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

#

#AUTHOR: Benoit Parmentier                                                                       

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

## TODO:

# Add options to run only specific stage + additional out_suffix?

# Make master script a function?

# Add log file for master script,add function to collect inputs and outputs

##################################################################################################

###Loading R library and packages   

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,"download_and_produce_MODIS_LST_climatology_05302013.R"))

source(file.path(script_path,"Database_stations_covariates_processing_function_05212013.R"))

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

source(file.path(script_path,"results_interpolation_date_output_analyses_06102013.R"))

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

var<-"TMAX" # variable being interpolated

#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="")

out_path <-paste(out_path,out_prefix,sep="")

if (!file.exists(out_path)){

#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

#infile_reg_outline <-"OR83M_state_outline.shp" #remove this parameter!!!

#this may be redundant with infile_reg_outline

#covar_names see stage 2

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

#"+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"

CRS_locs_WGS84<-CRS("+proj=longlat +ellps=WGS84 +datum=WGS84 +towgs84=0,0,0") #Station coords WGS84

#out_region_name<-"_venezuela_region" #generated on the fly

#The names of covariates can be changed...these names should be output/input from covar script!!!

rnames<-c("x","y","lon","lat","N","E","N_w","E_w","elev_s","slope","aspect","CANHEIGHT","DISTOC")

               "nobs_09","nobs_10","nobs_11","nobs_12")

covar_names<-c(rnames,lc_names,lst_names)

############ STAGE 1: LST Climatology ###############

#Parameters,Inputs from R to Python??

#list of 17 parameters

list_param_covar_production<-list(var,out_path,lc_path,infile_modis_grid,infile_elev,infile_canheight,

                                  infile_distoc,list_tiles_modis,infile_reg_outline,CRS_interp,CRS_locs_WGS84,out_region_name,

names(list_param_covar_production)<-c("var","out_path","lc_path","infile_modis_grid","infile_elev","infile_canheight",

                                      "infile_distoc","list_tiles_modis","infile_reg_outline","CRS_interp","CRS_locs_WGS84","out_region_name",

## Modify to store infile_covar_brick in output folder!!!

if (stages_to_run[2]==2){

  covar_obj <- covariates_production_temperature(list_param_covar_production)

  infile_covariates <- covar_obj$infile_covariates

  infile_reg_outline <- covar_obj$infile_reg_outline

}

#Note that if stages_to_run[2]!=2, then use values defined at the beginning of the script for infile_covariates and infile_reg_outline

range_years_clim<-c("2000","2011") #right bound not included in the range!!

infile_ghncd_data <-"/home/layers/data/climate/ghcn/v2.92-upd-2012052822/ghcnd-stations.txt"                              #This is the textfile of station locations from GHCND

#qc_flags_stations<-c("0","S")    #flags allowed for screening after the query from the GHCND??

#infile_covariates and infile_reg_outline defined in stage 2 or at the start of script...

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

#list_models<-c("y_var~ lat + lon + elev_",

#               "y_var~ I(lat*lon) + elev_s",

#              "y_var~ lat + lon + elev_s + N + E + DISTOC",