargassum_inundation.R
@@ -5,15 +5,15 @@ dev.off()
 library(maps)
 library(plotTimeSeries)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # define years  --------------------------------
 styear <- 1961
 enyear <- terminal_year
 
 # load data -------------------------------------
 
-d <- read.csv("../../indicator_data/sargassum_innundation_monthly_mean_hu.csv", skip = 2)
+d <- read.csv("indicator_data/sargassum_innundation_monthly_mean_hu.csv", skip = 2)
 
 d$yr <- substr(d$X, 1, 4)
 d$vars <- (d$ulim - d$X.1)^2
@@ -38,5 +38,5 @@ plotIndicatorTimeSeries(inddata)
 
 ind <- inddata
 
-save(ind, file = "../../indicator_objects/Sargassum.RData")
+save(ind, file = "indicator_objects/Sargassum.RData")
 
diff --git a/indicator_processing/non_automated/marine_debris.R b/indicator_processing/non_automated/marine_debris.R
@@ -11,7 +11,7 @@ library(plotTimeSeries)
 library(xml2)
 library(rvest)
 
-load("../spec_file.RData")
+load("indicator_processing/spec_file.RData")
 
 # download data directly from site -----------------------------
 
@@ -27,7 +27,7 @@ table <- html_table(page, fill = TRUE) #Parses tables into data frames
 table
 # automated download does not work ############
 
-dat <- read.csv("../../indicator_data/beach-litter.csv", skip = 0, header = T)
+dat <- read.csv("indicator_data/beach-litter.csv", skip = 0, header = T)
 
 d <- dat[which(dat$Entity == "Puerto Rico" | dat$Entity == "United States Virgin Islands"), ]
 d$Entity <- droplevels(d$Entity)
@@ -49,6 +49,6 @@ plotIndicatorTimeSeries(s, coltoplot = 1:2, plotrownum = 2, sublabel = T)
 
 ind <- s
 
-save(ind, file = "../../indicator_objects/marine_debris.RData")
+save(ind, file = "indicator_objects/marine_debris.RData")
 
 
diff --git a/indicator_processing/non_automated/pollution.R b/indicator_processing/non_automated/pollution.R
@@ -23,13 +23,15 @@ USVI_ind = USVI$sum
 # save as indicator object ----------------------
 datdata <- as.integer(USVI$year)
 inddata <- data.frame(PR_ind, USVI_ind)
-labs <- c("Pollution sites" , "Number added", "Puerto Rico",
-          "Pollution sites" , "Number added", "USVI")
+labs <- c("Pollution sites reported" , "Number added", "Puerto Rico",
+          "Pollution sites reported" , "Number added", "USVI")
 indnames <- data.frame(matrix(labs, nrow = 3, byrow = F))
 inddata <- list(labels = indnames, indicators = inddata, datelist = datdata)
 class(inddata) <- "indicatordata"
 
 # plot and save ----------------------------------
-save(inddata, file = "indicator_objects/pollution.RData")
+ind <- inddata
 
-plotIndicatorTimeSeries(inddata, coltoplot = 1:2, sublabel = TRUE)
+plotIndicatorTimeSeries(ind, plotrownum = 2, coltoplot = 1:2, sublabel = TRUE)
+
+save(ind, file = "indicator_objects/pollution.RData")