}

## Run function:

#list_tiles_modis <- c("h09v02,h10v02,h11v02,h12v02,h13v02,h14v02,h15v02") #tiles for Northenr America, Northern US...

#list_tiles_modis <- c("h10v04,h11v04,h12v04,h13v04,h14v04,h07v06") #tiles for Northenr America, Northern US...

#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 #defined above...

#list_tiles_modis <- c("h09v04,h09v04") #tiles for Oregon #defined above...

#list_tiles_modis <- c("h09v04,h09v04") #tiles for Oregon #defined above...

#list_tiles_modis <- c("h09v08,h09v07,h08v07,h0706,h08v06,h09v06,h10v06,h08v05,h09v05,h10v05,h11v05,h12v05") #tiles for Central America and Mexico Southern US...

#list_tiles_modis <- c("h09v09,h10v09,h11v09,h12v09,h13v09,h14v09")

script_path<-"/home/parmentier/Data/IPLANT_project/env_layers_scripts/"

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

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

#

#AUTHOR: Benoit Parmentier                                                                       

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

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")

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",