#Sep 2018 version of the NARCLIM suite of codes for OEH tech guide

Analysis/Code/NARCLIM_Download/R_Preparing_BASH_script_for_NARCLIM_batch_download.R

@@ -17,12 +17,13 @@
 # 'wssmean'		Surface wind speed standard_name: air_velocity units: m s-1
 # 'sstmean'   Sea surface temperatuer daily mean
 
-Clim_Var <- 'rldsmean'
+Clim_Var <- 'evspsblmean'
 Datatype <- 'T_GCMS'  #T_GCMS for GCM forcing, T_NNRP for reanalysis (only 1950-2009)
 Biasboolean <- 'False' #use bias corrected data?
+Location <- 'catchment' #location of coordinate
 
 Directory <- 'C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Data/NARCLIM_Site_CSVs/CASESTUDY2/'   
-Filename <- 'CASESTDUY2_NARCLIM_Point_Sites.csv'
+Filename <- 'CASESTUDY2_NARCLIM_Point_Sites.csv'
 
 #Load CSV with location names and lat lon coordinates
 Location.df <- data.frame(read.csv(paste(Directory, Filename, sep=""), header=T, fileEncoding="UTF-8-BOM"))
@@ -34,7 +35,7 @@ text1 <- c(paste("Datatype='",Datatype,"'", sep=""),
            paste("Bias_corrected='",Biasboolean,"'", sep=""), paste("ClimVarName='",Clim_Var,"'", sep=""))
 Vector.for.command.line.txt <- c(Vector.for.command.line.txt, text1)
 for (i in 1:(length(Location.df$Name))){
-  name<-as.character(Location.df$Name[i])
+  name <-as.character(Location.df$Name[i])
   #name<-gsub('([[:punct:]])|\\s+','_',name)
   # if(i<10){
   #   name<-paste('Catchment_0', as.character(i), sep="")
@@ -46,6 +47,10 @@ for (i in 1:(length(Location.df$Name))){
   if (Clim_Var == 'sstmean'){
     latitude=round(as.numeric(Location.df$Ocean_Lat[i]),3)
     longitude=round(as.numeric(Location.df$Ocean_Long[i]),3)
+  }
+  if (Location == 'catchment'){
+    latitude=round(as.numeric(Location.df$Catch_Lat[i]),3)
+    longitude=round(as.numeric(Location.df$Catch_Lon[i]),3)
     }
   text <- c(paste("latitude=",latitude,"", sep=""), paste("longitude=",longitude,"", sep=""),
 paste("name='",name,"'", sep=""),
@@ -56,7 +61,7 @@ P1_NARCliM_NC_to_CSV_CCRC_SS.py \\
   Vector.for.command.line.txt <- c(Vector.for.command.line.txt, text)
   if(i==10|i==20|i==31|i==length(Location.df$Name)){
     Vector.for.command.line.txt <- c(Vector.for.command.line.txt, " ")
-    text.file.name <- paste(Directory ,'/',Clim_Var, "_", Datatype, "_", Biasboolean,substring(as.character(i), 1,1), "_", ".txt", sep="")
+    text.file.name <- paste(Directory ,'/',Clim_Var, "_", Datatype, "_", Biasboolean,substring(as.character(i), 1,1), "_",Location, ".txt", sep="")
     #open and fill text file
     fileConn <- file(text.file.name)
     writeLines(Vector.for.command.line.txt, fileConn)

Analysis/Code/NARCLIM_Download/R_Preparing_BASH_script_for_NARCLIM_batch_download_GAB.R

@@ -0,0 +1,81 @@
+#code for preparing a text file with BASH code for batch download of NARCLIM data for the HUNTER WQ modeling of 
+#future climate scenarios 
+
+#NARCLIM Variables
+#evspsblmean   	water_evaporation flux (actual ET) long_name: Surface evaporation standard_name: water_evaporation_flux units: kg m-2 s-1
+#tasmean      mean near surface temperature
+#pracc 		precipitation daily precipitation sum (sum of convective prcacc and stratiform prncacc precip) 
+
+Clim_Var <- 'sstmean'
+Datatype <- 'T_NNRP'  #T_GCMS for GCM forcing, T_NNRP for reanalysis (only 1950-2009)
+Biasboolean <- 'False' #use bias corrected data? True or False python boolean
+
+Directory <- 'C:/Users/z5025317/OneDrive - UNSW/Hunter_CC_Modeling/07_Modelling/01_Input/BCGeneration/catchments/'   
+Filename <- 'Catchment_Prev_Hunter_Model_Centroids_VH_WGS84_attribute_Table.csv'
+
+Directory <- 'C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Data/NARCLIM_Site_CSVs/CASESTUDY_GAB/'
+Filename <- 'CASESTUDY2_GAB_NARCLIM_Point_Sites_V4.csv'
+
+#Load CSV with location names and lat lon coordinates
+Location.df <- data.frame(read.csv(paste(Directory, Filename, sep=""), header=T))
+
+for(type in c('min','max')){
+  #create empty vector for storing the command line text and open file
+  Vector.for.command.line.txt <- c()
+  Vector.for.command.line.txt <- c(Vector.for.command.line.txt, "module load python")
+  text1 <- c(paste("Datatype='",Datatype,"'", sep=""),
+  paste("Bias_corrected='",Biasboolean,"'", sep=""), paste("ClimVarName='",Clim_Var,"'", sep=""))
+  Vector.for.command.line.txt <- c(Vector.for.command.line.txt, text1)
+  
+  for (i in 1:(length(Location.df[,1]))){
+  #for (i in c(1,5,10)){ if only subset of catchments is needed like for Met file. 
+    #name<-as.character(Location.df$Name[i])
+    #name<-gsub('([[:punct:]])|\\s+','_',name)
+    if(type == 'min'){
+      #latlongs <- as.character(Location.df[,9])
+      name <- as.character(Location.df[,1][i])
+      latitude <- as.character(Location.df[,2][i])
+      longitude <- as.character(Location.df[,3][i])
+      }else if(type == 'max'){
+      name <- as.character(Location.df[,6][i])
+      latitude<-as.character(Location.df[,7][i])
+      longitude<-as.character(Location.df[,8][i])
+      }
+    # print(latlongs[i])
+    # names <- as.character(Location.df[,17])
+    # if(i<10){
+    #   name<-paste('Plant_0', as.character(i), sep="")
+    # }else{
+    #   name<-paste('Plant_', as.character(i), sep="")
+    # }
+    #print(name)
+    #print(names[i])
+    # latmin <- substr(latlongs[i], 5, 10)
+    # lonmin <- substr(latlongs[i], 18, 23)
+    # latmax <- substr(latlongs[i], 32, 37)
+    # lonmax <- substr(latlongs[i], 45, 50)
+    # latitude=latmax
+    # longitude=lonmax
+text <- c(paste("latitude=",latitude,"", sep=""), paste("longitude=",longitude,"", sep=""),
+paste("name='",name,"'", sep=""),
+"python /srv/ccrc/data02/z5025317/Code_execution/\\
+P1_NARCliM_NC_to_CSV_CCRC_SS.py \\
+--lat $latitude --lon $longitude --varName $ClimVarName --domain 'd01' --timestep \\
+'DAY' --LocationName $name --Datatype $Datatype --BiasBool $Bias_corrected")
+Vector.for.command.line.txt <- c(Vector.for.command.line.txt, text)
+    
+    if(i==10|i==20|i==30|i==40|i==45){
+      Vector.for.command.line.txt <- c(Vector.for.command.line.txt, " ")
+      text.file.name <- paste('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Data/NARCLIM_Site_CSVs/CASESTUDY_GAB/DataDownloadCCRC/',Clim_Var, "_", Datatype, "_", Biasboolean,as.character(i), type, ".txt", sep="")
+      #open and fill text file
+      fileConn <- file(text.file.name)
+      writeLines(Vector.for.command.line.txt, fileConn)
+      close(fileConn)
+      Vector.for.command.line.txt <- c()
+      Vector.for.command.line.txt <- c(Vector.for.command.line.txt, "module load python")
+      text1 <- c(paste("Datatype='",Datatype,"'", sep=""),
+                 paste("Bias_corrected='",Biasboolean,"'", sep=""), paste("ClimVarName='",Clim_Var,"'", sep=""))
+      Vector.for.command.line.txt <- c(Vector.for.command.line.txt, text1)
+      }
+    }
+}

Analysis/Code/P1_NARCliM_First_Pass_variab_deviation_plots.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+    # -*- coding: utf-8 -*-
 #==========================================================#
 #Last Updated - March 2018
 #@author: z5025317 Valentin Heimhuber
@@ -34,34 +34,38 @@ os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdo
      
 #loop through case study estuaries    
 Estuaries = ['HUNTER', 'RICHMOND', 'NADGEE', 'SHOALHAVEN', 'GEORGES','CATHIE']
-Estuaries = ['HUNTER']
+Estuaries = ['NADGEE','HUNTER', 'RICHMOND']
+
 for Est in Estuaries:
     
     #==========================================================#
     #set input parameters
     #==========================================================#
     Case_Study_Name = 'CASESTUDY2' 
-    Casestudy2_csv_path =  "Data/NARCLIM_Site_CSVs/CASESTUDY2/CASESTDUY2_NARCLIM_Point_Sites.csv"
+    Version = "V4"
+    OutVersion = "V4"
+    Casestudy2_csv_path =  'Data/NARCLIM_Site_CSVs/' + Case_Study_Name + '/' + Case_Study_Name + '_NARCLIM_Point_Sites.csv'
     #Estuary = 'HUNTER' # 'Belongil'
     Estuary = Est # 'Belongil'
     print Estuary
-    Base_period_start = '1970-01-01'        #Start of interval for base period of climate variability
+    Base_period_start = '1950-01-01'        #Start of interval for base period of climate variability
     Base_period_DELTA_start = '1990-01-01'   #Start of interval used for calculating mean and SD for base period (Delta base period)
     Base_period_end = '2009-01-01'          #use last day that's not included in period as < is used for subsetting
     Clim_var_type  = 'pracc'            #Name of climate variable in NARCLIM models  '*' will create pdf for all variables in folder
-    Stats = 'days_h_30'                  #'maxdaily' #maximum takes the annual max Precipitation instead of the sum
+    Stats = 'days_h_20'                  #'maxdaily' #maximum takes the annual max Precipitation instead of the sum 'days_h_30'
     
-    PD_Datasource = 'Station'                  #Source for present day climate data (historic time series) can be either: 'Station' or 'SILO'
-    SILO_Clim_var = ['max_temp']         #select the SILO clim variable to be used for base period. - see silo.py for detailed descriptions
+    PD_Datasource = 'SILO'                  #Source for present day climate data (historic time series) can be either: 'Station' or 'SILO'
+    SILO_Clim_var = ['daily_rain']         #select the SILO clim variable to be used for base period. - see silo.py for detailed descriptions
+    force_sea_levels = 'no'        #use fort denison sea levels to run the statistics
     Location = 'Estuary'                 # pick locaiton for extracting the SILO data can be: Estuary, Catchment, or Ocean
     
     Main_Plot = 'yes'
     presentdaybar = False               #include a bar for present day variability in the plots?
     present_day_plot = 'no'             #save a time series of present day  
     Allin1_delta_plot = 'yes'
-    Median_markers = 'no'              #plot the median horizontal lines on top of the delta range in the allin1 plot?      
-    Figure_headings = 'no'
-    Version = "V1"
+    Deltaxmin, Deltaymin = -20,40   #y limits for 0 baseline delta plots
+    Median_markers = 'yes'              #plot the median horizontal lines on top of the delta range in the allin1 plot?      
+    Figure_headings = 'yes'
     ALPHA_figs = 0                     #Set alpha of figure background (0 makes everything around the plot panel transparent)
     font = {'family' : 'sans-serif',        
         'weight' : 'normal',
@@ -72,7 +76,7 @@ for Est in Estuaries:
     
     #==========================================================#
     #set directory path for output files
-    output_directory = 'Output/' + Case_Study_Name + '/' + Estuary + '/' + '/Clim_Deviation_Plots/'
+    output_directory = 'Output/' + Case_Study_Name + '_' + OutVersion + '/' + Estuary + '/' + '/Clim_Deviation_Plots/'
     #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
     if not os.path.exists(output_directory):
         os.makedirs(output_directory)
@@ -86,7 +90,7 @@ for Est in Estuaries:
     #==========================================================#
     #read CSV file  
     #==========================================================#
-    Clim_Var_CSVs = glob.glob('./Output/' + Case_Study_Name + '/'  + Estuary + '/' + Estuary + '_' + Clim_var_type + '_' + Stats + '*')
+    Clim_Var_CSVs = glob.glob('./Output/' + Case_Study_Name + '_' + Version + '/'  + Estuary + '/' + Estuary + '_' + Clim_var_type + '_' + Stats + '*')
     clim_var_csv_path = Clim_Var_CSVs[0]
     Filename = os.path.basename(os.path.normpath(clim_var_csv_path))
     Clim_var_type = Filename.split('_', 2)[1]
@@ -117,6 +121,17 @@ for Est in Estuaries:
     if PD_Datasource == 'Station':
         Present_day_df,minplotDelta, maxplotDelta = fct.import_present_day_climdata_csv(Estuary, Clim_var_type)
     
+        if force_sea_levels == 'yes':
+            Estuary_Folder = "C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Data/Ocean_Data/Tide_Levels"
+            Present_day_df = pd.read_csv(Estuary_Folder + '/Fort_Denison_Daily_1900-2011.csv' , parse_dates=True, index_col=0)
+            Present_day_df = pd.read_csv(Estuary_Folder + '/Fort_Denison_Daily_1900-2011.csv' , parse_dates=True, index_col=0)
+            Present_day_df = Present_day_df.interpolate()
+            Present_day_df = pd.DataFrame(Present_day_df.loc[(Present_day_df.index >= Base_period_start) & (Present_day_df.index <= Base_period_end)])
+            [minplotDelta, maxplotDelta]=[1, 1]
+            
+            df = pd.read_csv(Estuary_Folder + '/Fort_Denison_Sub_Daily_1900-2011.csv',  parse_dates=[['Date', 'Time']])
+            df.index = pd.to_datetime(df.Date, format = 'dd/mm/Y') + pd.to_timedelta(df.Hour, unit='h')
+        
     if PD_Datasource == 'SILO':
         #read the CSV to extract the lat long and case stuy sites
         with open(Casestudy2_csv_path, mode='r') as infile:
@@ -162,7 +177,7 @@ for Est in Estuaries:
     
      #substract a constant from all values to convert from kelvin to celcius (temp)
     if Clim_var_type == 'sstmean':
-        Present_day_df = Present_day_df.iloc[:,0:(len(Present_day_df)-1)]-273.15
+        #Present_day_df = Present_day_df.iloc[:,0:(len(Present_day_df)-1)]-273.15
         Present_day_df.index = Present_day_df.index.to_period('D')
     #==========================================================#
     #create seasonal sums etc. 
@@ -172,7 +187,12 @@ for Est in Estuaries:
         Present_day_df_annual = Present_day_df_annual.replace(0, np.nan)
         Fdf_Seas_means = Present_day_df.resample('Q-NOV').max() #seasonal means
         Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
-    if(Stats[:4] =='days'):
+    elif Stats == 'maxmonthly':
+        Present_day_df_annual = Present_day_df.resample('M').max().resample('A').mean()
+        Present_day_df_annual = Present_day_df_annual.replace(0, np.nan)
+        Fdf_Seas_means = Present_day_df.resample('M').max().resample('Q-NOV').mean() #seasonal means
+        Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+    elif(Stats[:4] =='days'):
         Threshold = int(Stats[-2:])
         agg = ('>'+ str(Threshold) + '_count', lambda x: x.gt(Threshold).sum()),
         Present_day_df_annual = Present_day_df.resample('A').agg(agg)                
@@ -191,7 +211,30 @@ for Est in Estuaries:
             Present_day_df_weekly = Present_day_df.resample('W').mean()
             Fdf_Seas_means = Present_day_df.resample('Q-NOV').mean() #seasonal means
     #==========================================================#
-      
+    
+    #==========================================================# 
+    #calculate linear trend in present day series
+    #==========================================================#
+    if Stats == 'maxdaily' or Stats[:4] =='days' or Stats == 'maxmonthly':
+        coefficients, residuals, _, _, _ = np.polyfit(range(len(Present_day_df_annual.index)),Present_day_df_annual.values,1,full=True)
+        #mse = residuals[0]/(len(selected.index))
+        #nrmse = np.sqrt(mse)/(selected.max() - selected.min())
+        trend = coefficients[0]
+        print('Slope ' + str(coefficients[0]))
+        print(Base_period_start[:4]+ '-' + Base_period_end[:4] + ' trend was: ' + str(np.round(trend,4)) + ' units/year')
+    elif Stats == 'mean':
+        coefficients, residuals, _, _, _ = np.polyfit(range(len(Present_day_df.index)),Present_day_df.values,1,full=True)
+        #mse = residuals[0]/(len(selected.index))
+        #nrmse = np.sqrt(mse)/(selected.max() - selected.min())
+        if force_sea_levels == 'yes':
+            trend = coefficients[0]*12
+        else:
+            trend = coefficients[0]*365
+        print('Slope ' + str(coefficients[0]))
+        print(Base_period_start[:4]+ '-' + Base_period_end[:4] + ' trend was: ' + str(np.round(trend,5)) + ' units/year')
+        
+    #==========================================================#
+    
     
     #==========================================================#   
     #Loop through annual and seasons and create a deviation plot for each. 
@@ -224,7 +267,8 @@ for Est in Estuaries:
             if temp == 'SON':
                 Mean_df = Fdf_Seas_means[Fdf_Seas_means.index.quarter==4]
                 Column_names = ['Spring_near', 'Spring_far']
-            Present_Day_ref_df = Mean_df
+            Present_Day_ref_df = Mean_df  
+        
         #Subset to present day variability period
         Present_Day_ref_df = pd.DataFrame(Present_Day_ref_df.loc[(Present_Day_ref_df.index >= Base_period_start) & (Present_Day_ref_df.index <= Base_period_end)])
         #Subset to present day variability delta base period (this is the statistical baseline used for present day conditions)
@@ -284,8 +328,12 @@ for Est in Estuaries:
         Plot_in_df3['near future'] = df.iloc[1,0]
         Plot_in_df3['far future'] = df.iloc[0,0]
         Plot_in_df3 = Plot_in_df3.transpose()
-        plt.plot(Plot_in_df3['Med'], linestyle="", markersize=45, 
-             marker="_", color='darkblue', label="Median")
+#       plt.plot(Plot_in_df3['Med'], linestyle="", markersize=45, 
+#             marker="_", color='red', label="Median")
+        #Plot_in_df3['Med']
+        #Plot_in_df3['Med'].values
+        plt.plot(np.arange(2),Plot_in_df3['Med'].values[::-1], linestyle="", markersize=45, 
+             marker="_", color='red', label="Median")
         z = plt.axhline(float(Present_Day_Mean-2*Present_Day_SD), linestyle='-', color='black', alpha=.5)
         z.set_zorder(-1)
         z = plt.axhline(float(Present_Day_Mean+2*Present_Day_SD), linestyle='-', color='black', alpha=.5)
@@ -296,10 +344,10 @@ for Est in Estuaries:
         z.set_zorder(-1)
         z = plt.axhline(float(Present_Day_Mean), linestyle='--', color='red', alpha=.5)
         z.set_zorder(-1)
-        #plt.ylim(xmin, xmax)
-        plt.ylim(10, 140)
+        plt.ylim(xmin, xmax)
+        #plt.ylim(10, 140)
         if Figure_headings == 'yes':
-            plt.title(Clim_var_type + ' ' + temp )
+            plt.title(Clim_var_type + ' ' + temp)
         ax.grid(False)
         for tick in ax.get_xticklabels():
             tick.set_rotation(0)
@@ -321,17 +369,20 @@ for Est in Estuaries:
             z = plt.axhline(float(Present_Day_Mean), linestyle='--', color='red', alpha=.5)
             z.set_zorder(-1)
             #fig.patch.set_facecolor('deepskyblue')
-            plt.ylim(0, 40)
             fig.tight_layout()
             fig.patch.set_alpha(ALPHA_figs)
             if Figure_headings == 'yes':
-                plt.title(Clim_var_type + ' ' + Stats + ' ' + temp +' present day')
-            #plt.ylim(xmin, xmax)
+                #plt.title(Clim_var_type)
+                #plt.title(Clim_var_type + ' ' + Stats + ' ' + Base_period_start[:4] + '-' + Base_period_end[:4] + ' trend:' + str(np.round(trend,4)) + '/year')
+                plt.title(Base_period_start[:4] + '-' + Base_period_end[:4] + ' trend:' + str(np.round(trend,4)) + '/year')
+            plt.ylim(xmin, xmax)
+            #plt.ylim(0, 40)
             ax.grid(False)
             #if temp == 'MAM':
             i=i+4
         else:
             i=i+1
+        
         #create a data frame that contains all of the delta bars
         Plot_in_df_tp.index = Column_names
         Plot_in_df_tp['-2std'] = Plot_in_df_tp['-2std'] - Present_Day_Mean
@@ -349,11 +400,12 @@ for Est in Estuaries:
             else:
                 Plot_in_df_tp.plot.bar(stacked=True, color=uni_colors, edgecolor='none', legend=False, width=0.5,ax=ax)
             if Median_markers == 'yes':
-                plt.plot(Plot_in_df_tp.index, Plot_in_df_tp['Median'], linestyle="", markersize=13, 
-                     marker="_", color='darkblue', label="Median") 
+                plt.plot(np.arange(2),Plot_in_df_tp['Median'].values , linestyle="", markersize=45, 
+                     marker="_", color='red', label="Median") 
             z = plt.axhline(float(0), linestyle='--', color='red', alpha=.5)
             z.set_zorder(-1)
-            plt.ylim(-1, 20)
+            plt.ylim(Deltaxmin, Deltaymin)
+            #plt.ylim(xmin, xmax)
             if Figure_headings == 'yes':
                 plt.title(Clim_var_type + ' All Deltas ' + Stats)
             #ax.grid(False)
@@ -366,7 +418,7 @@ for Est in Estuaries:
     #plt.show()  
     if Main_Plot == 'yes': 
         if presentdaybar == False:
-            out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + PD_Datasource +  '_'  + SILO_Clim_var[0] +  '_' +  Version +  '_'  + '_NPDB.png'
+            out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + PD_Datasource +  '_'  + SILO_Clim_var[0] +  '_' + '_'  + Base_period_start +  '_'  + Base_period_end +  '_' +  Version +  '_'  + ' trend_' + str(np.round(trend[0],4)) + '.png'
         else:
             out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + PD_Datasource +  '_'  + SILO_Clim_var[0] +  '_' +  Version +  '_'  + '2.png'
         out_path = output_directory + '/' + out_file_name
@@ -387,17 +439,21 @@ for Est in Estuaries:
         else:
             Plot_in_df_tp.plot.bar(stacked=True, color=uni_colors, edgecolor='none', legend=False, width=0.5,ax=ax)
         if Median_markers == 'yes':
-            plt.plot(Plot_in_df_tp.index, Plot_in_df_tp['Median'], linestyle="", markersize=13, 
-                     marker="_", color='darkblue', label="Median") 
+#            plt.bar(Plot_in_df_tp.index, Plot_in_df_tp['Median'], linestyle="", markersize=13, 
+#                     marker="_", color='red', label="Median") 
+            plt.plot(np.arange(10), Plot_in_df_tp['Median'], linestyle="", markersize=13, 
+                     marker="_", color='red', label="Median")
         z = plt.axhline(float(0), linestyle='--', color='red', alpha=.5)
         z.set_zorder(-1)
-        plt.ylim(-5, 10)
+        plt.ylim(Deltaxmin, Deltaymin)
         if Figure_headings == 'yes':
             plt.title(Clim_var_type + ' All Delstas ' + Stats)
         #ax.grid(False)
         ax.xaxis.grid(False)
         for tick in ax.get_xticklabels():
-            tick.set_rotation(90)
+            tick.set_rotation(50)
+        plt.setp(ax.xaxis.get_majorticklabels(), ha='right')
+        #ax.set_xticklabels(xticklabels, rotation = 45, ha="right")
         fig.tight_layout()
         fig.patch.set_alpha(ALPHA_figs)
         plt.show()
@@ -450,7 +506,8 @@ for Est in Estuaries:
                 z.set_zorder(-1)
                 #fig.patch.set_facecolor('deepskyblue')
                 fig.patch.set_alpha(0)
-                plt.ylim(0, 400)
+                #plt.ylim(0, 400)
+                plt.ylim(xmin, xmax)
                 #export plot to png
             out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + Base_period_start +  '_'  + Base_period_end +  '_'  +  Version + 'Present_Day_Period.png'
             out_path = output_directory + '/' + out_file_name

Analysis/Code/P1_NARCliM_First_Pass_variab_deviation_plots_nonNARCLIM.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+    # -*- coding: utf-8 -*-
 """
 Created on Thu Jun 28 12:15:17 2018
 
@@ -53,16 +53,16 @@ Estuary = 'HUNTER' # 'Belongil'
 Base_period_start = '1970-01-01'        #Start of interval for base period of climate variability
 Base_period_DELTA_start = '1990-01-01'   #Start of interval used for calculating mean and SD for base period (Delta base period)
 Base_period_end = '2009-01-01'          #use last day that's not included in period as < is used for subsetting
-Clim_var_type  = 'Acidity'            #Name of climate variable in NARCLIM models  '*' will create pdf for all variables in folder
-[minplotDelta, maxplotDelta]=[0,1]
+Clim_var_type  = 'acidity'            #Name of climate variable in NARCLIM models  '*' will create pdf for all variables in folder
+[minplotDelta, maxplotDelta]=[0.5,1]
 
 #Source for present day climate data (historic time series) can be either: 'Station' or 'SILO'
 Location = 'Estuary'                 # pick locaiton for extracting the SILO data can be: Estuary, Catchment, or Ocean
 
 presentdaybar = False               #include a bar for present day variability in the plots?
 present_day_plot = 'yes'             #save a time series of present day        
-Version = "V1"
-Stats = 'mindaily' #'maxdaily' #maximum takes the annual max Precipitation instead of the sum
+Version = "V3"
+Stats = 'mean' #'maxdaily' #maximum takes the annual max Precipitation instead of the sum
 ALPHA_figs = 1 #Set alpha of figure background (0 makes everything around the plot panel transparent)
 #==========================================================#
 
@@ -70,7 +70,7 @@ ALPHA_figs = 1 #Set alpha of figure background (0 makes everything around the pl
 
 #==========================================================#
 #set directory path for output files
-output_directory = 'Output/' + Case_Study_Name + '/' + Estuary + '/' + '/Clim_Deviation_Plots/'
+output_directory = 'Output/' + Case_Study_Name +'_'+ Version + '/' + Estuary + '/' + '/Clim_Deviation_Plots/'
 #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
 if not os.path.exists(output_directory):
     os.makedirs(output_directory)
@@ -116,6 +116,9 @@ Present_day_df= Present_day_df['PH']
 if Stats == 'mindaily':
     Present_day_df_annual = Present_day_df.resample('A').min()
     Present_day_df_annual = Present_day_df_annual.replace(0, np.nan)
+if Stats == 'minmonthly':
+    Present_day_df_annual = Present_day_df.resample('M').resample('A').min()
+    Present_day_df_annual = Present_day_df_annual.replace(0, np.nan)
 if Stats == 'mean':
     Present_day_df_annual = Present_day_df.resample('A').mean()
     Present_day_df_annual = Present_day_df_annual.replace(0, np.nan)
@@ -146,10 +149,10 @@ index=['-2std', '-1std', 'Med', '1std', '2std']
 columns = ['near future', 'far future']
 Plot_in_df2 = pd.DataFrame(index=index, columns =columns )
 
-Plot_in_df2['near future'] = [float(Present_Day_Mean + Ensemble_Delta_df.near['10th']),np.NaN, float(Ensemble_Delta_df.near['Median']-Ensemble_Delta_df.near['10th']), 
-      np.NaN, float(Ensemble_Delta_df.near['90th']-Ensemble_Delta_df.near['Median'])]
-Plot_in_df2['far future'] = [float(Present_Day_Mean + Ensemble_Delta_df.far['10th']),np.NaN, float(Ensemble_Delta_df.far['Median']-Ensemble_Delta_df.far['10th']), 
-       np.NaN, float(Ensemble_Delta_df.far['90th']-Ensemble_Delta_df.far['Median'])]
+Plot_in_df2['near future'] = [float(Present_Day_Mean + Ensemble_Delta_df.near['90th']),np.NaN, float(Ensemble_Delta_df.near['Median']-Ensemble_Delta_df.near['90th']), 
+      np.NaN, float(Ensemble_Delta_df.near['10th']-Ensemble_Delta_df.near['Median'])]
+Plot_in_df2['far future'] = [float(Present_Day_Mean + Ensemble_Delta_df.far['90th']),np.NaN, float(Ensemble_Delta_df.far['Median']-Ensemble_Delta_df.far['90th']), 
+       np.NaN, float(Ensemble_Delta_df.far['10th']-Ensemble_Delta_df.far['Median'])]
 #transpose the data frame
 Plot_in_df_tp = Plot_in_df2.transpose()
 #do the individual plots
@@ -172,7 +175,7 @@ Plot_in_df3['near future'] = df.iloc[1,0]
 Plot_in_df3['far future'] = df.iloc[0,0]
 Plot_in_df3 = Plot_in_df3.transpose()
 plt.plot(Plot_in_df3['Med'], linestyle="", markersize=52, 
-     marker="_", color='darkblue', label="Median")
+     marker="_", color='red', label="Median")
 z = plt.axhline(float(Present_Day_Mean-2*Present_Day_SD), linestyle='-', color='black', alpha=.5)
 z.set_zorder(-1)
 z = plt.axhline(float(Present_Day_Mean+2*Present_Day_SD), linestyle='-', color='black', alpha=.5)
@@ -212,7 +215,7 @@ plt.ylim(xmin, xmax)
 ax.grid(False)
     
 if presentdaybar == False:
-    out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + Base_period_start +  '_'  + Base_period_end +  Version +  '_'  + '_NPDB.png'
+    out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_'  + Base_period_start +  '_'  + Base_period_end +  Version +  '_'  + '_NPDB2.png'
 out_path = output_directory + '/' + out_file_name
 fig.savefig(out_path)
     

Analysis/Code/P1_NARCliM_NC_to_CSV_CCRC_SS.py

@@ -1,4 +1,4 @@
-# -*- coding: utf-8 -*-
+`# -*- coding: utf-8 -*-
 from netCDF4 import *
 import numpy as np
 from numpy import *
@@ -152,6 +152,7 @@ if Bias_Correction_BOOL == 'True':
     #time.sleep(10) 
     #set up the loop variables for interrogating the entire NARCLIM raw data
     GCMs = ('CCCMA3.1','CSIRO-MK3.0','ECHAM5', 'MIROC3.2', 'NNRP')
+        #set up the loop variables for interrogating the entire NARCLIM raw data
     #
     #Define empty pandas data frames 
     Full_df = pd.DataFrame()

Analysis/Code/P1_NARCliM_NC_to_CSV_CCRC_SS_BASH_script_readme.txt

@@ -7,6 +7,7 @@ Variables available from NARCLIM (output):
 ‘pracc’ 		precipitation daily precipitation sum (sum of convective prcacc and stratiform prncacc precip) 
 ‘pr1Hmaxtstep’     	maximum 1 hour interval rainfall in a one day period
 'pr1Hmaxtstep' 		Max. 1-hour time-window moving averaged precipitation rate units: kg m-2 s-1 maximum 1-hour time-window moving averaged values from point values 60.0 second
+'pr30maxtstep'		Max. 30min time-window moving averaged precipitation rate units: kg m-2 s-1 maximum 1-hour time-window moving averaged values from point values 60.0 second
 'wss1Hmaxtstep'		Max. 1-hour time-window moving averaged surface wind speed units: m s-1 maximum 1-hour time-window moving averaged values from point values 60.0 second
 'wssmax' 		Surface wind speed standard_name: air_velocity units: m s-1 height: 10 m
 'wssmean'		Surface wind speed standard_name: air_velocity units: m s-1

Analysis/Code/P1_NARCliM_plots_Windows.py

@@ -25,6 +25,7 @@ matplotlib.style.use('ggplot')
 os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Analysis/Code')
 import climdata_fcts as fct
 import silo as sil
+
 ALPHA_figs = 0 
 font = {'family' : 'sans-serif',
         'weight' : 'normal',
@@ -39,10 +40,11 @@ os.chdir('C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdo
 #==========================================================#
 #set input parameters
 Case_Study_Name = 'CASESTUDY2'
+Version = 'V5' #V4 is latest for all model runs #V5 is just for the Hunter catchment climatology
 
 Estuaries = ['HUNTER', 'RICHMOND', 'NADGEE', 'SHOALHAVEN', 'GEORGES','CATHIE']
-Estuaries = ['HUNTER']
-
+Estuaries = ['HUNTER'] #,'HUNTER','RICHMOND']
+#Estuaries = ['SHOALHAVEN']
 for Est in Estuaries:
     #Estuary = 'HUNTER' # 'Belongil'
     Estuary = Est # 'Belongil'
@@ -56,16 +58,17 @@ for Est in Estuaries:
         #set input preferences
         #==========================================================#
         plot_pdf = 'no'
-        plot_pngs = 'yes'
+        plot_pngs = 'no'
         delta_csv = 'yes'
-        Stats = 'days_h_30'   # 'maxdaily', 'mean', 'days_h_25'
-        Version = 'V1'
-        #==========================================================#
-        
+        Stats = 'mean'   # 'maxdaily', 'mean', 'days_h_25'
+        DoMonthly = True
+        Perc_Vs_Abs = 'percent' #'percent' vs. 'absolute' deltas for near and far future
+        Location = 'Catchment'
+        #==========================================================# 
         
         #==========================================================#
         #set directory path for output files
-        output_directory = 'Output/' + Case_Study_Name + '/' + Estuary
+        output_directory = 'Output/' + Case_Study_Name + '_' + Version + '/' + Estuary
         #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
         if not os.path.exists(output_directory):
             os.makedirs(output_directory)
@@ -74,7 +77,7 @@ for Est in Estuaries:
             print('-------------------------------------------')
             
         #set directory path for individual png files
-        png_output_directory = 'Output/' + Case_Study_Name + '/' + Estuary + '/NARCLIM_Key_Figs'
+        png_output_directory = 'Output/' + Case_Study_Name +  '_' + Version + '/' + Estuary + '/NARCLIM_Key_Figs'
         #output_directory = 'J:/Project wrl2016032/NARCLIM_Raw_Data/Extracted'
         if not os.path.exists(png_output_directory):
             os.makedirs(png_output_directory)
@@ -82,13 +85,13 @@ for Est in Estuaries:
             print("output directory folder didn't exist and was generated")
             print('-------------------------------------------')
         #==========================================================#    
-        
-        
+                
         #==========================================================#
         Estuary_Folder = glob.glob('./Data/NARCLIM_Site_CSVs/'+ Case_Study_Name + '/' + Estuary + '*' )
+        if Location == 'Catchment':
+            Estuary_Folder = glob.glob('./Data/NARCLIM_Site_CSVs/'+ Case_Study_Name + '/' + Estuary + '*catch' )
         Clim_Var_CSVs = glob.glob(Estuary_Folder[0] + '/' + Clim_var_type + '*')
-        #==========================================================#
-        
+        #==========================================================#        
         
         #==========================================================#
         #read CSV files and start analysis
@@ -101,7 +104,7 @@ for Est in Estuaries:
         Full_df = pd.read_csv(clim_var_csv_path, index_col=0, parse_dates = True)
         #pandas datestamp index to period (we don't need the 12 pm info in the index (daily periods are enough))
         Full_df.index = Full_df.index.to_period('D')
-        Full_df = Full_df.drop(columns=['period'])
+        #Full_df = Full_df.drop(columns=['period'])
         Ncols_df = len(Full_df)
         #check data types of columns
         #Full_df.dtypes
@@ -119,7 +122,7 @@ for Est in Estuaries:
         if Clim_var_type in ['pr1Hmaxtstep']:
             Full_df = Full_df.iloc[:,0:(Ncols_df-1)]*60*60           
         if Clim_var_type in ['rsdsmean','rldsmean']:
-            Full_df = Full_df.iloc[:,0:(Ncols_df-1)]*60*60*24/1000000
+            Full_df = Full_df.iloc[:,0:(Ncols_df-1)]*60*60*24/1000000  #convert to unit used in SILO
         Fdf_1900_2080 = Full_df
         #==========================================================#
         
@@ -133,18 +136,40 @@ for Est in Estuaries:
                 Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
                 Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').max() #seasonal means
                 Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').max() #seasonal means
+                Fdf_Monthly_means = Fdf_Monthly_means.replace(0, np.nan)
+            elif(Stats[:4] =='days'):
+                Threshold = int(Stats[-2:])
+                #agg = ('abobe_27_count', lambda x: x.gt(27).sum()), ('average', 'mean')
+                agg = ('>'+ str(Threshold) + '_count', lambda x: x.gt(Threshold).sum()),
+                Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').agg(agg)                
+                #Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
+                Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').agg(agg)  #seasonal means
+                #Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').agg(agg)
             else:
                 Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').sum()
                 Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
                 Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').sum() #seasonal means
                 Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').sum() #Monthlyonal means
+                Fdf_Monthly_means = Fdf_Monthly_means.replace(0, np.nan)
         else:  
             if(Stats == 'maxdaily'):
                 Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').max()
                 Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
                 Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').max() #seasonal means
                 Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
-            if(Stats[:4] =='days'):
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').max() #Monthlyonal means
+                Fdf_Monthly_means = Fdf_Monthly_means.replace(0, np.nan)
+            elif(Stats == 'maxmonthly'):
+                Fdf_1900_2080_annual = Fdf_1900_2080.resample('M').max().resample('A').mean()
+                Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
+                Fdf_Seas_means = Fdf_1900_2080.resample('M').max().resample('Q-NOV').mean() #seasonal means
+                Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').max().resample('Q-NOV').mean() #Monthlyonal means
+                Fdf_Monthly_means = Fdf_Monthly_means.replace(0, np.nan)
+            elif(Stats[:4] =='days'):
                 Threshold = int(Stats[-2:])
                 #agg = ('abobe_27_count', lambda x: x.gt(27).sum()), ('average', 'mean')
                 agg = ('>'+ str(Threshold) + '_count', lambda x: x.gt(Threshold).sum()),
@@ -152,9 +177,11 @@ for Est in Estuaries:
                 #Fdf_1900_2080_annual = Fdf_1900_2080_annual.replace(0, np.nan)
                 Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').agg(agg)  #seasonal means
                 #Fdf_Seas_means = Fdf_Seas_means.replace(0, np.nan)
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').agg(agg)
             else:
                 Fdf_1900_2080_annual = Fdf_1900_2080.resample('A').mean()
                 Fdf_Seas_means = Fdf_1900_2080.resample('Q-NOV').mean() #seasonal means
+                Fdf_Monthly_means = Fdf_1900_2080.resample('M').mean() #seasonal means
         Fdf_1900_2080_means = Fdf_1900_2080.mean()
         #==========================================================#
         
@@ -179,14 +206,20 @@ for Est in Estuaries:
         #==========================================================#
         #Create Deltas of average change for annual and seasonal basis
         #==========================================================#
-        delta_all_df = fct.calculate_deltas_NF_FF2(Fdf_1900_2080_annual, Fdf_Seas_means, Stats)
-        
-        
+        delta_all_df = fct.calculate_deltas_NF_FF2(Fdf_1900_2080_annual, Fdf_Seas_means, Stats, Perc_Vs_Abs)
+        if DoMonthly ==True:
+            delta_all_df_monthly = fct.calculate_deltas_monthly(Fdf_Monthly_means, Stats, Perc_Vs_Abs)  
+            delta_all_df_monthly = pd.concat([delta_all_df_monthly.filter(regex= 'near'),delta_all_df_monthly.filter(regex= 'far')], axis=1)[-3:]  
+            
         #==========================================================#
         if delta_csv == 'yes':
             out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_NARCliM_ensemble_changes.csv'
             out_path = output_directory + '/' + out_file_name
             delta_all_df.to_csv(out_path)
+        if delta_csv == 'yes' and DoMonthly ==True:
+            out_file_name = Estuary  + '_' + Clim_var_type + '_' + Stats + '_NARCliM_ensemble_changes_monthly.csv'
+            out_path = output_directory + '/NARCLIM_Changes_Hunter/' + out_file_name
+            delta_all_df_monthly.to_csv(out_path)
         #==========================================================#
         
         #==========================================================#
@@ -216,6 +249,9 @@ for Est in Estuaries:
                  'tomato', 'royalblue', 'mediumpurple'  , 'tomato', 'royalblue', 'mediumpurple'  , 'tomato', 'royalblue', 'mediumpurple'  , 'tomato', 'royalblue', 'mediumpurple' ]
         plotcolours12 = ['darkolivegreen','turquoise', 'lightgreen', 'darkgreen',  'lightpink','slateblue', 'slategray', 'orange', 'tomato', 'peru', 'navy', 'teal']
         plotcolours15 = ['darkolivegreen','turquoise', 'lightgreen', 'darkgreen',  'lightpink','slateblue', 'slategray', 'orange', 'tomato', 'peru', 'navy', 'teal', 'lightgreen','lightpink','slateblue']
+        color_dict = {'CCCMA3.1_R1': 'darkolivegreen', 'CCCMA3.1_R2': 'turquoise', 'CCCMA3.1_R3': 'lightgreen', 'CSIRO-MK3.0_R2': 'darkgreen',
+                  'CSIRO-MK3.0_R1':'lightpink', 'CSIRO-MK3.0_R3':'slateblue','ECHAM5_R1':'slategray', 'ECHAM5_R2': 'orange', 'ECHAM5_R3':  'tomato',
+                  'MIROC3.2_R1': 'peru', 'MIROC3.2_R2': 'navy' ,'MIROC3.2_R3': 'teal', '10th':'lightgreen','median':'lightpink','90th':'slateblue'}
         #==========================================================#
          
          
@@ -284,27 +320,38 @@ for Est in Estuaries:
             #=========#
             # time series plot annual ALL models
             #=========#
-            png_out_file_name = Clim_var_type + '_' + Stats + '_TimeSeries_AllMods_' + Version + '.png'
+            png_out_file_name = Clim_var_type + '_' + Stats + '_TimeSeries_AllMods_' + Version + '3.png'
             png_out_path = png_output_directory + '/' + png_out_file_name
             plt.title(Clim_var_type + ' - ' + Stats + ' -  Time series - representative models')
             #prepare data
-            Mod_order = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,19,20,21,16,17,18,22,23,24,31,32,33,25,26,27,28,29,30,34,35,36]
-            test = Fdf_1900_2080_annual
-            Mod_Names = test.columns
-            New_Mod_Name = []
-            for i in range(0,len(Mod_Names)):
-                if(Stats[:4] =='days'):
-                    New_Mod_Name.append(str(Mod_order[i]+10) + '_' +  Mod_Names[i][0])
-                else:
-                    New_Mod_Name.append(str(Mod_order[i]+10) + '_' +  Mod_Names[i])
-            test.columns = New_Mod_Name
-            test_sorted = test.reindex_axis(sorted(test.columns), axis=1)
-            colnamest = test.columns
-            test_sorted.columns = [w[3:-5] for w in colnamest]
+#            Mod_order = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,19,20,21,16,17,18,22,23,24,31,32,33,25,26,27,28,29,30,34,35,36]
+#            test = Fdf_1900_2080_annual
+#            Mod_Names = test.columns
+#            New_Mod_Name = []
+#            for i in range(0,len(Mod_Names)):
+#                if(Stats[:4] =='days'):
+#                    New_Mod_Name.append(str(Mod_order[i]+10) + '_' +  Mod_Names[i][0])
+#                else:
+#                    New_Mod_Name.append(str(Mod_order[i]+10) + '_' +  Mod_Names[i])
+#            test.columns = New_Mod_Name
+#            test_sorted = test.reindex_axis(sorted(test.columns), axis=1)
+#            colnamest = test.columns
+#            test_sorted.columns = [w[3:-5] for w in colnamest]
+
             #plot
             fig = plt.figure(figsize=(8,7))
             ax=plt.subplot(2,1,1)
-            test_sorted.plot(ax=ax,color =  plotcolours36)
+            #test_sorted.plot(ax=ax) #,color =  plotcolours36)
+            Fdf_1900_2080_annual_b = Fdf_1900_2080_annual
+            New_Mod_Name = []
+            if(Stats[:4] =='days'):
+                for each in Fdf_1900_2080_annual_b.columns:
+                    New_Mod_Name.append(each[0][:-5])
+            else:
+                for each in Fdf_1900_2080_annual_b.columns:
+                    New_Mod_Name.append(each[:-5])
+            Fdf_1900_2080_annual_b.columns = New_Mod_Name
+            Fdf_1900_2080_annual_b.plot(ax=ax, color=[color_dict[x] for x in Fdf_1900_2080_annual_b.columns])
             plt.legend(loc=9, bbox_to_anchor=(0.5, -0.2))
             ax.xaxis.grid(False)
             fig.patch.set_alpha(ALPHA_figs)

Analysis/Code/climdata_fcts.py

@@ -71,9 +71,8 @@ def select_min_med_max_dif_model(NARCLIM_df):
     return dfall , dfmin, dfmed, dfmax, Min_dif_mod_name,Med_dif_mod_name, Max_dif_mod_name
 
 
-def calculate_deltas_NF_FF2(Annual_df, Seasonal_df, Stats):
+def calculate_deltas_NF_FF2(Annual_df, Seasonal_df, Stats, Perc_vs_Abs):
     """calculates the "deltas" between nearfuture and present day for annual or seasonal climate data in pandas TS format"""
-
     times = ['annual', 'DJF', 'MAM', 'JJA','SON']
     delta_all_df = pd.DataFrame()
     for temp in times:
@@ -106,10 +105,63 @@ def calculate_deltas_NF_FF2(Annual_df, Seasonal_df, Stats):
         for unique_model in unique_models:
             dfdiff = Mean_df.filter(regex= unique_model)
             type(dfdiff)
-            delta_NF = dfdiff[1] - dfdiff[0]
-            delta_NF_ensemble.append(delta_NF)
-            delta_FF = dfdiff[2] - dfdiff[1]
-            delta_FF_ensemble.append(delta_FF)
+            if Perc_vs_Abs == 'absolute':
+                delta_NF = dfdiff[1] - dfdiff[0]
+                delta_NF_ensemble.append(delta_NF)
+                delta_FF = dfdiff[2] - dfdiff[0]
+                delta_FF_ensemble.append(delta_FF)
+            if Perc_vs_Abs == 'percent':
+                delta_NF = ((dfdiff[1] - dfdiff[0])/dfdiff[0])*100
+                delta_NF_ensemble.append(delta_NF)
+                delta_FF = ((dfdiff[2] - dfdiff[0])/dfdiff[0])*100
+                delta_FF_ensemble.append(delta_FF)
+    
+        delta_df1=pd.DataFrame(delta_NF_ensemble, index=unique_models)
+        delta_df2=pd.DataFrame(delta_FF_ensemble, index=unique_models)
+        delta_df= pd.concat([delta_df1, delta_df2], axis=1)
+    
+        #rename columns
+        delta_df.columns = Column_names
+        #add a row with medians and 10 and 90th percentiles
+        delta_df.loc['10th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 10), Column_names[1]:np.percentile(delta_df[Column_names[1]], 10)})
+        delta_df.loc['median'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 50), Column_names[1]:np.percentile(delta_df[Column_names[1]], 50)})
+        delta_df.loc['90th'] = pd.Series({Column_names[0]:np.percentile(delta_df[Column_names[0]], 90), Column_names[1]:np.percentile(delta_df[Column_names[1]], 90)})
+        #append df to overall df
+        delta_all_df = pd.concat([delta_all_df, delta_df], axis=1)
+        if(Stats[:4] =='days'):
+            delta_all_df  = delta_all_df .astype(int).fillna(0.0)
+    return delta_all_df
+
+def calculate_deltas_monthly(Monthly_df, Stats, Perc_vs_Abs):  
+    """calculates the "deltas" between nearfuture and present day for annual or seasonal climate data in pandas TS format"""   
+    delta_all_df = pd.DataFrame()
+    for i in range(1, 13, 1):
+        Mean_df = Monthly_df[Monthly_df.index.month==i].mean()
+        Column_names = [str(i)+'_near', str(i)+'_far']
+        if(Stats[:4] =='days'):
+            models = list(Monthly_df.mean().index.get_level_values(0))
+        else:
+            models = list(Monthly_df.mean().index)
+        newmodel = []
+        for each in models:
+            newmodel.append(each[:-5])
+        unique_models = set(newmodel)
+        # calculate diff for each unique model
+        delta_NF_ensemble = []
+        delta_FF_ensemble = []
+        for unique_model in unique_models:
+            dfdiff = Mean_df.filter(regex= unique_model)
+            type(dfdiff)
+            if Perc_vs_Abs == 'absolute':
+                delta_NF = dfdiff[1] - dfdiff[0]
+                delta_NF_ensemble.append(delta_NF)
+                delta_FF = dfdiff[2] - dfdiff[0]
+                delta_FF_ensemble.append(delta_FF)
+            if Perc_vs_Abs == 'percent':
+                delta_NF = ((dfdiff[1] - dfdiff[0])/dfdiff[0])*100
+                delta_NF_ensemble.append(delta_NF)
+                delta_FF = ((dfdiff[2] - dfdiff[0])/dfdiff[0])*100
+                delta_FF_ensemble.append(delta_FF)
     
         delta_df1=pd.DataFrame(delta_NF_ensemble, index=unique_models)
         delta_df2=pd.DataFrame(delta_FF_ensemble, index=unique_models)
@@ -126,7 +178,6 @@ def calculate_deltas_NF_FF2(Annual_df, Seasonal_df, Stats):
         if(Stats[:4] =='days'):
             delta_all_df  = delta_all_df .astype(int).fillna(0.0)
     return delta_all_df
-  
     
 def import_present_day_climdata_csv(Estuary, Clim_var_type):
     """

Analysis/Code/ggplot_time_series_with_trends.R

@@ -19,30 +19,39 @@ setwd("C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/P
 #Set inputs
 ######################
 Case.Study <- "CASESTUDY2"
-Estuary <- "RICHMOND"
-Riv.Gauge.loc <- "OAKLANDROAD"     #GRETA 
-Est.Gauge.loc <-  "CORAKI"          #"RAYMONDTERRACE" # "HEXHAMBRIDGE"
+Estuary <- "HUNTER"
+Riv.Gauge.loc <- "GRETA"     #GRETA 
+Est.Gauge.loc <-  "RAYMONDTERRACE"   #"CORAKI"          #"RAYMONDTERRACE" # "HEXHAMBRIDGE"
 logtransformFlow <- TRUE
 ggplotGAM.k <- 15
 rivTempGAM.k <- 20
-Version <- 'V2'
+Version <- 'V3'
+
+Fontsize <- 12
 ######################
 
 ######################
-Output.Directory <- paste('./Output/', Case.Study, '/', Estuary,'/Recent_Trends/Riv_', Riv.Gauge.loc,'_Est_',Est.Gauge.loc,'_GAMk', ggplotGAM.k, '/', sep="")
+Output.Directory <- paste('./Output/CASESTUDY2_V4/', Estuary,'/Recent_Trends/', sep="")
 if (file.exists(Output.Directory)){
   print('output folder already existed and was not created again')
   } else {
   dir.create(file.path(Output.Directory))
   print('output folder did not exist and was created')
   }
+Output.Directory <- paste('./Output/CASESTUDY2_V4/', Estuary,'/Recent_Trends/Riv_', Riv.Gauge.loc,'_Est_',Est.Gauge.loc,'_GAMk', ggplotGAM.k, 'b/', sep="")
+if (file.exists(Output.Directory)){
+  print('output folder already existed and was not created again')
+} else {
+  dir.create(file.path(Output.Directory))
+  print('output folder did not exist and was created')
+}
 ######################
 
 ######################
 #Set input file paths
 ######################
 
-pattern = paste('SILO_climdata_', Estuary,'*', sep="")
+pattern = paste('SILO_climdata_', Estuary,'_Catchment*', sep="")
 AirT_CSV_Path <- list.files(paste("./Data/SILO/",Case.Study, '/',sep=""), pattern, full.names=T, recursive=T)
 
 pattern = paste(Estuary,'@', Riv.Gauge.loc, '.*.ALL.csv', sep="")
@@ -114,6 +123,12 @@ RivT.full.pvalNCV_ECall <- summary(linear.trend.model_EC_all )$coefficients[2,4]
 RivT.full.lintrend <- summary(linear.trend.model_EC_all )$coefficients[2,1] * 356
 ############River temp
 
+#export interpolated data as csv
+#csv.name <- "C:/Users/z5025317/OneDrive - UNSW/CC_Estuaries_CASESTUDY2/Data/River_Gauge_Data/HUNTER@Greta_210064_Temp_interpolated.csv"
+#write.csv(RivT.df, csv.name)
+
+
+
 ############River flow
 #Load a daily (no gaps) time series as a time serie baseline for other time series used here
 #Here we use the raw DPI CSV format that comes with a bunch of metadata
@@ -128,7 +143,8 @@ rm(dat,char.df)
 #RivQ.full.TS <- zoo(log10((as.numeric(as.character(RivQ.df$Flow))) +1) , order.by= as.Date(RivQ.df[,"Date"], format = "%d/%m/%Y")) #=daily time series of rainfall for creation of clean, daily TS of ET and Q
 RivQ.full.TS <- zoo(as.numeric(as.character(RivQ.df$Flow)), order.by= as.Date(RivQ.df[,"Date"], format = "%d/%m/%Y")) #=daily time series of rainfall for creation of clean, daily TS of ET and Q
 
-RivQ.TS <- window(RivQ.full.TS, start=as.Date("1990-01-01"), end=as.Date("2018-01-01"))
+#RivQ.TS <- window(RivQ.full.TS, start=as.Date("1990-01-01"), end=as.Date("2018-01-01"))
+RivQ.full.TS <- window(RivQ.full.TS, start=as.Date("2013-06-01"), end=as.Date("2018-06-01"))
 RivQ.full.df <- data.frame(RivQ.full.TS)   ### This is only done because 
 RivQ.df <- data.frame(RivQ.TS)
 colnames(RivQ.df) <- 'RivQmean'
@@ -149,7 +165,10 @@ RivQ.full.lintrend <- summary(linear.trend.model_EC_all )$coefficients[2,1] * 35
 #Load a daily (no gaps) time series as a time serie baseline for other time series used here
 SST.df <- data.frame(read.csv(SST_CSV_Path))
 SST.full.TS <- zoo(SST.df$NNRP_R1_1950-273.15, order.by= as.Date(SST.df[,"X"], format = "%Y-%m-%d")) #=daily time series of rainfall for creation of clean, daily TS of ET and Q
-SST.TS <- window(SST.full.TS, start=as.Date("1990-01-01"), end=as.Date("2018-01-01"))
+#SST.TS <- window(SST.full.TS, start=as.Date("1990-01-01"), end=as.Date("2018-01-01"))
+
+SST.full.TS <- window(SST.full.TS, start=as.Date("2013-06-01"), end=as.Date("2018-06-01"))
+
 SST.full.df <- data.frame(SST.full.TS)
 SST.df <- data.frame(SST.TS)
 str(SST.df)
@@ -185,8 +204,7 @@ rm(dat,char.df)
 #replace negative values with NA
 EstT.df$Temp <- replace(EstT.df$Temp, which(as.numeric(as.character(EstT.df$Temp)) < 11), NA)
 EstT.full.TS <- zoo(as.numeric(as.character(EstT.df$Temp)), order.by= as.Date(EstT.df[,"Date"], format = "%d/%m/%Y")) #=daily time series of rainfall for creation of clean, daily TS of ET and Q
-plot(EstT.full.TS)
-EstT.TS <- window(EstT.full.TS, start=as.Date("2013-06-01"), end=as.Date("2018-01-01"))
+EstT.TS <- window(EstT.full.TS, start=as.Date("2013-06-01"), end=as.Date("2018-06-01"))
 EstT.full.TS <- EstT.TS
 EstT.full.df <- data.frame(EstT.TS)   ### This is only done because of poor data at beginning
 EstT.df <- data.frame(EstT.TS)
@@ -211,7 +229,7 @@ EstT.full.lintrend <- summary(linear.trend.model_EC_all )$coefficients[2,1] * 35
 ##################################### Full Time Period
 #Air temp Full period 
 p1air <- ggplot(AirT.full.df, aes(y=tasmean, x=index(AirT.full.TS))) + geom_line(alpha=0.5) + 
-  ggtitle(paste(Estuary," Catchment Centroid - Linear and smooth trend in catchment airT (SILO) lin trend was ",
+  ggtitle(paste(Estuary," Catchment Centroid - Linear and smooth trends in catchment airT (SILO) lin trend was ",
                 round(AirT.full.lintrend,3), ' C°/year with p=', round(AirT.full.pvalNCV_ECall,10), sep=" ")) +
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
@@ -219,12 +237,14 @@ p1air <- ggplot(AirT.full.df, aes(y=tasmean, x=index(AirT.full.TS))) + geom_line
   ylab("Air Temperature [C°]") + xlab("Time")
 
 p1riv <- ggplot(RivT.full.df, aes(y=rivTmean, x=index(RivT.TS))) + geom_line(alpha=0.5) + 
-  ggtitle(paste(Estuary,'@', Riv.Gauge.loc, " - Linear and smooth trend in river temperature (GAUGE) lin trend was ",
-                round(RivT.full.lintrend,3), ' C°/year with p=', round(RivT.full.pvalNCV_ECall,10), sep=" ")) +
+  ggtitle(paste(Estuary, " - Linear and smooth trends in gauged river temperature (@", Riv.Gauge.loc  ,") - Linear trend was ",
+                round(RivT.full.lintrend,3), 'C°/year with p=', sprintf("%.5f",round(RivT.full.pvalNCV_ECall,10)), sep="")) +
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("River Temperature [C°]") + xlab("Time")
+  ylab("River Temperature [C°]") + xlab("Time") + xlab(NULL) +  
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 
 if(logtransformFlow ==TRUE){
@@ -234,7 +254,9 @@ p1rivQ <- ggplot(RivQ.full.df, aes(y=log10(RivQmean+2), x=index(RivQ.full.TS)))
     theme(plot.title=element_text(face="bold", size=9)) +
     geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
     stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-    ylab(expression(paste("log10(River Flow [ML/day] + 2)", sep=""))) + xlab("Time")
+    ylab(expression(paste("log10(River Flow [ML/day] + 2)", sep=""))) + xlab("Time") +
+    theme(axis.text=element_text(size=Fontsize)) +
+    theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
   } else {
   p1rivQ <- ggplot(RivQ.full.df, aes(y=RivQmean, x=index(RivQ.full.TS))) + geom_line(alpha=0.5) + 
     ggtitle(paste(Estuary,'@', Riv.Gauge.loc, " - Linear and smooth trend in river flow (GAUGE) lin trend was ",
@@ -242,28 +264,54 @@ p1rivQ <- ggplot(RivQ.full.df, aes(y=log10(RivQmean+2), x=index(RivQ.full.TS)))
     theme(plot.title=element_text(face="bold", size=9)) +
     geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
     stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-    ylab(expression(paste("River Flow [ML/day]", sep=""))) + xlab("Time") 
+    ylab(expression(paste("River Flow [ML/day]", sep=""))) + xlab("Time") +
+    theme(axis.text=element_text(size=Fontsize)) +    
+    theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
     }
 
 
 #Sea temp Full period 
 p1sst <- ggplot(SST.full.df, aes(y=SSTmean, x=index(SST.full.TS))) + geom_line(alpha=0.5) + 
-  ggtitle(paste(Estuary, "NNRP (NARCLIM reanalysis) - Linear and smooth trend in sea surface temperature (NNRP) lin trend was ",
-                round(SST.full.lintrend,3), ' C°/year with p=', round(SST.full.pvalNCV_ECall,10), sep=" ")) +
+  ggtitle(paste(Estuary, " offshore - Linear and smooth trends in sea surface temperature (NNRP NARCLIM reanalysis) linear trend was ",
+                round(SST.full.lintrend,3), 'C°/year with p=', sprintf("%.5f",round(SST.full.pvalNCV_ECall,10)), sep=" ")) +
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("Sea Surface Temperature [C°]") + xlab("Time")
+  ylab("Sea Surface Temperature [C°]") + xlab("Time")+ xlab(NULL) +
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 p1Est <- ggplot(EstT.full.df, aes(y=EstTmean, x=index(EstT.TS))) + geom_line(alpha=0.5) + 
   ggtitle(paste(Estuary,'@', Est.Gauge.loc, " - Linear and smooth trend in Estuary temperature (GAUGE) lin trend was ",
-                round(EstT.full.lintrend,3), ' C°/year with p=', round(EstT.full.pvalNCV_ECall,10), sep=" ")) +
+                round(EstT.full.lintrend,3), 'C°/year with p=', round(EstT.full.pvalNCV_ECall,10), sep=" ")) +
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("Estuary Temperature [C°]") + xlab("Time")
+  ylab("Estuary Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
+p1Est2 <- ggplot(EstT.full.df, aes(y=EstTmean, x=index(EstT.TS))) + geom_line(alpha=0.5) + 
+  ggtitle(paste(Estuary,'@', Est.Gauge.loc, " - Linear and smooth trend in Estuary temperature (GAUGE) lin trend was ",
+                round(EstT.full.lintrend,3), 'C°/year with p=', round(EstT.full.pvalNCV_ECall,10), sep=" ")) +
+  theme(plot.title=element_text(face="bold", size=9)) +
+  geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
+  #stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
+  binomial_smooth(formula = y ~ splines::ns(x, 2)) +
+  ylab("Estuary Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
+png.name <- paste(Output.Directory, Estuary, '@', Est.Gauge.loc, '_Trends_estTmean_full_period_', Sys.Date(),"nosmoothb3.png", sep="")
+png(file = png.name, width = 10.5, height = 4, units='in', res=500)
+grid.arrange(p1Est2,ncol=1)
+dev.off()
 
 
+gA1 <- ggplotGrob(p1riv)
+gA2 <- ggplotGrob(p1sst)
+gA1$widths <- gA2$widths
+
 #export to png
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_tasmean_full_period_', Sys.Date(),".png", sep="")
 png(file = png.name, width = 10.5, height = 7, units='in', res=500)
@@ -271,7 +319,11 @@ grid.arrange(p1air,ncol=1)
 dev.off()
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_rivTmean_full_period_', Sys.Date(),".png", sep="")
 png(file = png.name, width = 10.5, height = 7, units='in', res=500)
-grid.arrange(p1riv,ncol=1)
+grid.arrange(p1riv,p1riv,ncol=1)
+dev.off()
+png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_rivTmean_SSTmean_full_period4_', Sys.Date(),".png", sep="")
+png(file = png.name, width = 10.5, height = 7, units='in', res=500)
+grid.arrange(gA1,gA2,ncol=1)
 dev.off()
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_RivQmean_full_period_', Sys.Date(),".png", sep="")
 png(file = png.name, width = 10.5, height = 7, units='in', res=500)
@@ -279,12 +331,18 @@ grid.arrange(p1rivQ,ncol=1)
 dev.off()
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_SSTmean_full_period_', Sys.Date(),".png", sep="")
 png(file = png.name, width = 10.5, height = 7, units='in', res=500)
-grid.arrange(p1sst,ncol=1)
+grid.arrange(p1sst,p1sst,ncol=1)
 dev.off()
-png.name <- paste(Output.Directory, Estuary, '@', Est.Gauge.loc, '_Trends_estTmean_full_period_', Sys.Date(),".png", sep="")
-png(file = png.name, width = 10.5, height = 7, units='in', res=500)
+png.name <- paste(Output.Directory, Estuary, '@', Est.Gauge.loc, '_Trends_estTmean_full_period_', Sys.Date(),"b.png", sep="")
+png(file = png.name, width = 10.5, height = 4, units='in', res=500)
 grid.arrange(p1Est,ncol=1)
 dev.off()
+
+png.name <- paste(Output.Directory, Estuary, '@', Est.Gauge.loc, '_Trends_estTmean_full_period_', Sys.Date(),"nosmoothb.png", sep="")
+png(file = png.name, width = 10.5, height = 4, units='in', res=500)
+grid.arrange(p1Est2,ncol=1)
+dev.off()
+
 ##################################### Full Time Period
 
 
@@ -300,7 +358,9 @@ p2air <- ggplot(combined.df, aes(y=tasmean, x=index(combined.TS))) + geom_line(a
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("Air Temperature [C°]") + xlab("Time")
+  ylab("Air Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) + 
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 #Riv temp 
 p2riv <- ggplot(combined.df, aes(y=rivTmean, x=index(combined.TS))) + geom_line(alpha=0.5) + 
@@ -309,7 +369,9 @@ p2riv <- ggplot(combined.df, aes(y=rivTmean, x=index(combined.TS))) + geom_line(
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("River Temperature [C°]") + xlab("Time")
+  ylab("River Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) + 
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 #Riv flow
 if(logtransformFlow ==TRUE){
@@ -319,7 +381,9 @@ if(logtransformFlow ==TRUE){
     theme(plot.title=element_text(face="bold", size=9)) +
     geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
     stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-    ylab(expression(paste("log10(River Flow [ML/day] + 2)", sep=""))) + xlab("Time")
+    ylab(expression(paste("log10(River Flow [ML/day] + 2)", sep=""))) + xlab("Time")+
+    theme(axis.text=element_text(size=Fontsize)) + 
+    theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
   } else {
   p2rivQ <- ggplot(combined.df, aes(y=rivQmean, x=index(combined.TS))) + geom_line(alpha=0.5) + 
     ggtitle(paste(Estuary,'@', Riv.Gauge.loc, " - Linear and smooth trend in river flow (GAUGE) lin trend was ",
@@ -327,7 +391,9 @@ if(logtransformFlow ==TRUE){
     theme(plot.title=element_text(face="bold", size=9)) +
     geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
     stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-    ylab(expression(paste("River Flow [ML/day]", sep=""))) + xlab("Time")
+    ylab(expression(paste("River Flow [ML/day]", sep=""))) + xlab("Time")+
+    theme(axis.text=element_text(size=Fontsize)) + 
+    theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
     }
 
 #Sea temp 
@@ -337,7 +403,9 @@ p2sst <- ggplot(combined.df, aes(y=SSTmean, x=index(combined.TS))) + geom_line(a
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("Sea Surface Temperature [C°]") + xlab("Time")
+  ylab("Sea Surface Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) + 
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 #sst temp 
 p2Est <- ggplot(combined.df, aes(y=EstTmean, x=index(combined.TS))) + geom_line(alpha=0.5) + 
@@ -346,7 +414,9 @@ p2Est <- ggplot(combined.df, aes(y=EstTmean, x=index(combined.TS))) + geom_line(
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   #stat_smooth(method=gam, formula=y~s(x, k=ggplotGAM.k), se=T, size=0.5) +
-  ylab("Estuary Temperature [C°]") + xlab("Time")
+  ylab("Estuary Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +  
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
 
 #export to png
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_tasmean_1990-present_', Sys.Date(),".png", sep="")
@@ -382,6 +452,11 @@ png(file = png.name, width = 10.5, height = 7, units='in', res=500)
 grid.arrange(gA,gB ,gC,ncol=1)
 dev.off()
 
+png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_SST_RivT_1990-present_', Sys.Date(),".png", sep="")
+png(file = png.name, width = 10.5, height = 7, units='in', res=500)
+grid.arrange(gB,gC, ncol=1)
+dev.off()
+
 png.name <- paste(Output.Directory, Estuary, '@', Riv.Gauge.loc, '_Trends_SST_RivT_EstT_1990-present_', Sys.Date(),".png", sep="")
 png(file = png.name, width = 10.5, height = 7, units='in', res=500)
 grid.arrange(gB,gD,gC,ncol=1)
@@ -413,3 +488,4 @@ dev.off()
 
 
 
+

Analysis/Code/ggplot_time_series_with_trends_Waves_SST_OEH.R

@@ -19,7 +19,7 @@ setwd("C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/P
 #Set inputs
 ######################
 Case.Study <- "CASESTUDY2"
-Estuary <- "RICHMOND"
+Estuary <- "GEORGES"
 Climvar <- 'tasmean'
 ggplotGAM.k <- 7
 ######################
@@ -43,7 +43,7 @@ pattern = paste(Estuary, '.*.csv', sep="")
 Buoy_CSV_Path <- list.files("./Data/Ocean_Data/Waves_SST/", pattern, full.names=T)
 Buoy.name <- substr(list.files("./Data/Ocean_Data/Waves_SST/", pattern, full.names=F), nchar(Estuary)+2, nchar(Estuary)+7)
 
-SST.df <- data.frame(read.csv(AirT_CSV_Path, colClasses = "character"))
+SST.df <- data.frame(read.csv(Buoy_CSV_Path, colClasses = "character"))
 colnames(SST.df) <- as.character(SST.df[9,])
 SST.df = SST.df[-c(1:9), ] 
 
@@ -95,6 +95,13 @@ SST.full.df$Julday1 <- seq(1,length(SST.full.df[,1]),1)
 linear.trend.model_EC_all <- lm(SSTmean ~ Julday1, SST.full.df)
 SST.pvalNCV_ECall <- summary(linear.trend.model_EC_all )$coefficients[2,4] 
 SST.lintrend <- summary(linear.trend.model_EC_all )$coefficients[2,1] * 365
+
+
+
+#export interpolated data as csv
+csv.name <- paste("C:/Users/z5025317/OneDrive - UNSW/WRL_Postdoc_Manual_Backup/WRL_Postdoc/Projects/Paper#1/Data/Ocean_Data/Waves_SST/Processed/",Estuary , "_SST_Daily.csv", sep="")
+write.csv(SST.full.df, csv.name)
+
 ######################
 
 
@@ -109,7 +116,10 @@ p1air <- ggplot(Hsig.full.df, aes(y=Hsigmean, x=index(Hsig.full.TS))) + geom_lin
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x,  k=4), se=T, size=0.5, col="red") +
-  ylab("Significant Wave Height [m]") + xlab("Time")
+  ylab("Significant Wave Height [m]") + xlab("Time")  +
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
 
 #export to png
 png.name <- paste(Output.Directory, '/Trends_Significant_Wave_Height_',Buoy.name,  '_full_period_', Sys.Date(),".png", sep="")
@@ -125,7 +135,10 @@ p1air <- ggplot(Hsig.full.df, aes(y=Hsigmean, x=index(Hsig.full.TS))) + geom_lin
   stat_smooth(method=gam, formula=y~s(x,  k=13), se=T, size=0.5, col="red") +
   #stat_smooth(method=gam, formula=y~s(x,  k=8), se=T, size=0.5, cor="blue") +
   stat_smooth(method=gam, formula=y~s(x,  k=5), se=T, size=0.5, col="green") +
-  ylab("Significant Wave Height [m]") + xlab("Time")
+  ylab("Significant Wave Height [m]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
 
 #export to png
 png.name <- paste(Output.Directory, '/Trends_Significant_Wave_Height_',Buoy.name,  '_MultiGAM_full_period_', Sys.Date(),".png", sep="")
@@ -140,7 +153,10 @@ p1air <- ggplot(SST.full.df, aes(y=SSTmean, x=index(SST.full.TS))) + geom_line(a
   theme(plot.title=element_text(face="bold", size=9)) +
   geom_smooth(method='lm',fill="green", formula=y~x, colour="darkgreen", size = 0.5) +
   stat_smooth(method=gam, formula=y~s(x,  k=4), se=T, size=0.5, col="red") +
-  ylab("Sea Surface Temperature [C°]") + xlab("Time")
+  ylab("Sea Surface Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
 
 #export to png
 png.name <- paste(Output.Directory, '/Trends_SST_',Buoy.name,  '_full_period_',  Sys.Date(),".png", sep="")
@@ -156,7 +172,10 @@ p1air <- ggplot(SST.full.df, aes(y=SSTmean, x=index(SST.full.TS))) + geom_line(a
   stat_smooth(method=gam, formula=y~s(x,  k=13), se=T, size=0.5, col="red") +
   #stat_smooth(method=gam, formula=y~s(x,  k=8), se=T, size=0.5, cor="blue") +
   stat_smooth(method=gam, formula=y~s(x,  k=5), se=T, size=0.5, col="green") +
-  ylab("Sea Surface Temperature [C°]") + xlab("Time")
+  ylab("Sea Surface Temperature [C°]") + xlab("Time")+
+  theme(axis.text=element_text(size=Fontsize)) +
+  theme(panel.grid.major.x = element_blank() ,panel.grid.minor.x = element_blank(), panel.grid.major.y = element_line( size=.1, color="white" ))
+
 
 #export to png
 png.name <- paste(Output.Directory, '/Trends_SST_',Buoy.name, '_MultiGAM_full_period_', Sys.Date(),".png", sep="")