#DATE: 03/21/2013                                                                                 

#master_script_temp_03192013.R

#CALLED FROM MASTER SCRIPT:

#/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03192013.py

source(file.path(script_path,"covariates_production_temperatures_03212013.R"))

source(file.path(script_path,"Database_stations_covariates_processing_function_03132013.R"))

source(file.path(script_path,"GAM_fusion_analysis_raster_prediction_multisampling_03182013.R"))

source(file.path(script_path,"results_interpolation_date_output_analyses_03182013.R"))

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

source(file.path(script_path,"GAM_fusion_function_multisampling_03142013.R")) #Include GAM_CAI

source(file.path(script_path,"GAM_fusion_function_multisampling_validation_metrics_03182013.R"))

  #/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/climatology_03182013.py

##Paths to inputs and output

var<-"TMIN"

in_path <- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/input_data/"

out_path<- "/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/output_data/"

lc_path<-"/home/layers/data/land-cover/lc-consensus-global"

infile_modis_grid<-"modis_sinusoidal_grid_world.shp"

infile_elev<-"/home/layers/data/terrain/dem-cgiar-srtm-1km-tif/srtm_1km.tif"  #this is the global file: replace later with the input produced by the DEM team

infile_canheight<-"Simard_Pinto_3DGlobalVeg_JGR.tif"              #Canopy height

list_tiles_modis = c('h11v08','h11v07','h12v07','h12v08','h10v07','h10v08') #tile for Venezuel and surrounding area

infile_reg_outline=""  #input region outline defined by polygon

CRS_interp<-"+proj=sinu +lon_0=0 +x_0=0 +y_0=0 +a=6371007.181 +b=6371007.181 +units=m +no_defs";

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

out_suffix<-"_VE_03192013"

ref_rast_name<-""  #local raster name defining resolution, exent, local projection--. set 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","slope","aspect","CANHEIGHT","DISTOC")

lc_names<-c("LC1","LC2","LC3","LC4","LC5","LC6","LC7","LC8","LC9","LC10","LC11","LC12")

lst_names<-c("mm_01","mm_02","mm_03","mm_04","mm_05","mm_06","mm_07","mm_08","mm_09","mm_10","mm_11","mm_12",

             "nobs_01","nobs_02","nobs_03","nobs_04","nobs_05","nobs_06","nobs_07","nobs_08",

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

covar_names<-c(rnames,lc_names,lst_names)

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

                                  list_tiles_modis,infile_reg_outline,CRS_interp,CRS_locs_WGS84,out_region_name,

                                  out_suffix,ref_rast_name,covar_names) 

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

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

                                      "out_suffix","ref_rast_name","covar_names") 

  #/home/parmentier/Data/IPLANT_project/Venezuela_interpolation/Venezuela_01142013/covariates_production_temperatures_03212013.R

  infile_covar_brick<-covariates_production_temperature(list_param_covar_production)

#set up earlier

infile_covariates<-"covariates__venezuela_region__VE_01292013.tif" #this is an output from covariate script and used in stage 3 and stage 4

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

infile1<- "outline_venezuela_region__VE_01292013.shp"      #This is the shape file of outline of the study area                                                      #It is an input/output of the covariate script

#covar_names see stage 2

var <- "TMAX"           # name of the variables to keep: TMIN, TMAX or PRCP

#specific to this stage

#source(file.path(script_path,"results_interpolation_date_output_analyses_03052013.R"))

#Call as function...