#STAGE 5: Output analyses: assessment of results for specific dates...

#

#AUTHOR: Benoit Parmentier                                                                       

#PROJECT: NCEAS INPLANT: Environment and Organisms --TASK#363, TASK$568--   

library(fields)                              # NCAR Spatial Interpolation methods such as kriging, splines

library(raster)                              # Hijmans et al. package for raster processing

library(rasterVis)

library(reshape)

library(plotrix)

modis_download_script <- file.path(script_path,"modis_download_05142013.py") # LST modis download python script

clim_script <- file.path(script_path,"climatology_05312013.py") # LST climatology python script

grass_setting_script <- file.path(script_path,"grass-setup.R") #Set up system shell environment for python+GRASS

source(file.path(script_path,"covariates_production_temperatures_06272013.R"))

source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_06082013.R"))

#source(file.path(script_path,"results_covariates_database_stations_output_analyses_04012013.R")) #to be completed

#FUNCTIONS CALLED FROM GAM ANALYSIS RASTER PREDICTION ARE FOUND IN...

source(file.path(script_path,"sampling_script_functions_03122013.R"))

source(file.path(script_path,"interpolation_method_day_function_multisampling_06082013.R")) #Include GAM_day

source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_05062013.R"))

stages_to_run<-c(0,2,3,4,5) #May decide on antoher strategy later on...

var<-"TMAX" # variable being interpolated

out_suffix_modis <-"_05302013" #use tiles produce previously

#interpolation_method<-c("gam_fusion","gam_CAI","gam_daily") #other otpions to be added later

#interpolation_method<-c("gam_CAI") #other otpions to be added later

#interpolation_method<-c("gam_daily") #other otpions to be added later

#interpolation_method<-c("kriging_daily") #other otpions to be added later

#out_path <- paste("/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data",

#                  out_prefix,"/",sep="")

#infile_reg_outline<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/outline_venezuela_region__VE_01292013.shp" 

#infile_covariates<-"/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates__venezuela_region_TMIN__VE_03192013.tif" #covariates stack for TMIN

#infile_covariates<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates_Oregon_region_TMAX__OR_04052013.tif" #Oregon covar TMAX from earlier codes...for continuity

#This is the shape file of outline of the study area                                                      #It is an input/output of the covariate script

#this may be redundant with infile_reg_outline

buffer_dist<-0 #not in use yet, must change climatology step to make sure additional tiles are downloaded and LST averages

               #must also be calculated for neighbouring tiles.

#list_tiles_modis <- c("h11v08,h11v07,h12v07,h12v08,h10v07,h10v08") #tile for Venezuela and surrounding area

list_tiles_modis <- c("h08v04,h09v04") #tiles for Oregon

#CRS_interp <-"+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +ellps=GRS80 +units=m +no_defs";

#"+proj=lcc +lat_1=43 +lat_2=45.5 +lat_0=41.75 +lon_0=-120.5 +x_0=400000 +y_0=0 +datum=NAD83 +units=m +no_defs +ellps=GRS80"

covar_names<-c(rnames,lc_names,lst_names)

list_val_range <-c("lon,-180,180","lat,-90,90","N,-1,1","E,-1,1","N_w,-1,1","E_w,-1,1","elev_s,0,6000","slope,0,90",

                   "mm_02,-15,50","mm_03,-15,50","mm_04,-15,50","mm_05,-15,50","mm_06,-15,50","mm_07,-15,50",

                   "mm_08,-15,50","mm_09,-15,50","mm_10,-15,50","mm_11,-15,50","mm_12,-15,50")

#Models to run...this can be change for each run

#               "y_var ~ lat + lon + elev_s",

#               "y_var ~ lat*lon*elev_s",

#               "y_var ~ lat*lon + elev_s + N_w*E_w + LST",