--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/clim_data.R	Thu Aug 09 05:01:04 2018 -0400
@@ -0,0 +1,136 @@
+#!/usr/bin/env Rscript
+
+
+args <- commandArgs(trailingOnly = TRUE)
+
+#Rscript clim_data.R 'worldclim' 'var' 'resolution' 'OutputFormat' #'FRA' #'prec1'
+if (length(args)==0 | args[1]=="-h" | args[1]=="--help"){
+  print ("general script execution : Rscript clim_data.R \'worldclim\' \'var\' resolution \'OutputFormat\' #\'variable-to-plot\' #\'region_code\'")
+  print ("eg : Rscript clim_data.R \'worldclim\' \'prec\' 10 \'raster\' #\'prec1' #\'FRA\'")
+  q('no')
+} 
+
+
+#Climatic variables dictionaries
+months<-c("January","February","March","April","May","June","July","August","September","October","November","December")
+bioclimatic_vars<-c("Annual Mean Temperature", "Mean Diurnal Range (Mean of monthly (max temp - min temp))", "Isothermality (BIO2/BIO7) (x 100)","Temperature Seasonality (standard deviation x100)","Max Temperature of Warmest Month","Min Temperature of Coldest Month","Temperature Annual Range (BIO5-BIO6)","Mean Temperature of Wettest Quarter","Mean Temperature of Driest Quarter","Mean Temperature of Warmest Quarter","Mean Temperature of Coldest Quarter","Annual Precipitation","Precipitation of Wettest Month","Precipitation of Driest Month","Precipitation Seasonality (Coefficient of Variation)","Precipitation of Wettest Quarter","Precipitation of Driest Quarter","Precipitation of Warmest Quarter","Precipitation of Coldest Quarter")
+
+#Function to create custom plot title
+get_plot_title<-function(usr_var,usr_var_to_plot){
+  match<-str_extract(usr_var_to_plot,"[0-9]+")
+  if(usr_var %in% c("prec","tmin","tmax")){
+      printable_var<-(months[as.integer(match)])
+      if(usr_var=="prec"){
+        printable_var<-paste(printable_var," precipitations (mm)",sep="")
+      }else if(usr_var=="tmin"){
+        printable_var<-paste(printable_var," minimum temperature (°C *10)",sep="")
+      }else{
+        printable_var<-paste(printable_var," maximum temperature (°C *10)",sep="")
+      }
+  }else if(usr_var=="bio"){
+      printable_var<-(bioclimatic_vars[as.integer(match)])
+      printable_var<-paste("Bioclimatic variable - ",printable_var,sep="")
+  }
+  title<-paste("Worldclim data - ",printable_var,".",sep="")
+  return(title)
+}
+
+
+#Call libraries
+library('raster',quietly=TRUE) 
+library(sp,quietly = TRUE, warn.conflicts = FALSE)
+library(ncdf4,quietly = TRUE, warn.conflicts = FALSE)
+library(rgdal,quietly = TRUE, warn.conflicts = FALSE) #To save as geotif
+library(stringr)
+
+
+#Get args
+usr_data=args[1]
+usr_var=args[2]
+usr_res=as.numeric(args[3])
+usr_of=args[4]
+
+
+# Retrieve 'var' data from WorldClim
+global.var <- getData(usr_data, download = TRUE, var = usr_var, res = usr_res)
+
+# Check if we actualy get some
+if (length(global.var)==0){
+  cat("No data found.")
+}else{
+  writeRaster(global.var, "output_writeRaster", format=usr_of,overwrite=TRUE)
+  final_msg<-paste("WorldClim data for ", usr_var, " at resolution ", usr_res, " in ", usr_of, " format\n", sep="")
+  cat(final_msg)
+}
+
+
+
+
+
+
+#################
+##Visualisation##
+#################
+
+#Get args
+if(length(args[5])>=0 && length(args[6])>=0){
+  usr_var_to_plot=args[5]
+  usr_plot_region=args[6]
+}else{q('no')}
+
+list_region_mask<-c("FRA","DEU","GBR","ESP","ITA")
+
+if(usr_plot_region %in% list_region_mask){
+#Country mask
+  region <- getData("GADM",country=usr_plot_region,level=0)
+  region_mask <- mask(global.var, region)
+  region_var_to_plot_expression<-paste("region_mask$",usr_var_to_plot,sep="")
+}else{ #All map and resize manualy
+  region_var_to_plot_expression<-paste("global.var$",usr_var_to_plot,sep="")
+}
+
+
+region_var_to_plot<-eval(parse(text=region_var_to_plot_expression))
+
+#PLotmap
+jpeg(file="worldclim_plot_usr_region.jpeg",bg="white")
+
+title<-get_plot_title(usr_var,usr_var_to_plot)
+
+
+if(usr_plot_region=="FRA"){
+  #FRA
+  plot(region_var_to_plot, xlim = c(-7, 12), ylim = c(40, 52), axes=TRUE,xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="GBR"){
+  #GBR
+  plot(region_var_to_plot, xlim = c(-10, 5), ylim = c(46, 63), axes=TRUE,xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="NA"){
+  #North America : 
+  plot(region_ar_to_plot,xlim=c(-180,-50),ylim=c(10,75),xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="EU"){
+  #Europe
+  plot(region_var_to_plot,xlim=c(-28,48),ylim=c(34,72),xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="DEU"){
+  #DEU
+  plot(region_var_to_plot, xlim = c(5, 15), ylim = c(45, 57),axes=TRUE,xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="ESP"){
+  #ESP
+  plot(region_var_to_plot, xlim = c(-10, 6), ylim = c(35, 45), axes=TRUE,xlab="Longitude",ylab="Latitude", main=title)
+}else if(usr_plot_region=="ITA"){
+  #ITA
+  plot(region_var_to_plot, xlim = c(4, 20), ylim = c(35, 48), axes=TRUE,xlab="Longitude",ylab="Latitude", main=title)
+}else if(usr_plot_region=="WM"){
+  #Worldmap
+  plot(region_var_to_plot,xlab="Longitude",ylab="Latitude",main=title)
+}else if(usr_plot_region=="AUS"){
+  #AUS
+  plot(region_var_to_plot,xlim=c(110,155),ylim=c(-45,-10),xlab="Longitude",ylab="Latitude",axes=TRUE,main=title)
+}else{
+  write("Error with country code.", stderr())  
+  q('no')
+}
+
+garbage_output<-dev.off
+ 
+#Exit
+q('no')